Biological Potential in Serpentinizing Systems

Science.gov (United States)

Hoehler, Tori M.

2016-01-01

Generation of the microbial substrate hydrogen during serpentinization, the aqueous alteration of ultramafic rocks, has focused interest on the potential of serpentinizing systems to support biological communities or even the origin of life. However the process also generates considerable alkalinity, a challenge to life, and both pH and hydrogen concentrations vary widely across natural systems as a result of different host rock and fluid composition and differing physical and hydrogeologic conditions. Biological potential is expected to vary in concert. We examined the impact of such variability on the bioenergetics of an example metabolism, methanogenesis, using a cell-scale reactive transport model to compare rates of metabolic energy generation as a function of physicochemical environment. Potential rates vary over more than 5 orders of magnitude, including bioenergetically non-viable conditions, across the range of naturally occurring conditions. In parallel, we assayed rates of hydrogen metabolism in wells associated with the actively serpentinizing Coast Range Ophiolite, which includes conditions more alkaline and considerably less reducing than is typical of serpentinizing systems. Hydrogen metabolism is observed at pH approaching 12 but, consistent with the model predictions, biological methanogenesis is not observed.

Mechanisms of radiation interaction with DNA: Potential implications for radiation protection

International Nuclear Information System (INIS)

Sinclair, W.K.; Fry, R.J.M.

1987-01-01

An overview of presentations and discussions which took place at the US Department of Energy/Commission of European Communities (DOE/CEC) workshop on ''Mechanisms of Radiation Interaction with DNA: Potential Implications for Radiation Protection,'' held at San Diego, California, January 21-22, 1987, is provided. The Department has traditionally supported fundamental research on interactions of ionizing radiation with different biological systems and at all levels of biological organization. The aim of this workshop was to review the base of knowledge in the area of mechanisms of radiation action at the DNA level, and to explore ways in which this information can be applied to the development of scientifically sound concepts and procedures for use in the field of radiation protection

Biological interactions and human health effects of static magnetic fields

International Nuclear Information System (INIS)

Tenforde, T.S.

1994-09-01

Mechanisms through which static magnetic fields interact with living systems will be described and illustrated by selected experimental observations. These mechanisms include electrodynamic interactions with moving ionic charges (blood flow and nerve impulse conduction), magnetomechanical interactions (orientation and translation of molecular structures and magnetic particles), and interactions with electronic spin states in charge transfer reactions (photo-induced electron transfer in photosynthesis). A general summary will also be presented of the biological effects of static magnetic fields studied in the laboratory and in natural settings. One aspect of magnetic field effects that merits special concern is their influence on implanted medical electronic devices such as cardiac pacemakers. Several extensive studies have demonstrated closure of the reed switch in pacemakers exposed to relatively weak static magnetic fields, thereby causing them to revert to an asynchronous mode of operation that is potentially hazardous. Recommendations for human exposure limits are provided

Interaction of phosphorylcholine with fibronectin coatings: Surface characterization and biological performances

Energy Technology Data Exchange (ETDEWEB)

Montaño-Machado, Vanessa, E-mail: vanessa.montano-machado.1@ulaval.ca [Laboratory for Biomaterials and Bioengineering, Dept. of Min-Met-Materials Eng., & University Hospital Research Center, Laval University, University Campus, PLT-1745G, Québec, Québec, G1 V 0A6 (Canada); ERRMECe, University of Cergy-Pontoise, Site Saint-Martin, 2 Avenue Adolphe Chauvin, 95302 Cergy-Pontoise Cedex (France); Noël, Céline, E-mail: celine.noel@unamur.be [Research Centre in Physics of Matter and Radiation (PMR), Université de Namur, 61 rue de Bruxelles, B-5000 Namur (Belgium); Chevallier, Pascale, E-mail: pascale.chevallier@crchudequebec.ulaval.ca [Laboratory for Biomaterials and Bioengineering, Dept. of Min-Met-Materials Eng., & University Hospital Research Center, Laval University, University Campus, PLT-1745G, Québec, Québec, G1 V 0A6 (Canada); Turgeon, Stéphane, E-mail: stephane.turgeon@crchudequebec.ulaval.ca [Laboratory for Biomaterials and Bioengineering, Dept. of Min-Met-Materials Eng., & University Hospital Research Center, Laval University, University Campus, PLT-1745G, Québec, Québec, G1 V 0A6 (Canada); Houssiau, Laurent, E-mail: laurent.houssiau@unamur.be [Research Centre in Physics of Matter and Radiation (PMR), Université de Namur, 61 rue de Bruxelles, B-5000 Namur (Belgium); Pauthe, Emmanuel, E-mail: emmanuel.pauthe@u-cergy.fr [ERRMECe, University of Cergy-Pontoise, Site Saint-Martin, 2 Avenue Adolphe Chauvin, 95302 Cergy-Pontoise Cedex (France); and others

2017-02-28

Highlights: • Fibronectin/phosphorylcholine coatings on plasma deposited fluorocarbon films were created. • The effect of several coating techniques on the surface biological performances was evaluated. • XPS, DWCA, immunostaining and ToF-SIMS (imaging and depth profiling) techniques were applied. • Potential for cardiovascular applications was showed by endothelial cell and blood interactions. - Abstract: Coating medical devices with several bioactive molecules is an interesting approach to achieve specific biological targets upon the interaction of the biomaterial with the living environment. In this work, a fluorocarbon polymer (CF{sub x}) was first deposited by plasma treatment on stainless steel (SS) substrate and thereafter, coatings containing fibronectin (FN) and phosphorylcholine (PRC) were created for cardiovascular applications. These two biomolecules were chosen to promote endothelialization and to avoid thrombus formation, respectively. Adsorption and grafting techniques were applied – and combined – to accomplish 4 different coatings containing both molecules. However, big challenge was found to characterize a small molecule (PRC: 184 g/mol) interacting with a protein (FN: 450 kD). For the first time XPS, dynamic water contact angle, immunostaining and ToF-SIMS (imaging and depth profiling) analyses were combined to accomplish the characterization of such a coating. The most encouraging biological performances were obtained for samples where FN was grafted to the CF{sub x} film followed by the adsorption of PRC: proliferation of endothelial cells and hemocompatibility properties were observed. Promising coatings for cardiovascular applications were developed. The relevance of characterizing the coatings with high sensitive techniques and the further correlation with their biological performances were evidenced.

Floral biology and the effects of plant-pollinator interaction on ...

African Journals Online (AJOL)

Reproductive biology and patterns of plant-pollinator interaction are fundamental to gene flow, diversity and evolutionary success of plants. Consequently, we examined the magnitude of insect-plant interaction based on the dynamics of breeding systems and floral biology and their effects on pollination intensity, fruit and ...

Laser interaction with biological material mathematical modeling

CERN Document Server

Kulikov, Kirill

2014-01-01

This book covers the principles of laser interaction with biological cells and tissues of varying degrees of organization. The problems of biomedical diagnostics are considered. Scattering of laser irradiation of blood cells is modeled for biological structures (dermis, epidermis, vascular plexus). An analytic theory is provided which is based on solving the wave equation for the electromagnetic field. It allows the accurate analysis of interference effects arising from the partial superposition of scattered waves. Treated topics of mathematical modeling are: optical characterization of biological tissue with large-scale and small-scale inhomogeneities in the layers, heating blood vessel under laser irradiation incident on the outer surface of the skin and thermo-chemical denaturation of biological structures at the example of human skin.

Intermolecular interaction of thiosemicarbazone derivatives to solvents and a potential Aedes aegypti target

Science.gov (United States)

da Silva, João Bosco P.; Hallwass, Fernando; da Silva, Aluizio G.; Moreira, Diogo Rodrigo; Ramos, Mozart N.; Espíndola, José Wanderlan P.; de Oliveira, Ana Daura T.; Brondani, Dalci José; Leite, Ana Cristina L.; Merz, Kenneth M.

2015-08-01

DFT calculations were used to access information about structure, energy and electronic properties of series of phenyl- and phenoxymethyl-(thio)semicarbazone derivatives with demonstrated activity against the larvae of Aedes aegypti in stage L4. The way as the thiosemicarbazone derivatives can interact with solvents like DMSO and water were analyzed from the comparison between calculated and experimental 1H NMR chemical shifts. The evidences of thiosemicarbazone derivatives making H-bond interaction to solvent have provide us insights on how they can interact with a potential A. aegypti's biological target, the Sterol Carrier Protein-2.

Interaction of Ulocladium atrum, a Potential Biological Control Agent, with Botrytis cinerea and Grapevine Plantlets

Directory of Open Access Journals (Sweden)

Sébastien Ronseaux

2013-09-01

Full Text Available The effectiveness of biological control agent, Ulocladium atrum (isolates U13 and U16 in protecting Vitis vinifera L. cv. Chardonnay against gray mold disease caused by Botrytis cinerea, and simulation of the foliar defense responses was investigated. A degraded mycelium structure during cultural assay on potato dextrose agar revealed that U. atrum isolates U13 and U16 were both antagonistic to B. cinerea, mainly when isolates were inoculated two days before Botrytis. Under in vitro conditions, foliar application of U. atrum protected grapevine leaves against gray mold disease. An increase in chitinase activity was induced by the presence of U. atrum isolates indicating that the biological control agents triggered plant defense mechanisms. Moreover, U13 has the potential to colonize the grapevine plantlets and to improve their growth. The ability of U. atrum isolates to exhibit an antagonistic effect against B. cinerea in addition to their aptitude to induce plant resistance and to promote grapevine growth may explain a part of their biological activity. Hence, this study suggests that U. atrum provides a suitable biocontrol agent against gray mold in grapevines.

"Cancer Cell Biology:" A Student-Centered Instructional Module Exploring the Use of Multimedia to Enrich Interactive, Constructivist Learning of Science

Science.gov (United States)

Bockholt, Susanne M.; West, J. Paige; Bollenbacher, Walter E.

2003-01-01

Multimedia has the potential of providing bioscience education novel learning environments and pedagogy applications to foster student interest, involve students in the research process, advance critical thinking/problem-solving skills, and develop conceptual understanding of biological topics. "Cancer Cell Biology," an interactive, multimedia,…

Environmental radiation: basic principles, biological facts, potential risks

International Nuclear Information System (INIS)

Rodemann, H.P.

2000-01-01

This book describes the complex processes that underlie the effects of different types of radiation at the cellular, organ and organismic level. Technical terms central to the subject matter are printed in italicize and explained in a glossary along with all physical quantities and dimensional units referred to. Through a systematic presentation of various aspects of the effects of environmental radiation on humans the author has endeavoured to make it clear that any discussion on potential health hazards must be conducted specific to the type of radiation in question. Furthermore, to study these issues meaningfully one must have a knowledge of the scientific basis of interactions between the various types of radiation and biological systems and be able to assess the relative impact of environmental radiation compared with other environmental health hazards

Macroscopic Quantum-Type Potentials in Theoretical Systems Biology

Directory of Open Access Journals (Sweden)

Laurent Nottale

2013-12-01

Full Text Available We review in this paper the use of the theory of scale relativity and fractal space-time as a tool particularly well adapted to the possible development of a future genuine systems theoretical biology. We emphasize in particular the concept of quantum-type potentials, since, in many situations, the effect of the fractality of space—or of the underlying medium—can be reduced to the addition of such a potential energy to the classical equations of motion. Various equivalent representations—geodesic, quantum-like, fluid mechanical, stochastic—of these equations are given, as well as several forms of generalized quantum potentials. Examples of their possible intervention in high critical temperature superconductivity and in turbulence are also described, since some biological processes may be similar in some aspects to these physical phenomena. These potential extra energy contributions could have emerged in biology from the very fractal nature of the medium, or from an evolutive advantage, since they involve spontaneous properties of self-organization, morphogenesis, structuration and multi-scale integration. Finally, some examples of applications of the theory to actual biological-like processes and functions are also provided.

Social-Biological Interactions in Oral Disease: A 'Cells to Society' View.

Directory of Open Access Journals (Sweden)

Noha Gomaa

Full Text Available Oral diseases constitute a major worldwide public health problem, with their burden concentrating in socially disadvantaged and less affluent groups of the population, resulting in significant oral health inequalities. Biomedical and behavioural approaches have proven relatively ineffective in reducing these inequalities, and have potentially increased the health gap between social groups. Some suggest this stems from a lack of understanding of how the social and psychosocial contexts in which behavioural and biological changes occur influence oral disease. To unravel the pathways through which social factors affect oral health outcomes, a better understanding is thus needed of how the social 'gets under the skin,' or becomes embodied, to alter the biological. In this paper, we present the current knowledge on the interplay between social and biological factors in oral disease. We first provide an overview of the process of embodiment in chronic disease and then evaluate the evidence on embodiment in oral disease by reviewing published studies in this area. Results show that, in periodontal disease, income, education and perceived stress are correlated with elevated levels of stress hormones, disrupted immune biomarkers and increased allostatic load. Similarly, socioeconomic position and increased financial stress are related to increased stress hormones and cariogenic bacterial counts in dental caries. Based on these results, we propose a dynamic model depicting social-biological interactions that illustrates potential interdependencies between social and biological factors that lead to poor oral health. This work and the proposed model may aid in developing a better understanding of the causes of oral health inequalities and implicate the importance of addressing the social determinants of oral health in innovating public health interventions.

Synthesis of novel (-)-epicatechin derivatives as potential endothelial GPER agonists: Evaluation of biological effects.

Science.gov (United States)

Sarmiento, Viviana; Ramirez-Sanchez, Israel; Moreno-Ulloa, Aldo; Romero-Perez, Diego; Chávez, Daniel; Ortiz, Miguel; Najera, Nayelli; Correa-Basurto, Jose; Villarreal, Francisco; Ceballos, Guillermo

2018-02-15

To potentially identify proteins that interact (i.e. bind) and may contribute to mediate (-)-epicatechin (Epi) responses in endothelial cells we implemented the following strategy: 1) synthesis of novel Epi derivatives amenable to affinity column use, 2) in silico molecular docking studies of the novel derivatives on G protein-coupled estrogen receptor (GPER), 3) biological assessment of the derivatives on NO production, 4) implementation of an immobilized Epi derivative affinity column and, 5) affinity column based isolation of Epi interacting proteins from endothelial cell protein extracts. For these purposes, the Epi phenol and C3 hydroxyl groups were chemically modified with propargyl or mesyl groups. Docking studies of the novel Epi derivatives on GPER conformers at 14 ns and 70 ns demostrated favorable thermodynamic interactions reaching the binding site. Cultures of bovine coronary artery endothelial cells (BCAEC) treated with Epi derivatives stimulated NO production via Ser1179 phosphorylation of eNOS, effects that were attenuated by the use of the GPER blocker, G15. Epi derivative affinity columns yielded multiple proteins from BCAEC. Proteins were electrophoretically separated and inmmunoblotting analysis revealed GPER as an Epi derivative binding protein. Altogether, these results validate the proposed strategy to potentially isolate and identify novel Epi receptors that may account for its biological activity. Copyright © 2018 Elsevier Ltd. All rights reserved.

Electrical circuit modeling and analysis of microwave acoustic interaction with biological tissues.

Science.gov (United States)

Gao, Fei; Zheng, Qian; Zheng, Yuanjin

2014-05-01

Numerical study of microwave imaging and microwave-induced thermoacoustic imaging utilizes finite difference time domain (FDTD) analysis for simulation of microwave and acoustic interaction with biological tissues, which is time consuming due to complex grid-segmentation and numerous calculations, not straightforward due to no analytical solution and physical explanation, and incompatible with hardware development requiring circuit simulator such as SPICE. In this paper, instead of conventional FDTD numerical simulation, an equivalent electrical circuit model is proposed to model the microwave acoustic interaction with biological tissues for fast simulation and quantitative analysis in both one and two dimensions (2D). The equivalent circuit of ideal point-like tissue for microwave-acoustic interaction is proposed including transmission line, voltage-controlled current source, envelop detector, and resistor-inductor-capacitor (RLC) network, to model the microwave scattering, thermal expansion, and acoustic generation. Based on which, two-port network of the point-like tissue is built and characterized using pseudo S-parameters and transducer gain. Two dimensional circuit network including acoustic scatterer and acoustic channel is also constructed to model the 2D spatial information and acoustic scattering effect in heterogeneous medium. Both FDTD simulation, circuit simulation, and experimental measurement are performed to compare the results in terms of time domain, frequency domain, and pseudo S-parameters characterization. 2D circuit network simulation is also performed under different scenarios including different sizes of tumors and the effect of acoustic scatterer. The proposed circuit model of microwave acoustic interaction with biological tissue could give good agreement with FDTD simulated and experimental measured results. The pseudo S-parameters and characteristic gain could globally evaluate the performance of tumor detection. The 2D circuit network

Computing paths and cycles in biological interaction graphs

Directory of Open Access Journals (Sweden)

von Kamp Axel

2009-06-01

Full Text Available Abstract Background Interaction graphs (signed directed graphs provide an important qualitative modeling approach for Systems Biology. They enable the analysis of causal relationships in cellular networks and can even be useful for predicting qualitative aspects of systems dynamics. Fundamental issues in the analysis of interaction graphs are the enumeration of paths and cycles (feedback loops and the calculation of shortest positive/negative paths. These computational problems have been discussed only to a minor extent in the context of Systems Biology and in particular the shortest signed paths problem requires algorithmic developments. Results We first review algorithms for the enumeration of paths and cycles and show that these algorithms are superior to a recently proposed enumeration approach based on elementary-modes computation. The main part of this work deals with the computation of shortest positive/negative paths, an NP-complete problem for which only very few algorithms are described in the literature. We propose extensions and several new algorithm variants for computing either exact results or approximations. Benchmarks with various concrete biological networks show that exact results can sometimes be obtained in networks with several hundred nodes. A class of even larger graphs can still be treated exactly by a new algorithm combining exhaustive and simple search strategies. For graphs, where the computation of exact solutions becomes time-consuming or infeasible, we devised an approximative algorithm with polynomial complexity. Strikingly, in realistic networks (where a comparison with exact results was possible this algorithm delivered results that are very close or equal to the exact values. This phenomenon can probably be attributed to the particular topology of cellular signaling and regulatory networks which contain a relatively low number of negative feedback loops. Conclusion The calculation of shortest positive

Recent developments in systems biology and metabolic engineering of plant microbe interactions

Directory of Open Access Journals (Sweden)

Vishal Kumar

2016-09-01

Full Text Available Microorganisms play a crucial role in the sustainability of the various ecosystems. The characterization of various interactions between microorganisms and other biotic factors is a necessary footstep to understand the association and functions of microbial communities. Among the different microbial interactions in an ecosystem, plant-microbe interaction plays an important role to balance the ecosystem. The present review explores plant microbe interactions using gene editing and system biology tools towards the comprehension in improvement of plant traits. Further, system biology tools like FBA, OptKnock and constrain based modeling helps in understanding such interactions as a whole. In addition, various gene editing tools have been summarized and a strategy has been hypothesized for the development of disease free plants. Furthermore, we have tried to summarize the predictions through data retrieved from various types of sources such as high throughput sequencing data (e.g. single nucleotide polymorphism (SNP detection, RNA-seq, proteomics and metabolic models have been reconstructed from such sequences for species communities. It is well known fact that systems biology approaches and modeling of biological networks will enable us to learn the insight of such network and will also help further in understanding these interactions.

Finding optimal interaction interface alignments between biological complexes

KAUST Repository

Cui, Xuefeng

2015-06-13

Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting their structural similarities, which are keys to understanding their evolutionary histories and functions. Although various structure alignment methods have been developed to successfully access the similarities of protein structures or certain types of interaction interfaces, existing alignment tools cannot directly align arbitrary types of interfaces formed by protein, DNA or RNA molecules. Specifically, they require a \\'blackbox preprocessing\\' to standardize interface types and chain identifiers. Yet their performance is limited and sometimes unsatisfactory. Results: Here we introduce a novel method, PROSTA-inter, that automatically determines and aligns interaction interfaces between two arbitrary types of complex structures. Our method uses sequentially remote fragments to search for the optimal superimposition. The optimal residue matching problem is then formulated as a maximum weighted bipartite matching problem to detect the optimal sequence order-independent alignment. Benchmark evaluation on all non-redundant protein-DNA complexes in PDB shows significant performance improvement of our method over TM-align and iAlign (with the \\'blackbox preprocessing\\'). Two case studies where our method discovers, for the first time, structural similarities between two pairs of functionally related protein-DNA complexes are presented. We further demonstrate the power of our method on detecting structural similarities between a protein-protein complex and a protein-RNA complex, which is biologically known as a protein-RNA mimicry case. © The Author 2015. Published by Oxford University Press.

Biological interactions and cooperative management of multiple species.

Science.gov (United States)

Jiang, Jinwei; Min, Yong; Chang, Jie; Ge, Ying

2017-01-01

Coordinated decision making and actions have become the primary solution for the overexploitation of interacting resources within ecosystems. However, the success of coordinated management is highly sensitive to biological, economic, and social conditions. Here, using a game theoretic framework and a 2-species model that considers various biological relationships (competition, predation, and mutualism), we compute cooperative (or joint) and non-cooperative (or separate) management equilibrium outcomes of the model and investigate the effects of the type and strength of the relationships. We find that cooperation does not always show superiority to non-cooperation in all biological interactions: (1) if and only if resources are involved in high-intensity predation relationships, cooperation can achieve a win-win scenario for ecosystem services and resource diversity; (2) for competitive resources, cooperation realizes higher ecosystem services by sacrificing resource diversity; and (3) for mutual resources, cooperation has no obvious advantage for either ecosystem services or resource evenness but can slightly improve resource abundance. Furthermore, by using a fishery model of the North California Current Marine Ecosystem with 63 species and seven fleets, we demonstrate that the theoretical results can be reproduced in real ecosystems. Therefore, effective ecosystem management should consider the interconnection between stakeholders' social relationship and resources' biological relationships.

PathSys: integrating molecular interaction graphs for systems biology

Directory of Open Access Journals (Sweden)

Raval Alpan

2006-02-01

Full Text Available Abstract Background The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. Results Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping. Conclusion Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks.

Diatomic interaction potential theory applications

CERN Document Server

Goodisman, Jerry

2013-01-01

Diatomic Interaction Potential Theory, Volume 2: Applications discusses the variety of applicable theoretical material and approaches in the calculations for diatomic systems in their ground states. The volume covers the descriptions and illustrations of modern calculations. Chapter I discusses the calculation of the interaction potential for large and small values of the internuclear distance R (separated and united atom limits). Chapter II covers the methods used for intermediate values of R, which in principle means any values of R. The Hartree-Fock and configuration interaction schemes des

Analysis of Biological Interactions by Affinity Chromatography: Clinical and Pharmaceutical Applications.

Science.gov (United States)

Hage, David S

2017-06-01

The interactions between biochemical and chemical agents in the body are important in many clinical processes. Affinity chromatography and high-performance affinity chromatography (HPAC), in which a column contains an immobilized biologically related binding agent, are 2 methods that can be used to study these interactions. This review presents various approaches that can be used in affinity chromatography and HPAC to characterize the strength or rate of a biological interaction, the number and types of sites that are involved in this process, and the interactions between multiple solutes for the same binding agent. A number of applications for these methods are examined, with an emphasis on recent developments and high-performance affinity methods. These applications include the use of these techniques for fundamental studies of biological interactions, high-throughput screening of drugs, work with modified proteins, tools for personalized medicine, and studies of drug-drug competition for a common binding agent. The wide range of formats and detection methods that can be used with affinity chromatography and HPAC for examining biological interactions makes these tools attractive for various clinical and pharmaceutical applications. Future directions in the development of small-scale columns and the coupling of these methods with other techniques, such as mass spectrometry or other separation methods, should continue to increase the flexibility and ease with which these approaches can be used in work involving clinical or pharmaceutical samples. © 2016 American Association for Clinical Chemistry.

A new methodology for studying nanoparticle interactions in biological systems: Dispersing titania in biocompatible media using chemical stabilisers

Science.gov (United States)

Ramirez-Garcia, Sonia; Chen, Lan; Morris, Michael A.; Dawson, Kenneth A.

2011-11-01

We report here a highly successful and original protocol for the dispersion of nanoparticles in biocompatible fluids for in vitro and in vivo studies of the nanoparticle-biology interaction. Titania is chosen as a suitable model as it is one of the priority materials listed by the OECD and small particles of the anatase structure are extensively used as e.g. photocatalysts in solar cells. Consequently, its delivery into the environment and its interaction with biological organisms is unavoidable. Therefore, its biological effect needs to be understood. In this work, we prepared stable nanoparticle dispersions of anatase aggregates using citrate stabilisations between 45 and 55 nm at concentrations of up to 10 mg mL-1. The optimum pH for this type of suspension was 7, resulting in ζ-potentials of approximately -50 mV. The stabilised aggregates were the subject of dialysis to produce stable dispersions without the chemical stabiliser, thus allowing studies in the absence of potentially toxic chemicals. Different sizing techniques such as Dynamic Light Scattering (DLS), Nanoparticle Tracking Analysis (NTA) and Differential Centrifuge Sedimentation (DCS) were used to characterise the different suspensions. The results obtained with each of these techniques are compared and a critical analysis of the suitability of each technique is given.We report here a highly successful and original protocol for the dispersion of nanoparticles in biocompatible fluids for in vitro and in vivo studies of the nanoparticle-biology interaction. Titania is chosen as a suitable model as it is one of the priority materials listed by the OECD and small particles of the anatase structure are extensively used as e.g. photocatalysts in solar cells. Consequently, its delivery into the environment and its interaction with biological organisms is unavoidable. Therefore, its biological effect needs to be understood. In this work, we prepared stable nanoparticle dispersions of anatase aggregates

Research on the potential use of interactive materials on astronomy education

Science.gov (United States)

Voelzke, Marcos Rincon; Macedo, Josue

2016-07-01

This study presents results of a survey conducted at the Federal Institution of Education, Science and Technology in the North of Minas Gerais (IFNMG), and aimed to investigate the potentialities of the use of interactive materials in the teaching of astronomy. An advanced training course with involved learning activities about basic concepts of astronomy was offered to thirty-two Licenciate students in Physics, Mathematics and Biological Sciences, using the mixed methodology, combined with the three pedagogical moments. Among other aspects, the viability of the use of resources was noticed, involving digital technologies and interactive materials on teaching of astronomy, which may contribute to the broadening of methodological options for future teachers and meet their training needs.

Integrating interactive computational modeling in biology curricula.

Directory of Open Access Journals (Sweden)

Tomáš Helikar

2015-03-01

Full Text Available While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

Integrating interactive computational modeling in biology curricula.

Science.gov (United States)

Helikar, Tomáš; Cutucache, Christine E; Dahlquist, Lauren M; Herek, Tyler A; Larson, Joshua J; Rogers, Jim A

2015-03-01

While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology) class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

Students' Evaluation of Classroom Interactions of Their Biology ...

African Journals Online (AJOL)

Nekky Umera

teacher classroom interactions were positively correlated and uncertainty, ... implementation is that, if biology teachers were to display more leadership, helpful and ... Accepted methods to overcome poor academic achievement in science have ... activities and experiences through which teachers; curriculum, materials, and.

Biana: a software framework for compiling biological interactions and analyzing networks.

Science.gov (United States)

Garcia-Garcia, Javier; Guney, Emre; Aragues, Ramon; Planas-Iglesias, Joan; Oliva, Baldo

2010-01-27

The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties. We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php. BIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules.

Institute for Multiscale Modeling of Biological Interactions

Energy Technology Data Exchange (ETDEWEB)

Paulaitis, Michael E; Garcia-Moreno, Bertrand; Lenhoff, Abraham

2009-12-26

The Institute for Multiscale Modeling of Biological Interactions (IMMBI) has two primary goals: Foster interdisciplinary collaborations among faculty and their research laboratories that will lead to novel applications of multiscale simulation and modeling methods in the biological sciences and engineering; and Building on the unique biophysical/biology-based engineering foundations of the participating faculty, train scientists and engineers to apply computational methods that collectively span multiple time and length scales of biological organization. The success of IMMBI will be defined by the following: Size and quality of the applicant pool for pre-doctoral and post-doctoral fellows; Academic performance; Quality of the pre-doctoral and post-doctoral research; Impact of the research broadly and to the DOE (ASCR program) mission; Distinction of the next career step for pre-doctoral and post-doctoral fellows; and Faculty collaborations that result from IMMBI activities. Specific details about accomplishments during the three years of DOE support for IMMBI have been documented in Annual Progress Reports (April 2005, June 2006, and March 2007) and a Report for a National Academy of Sciences Review (October 2005) that were submitted to DOE on the dates indicated. An overview of these accomplishments is provided.

Calculation of Rydberg interaction potentials

International Nuclear Information System (INIS)

Weber, Sebastian; Büchler, Hans Peter; Tresp, Christoph; Urvoy, Alban; Hofferberth, Sebastian; Menke, Henri; Firstenberg, Ofer

2017-01-01

The strong interaction between individual Rydberg atoms provides a powerful tool exploited in an ever-growing range of applications in quantum information science, quantum simulation and ultracold chemistry. One hallmark of the Rydberg interaction is that both its strength and angular dependence can be fine-tuned with great flexibility by choosing appropriate Rydberg states and applying external electric and magnetic fields. More and more experiments are probing this interaction at short atomic distances or with such high precision that perturbative calculations as well as restrictions to the leading dipole–dipole interaction term are no longer sufficient. In this tutorial, we review all relevant aspects of the full calculation of Rydberg interaction potentials. We discuss the derivation of the interaction Hamiltonian from the electrostatic multipole expansion, numerical and analytical methods for calculating the required electric multipole moments and the inclusion of electromagnetic fields with arbitrary direction. We focus specifically on symmetry arguments and selection rules, which greatly reduce the size of the Hamiltonian matrix, enabling the direct diagonalization of the Hamiltonian up to higher multipole orders on a desktop computer. Finally, we present example calculations showing the relevance of the full interaction calculation to current experiments. Our software for calculating Rydberg potentials including all features discussed in this tutorial is available as open source. (tutorial)

Biology of Leptoypha hospita (Hemiptera: Tingidae), a Potential Biological Control Agent of Chinese Privet

Science.gov (United States)

Yanzhuo Zhang; James L. Hanula; Scott Horn; Kristine Braman; Jianghua Sun

2011-01-01

The biology of Leptoypha hospita Drake et Poor (Hemiptera: Tingidae), a potential biological control agent from China for Chinese privet, Ligustrum sinense Lour., was studied in quarantine in the United States. Both nymphs and adults feed on Chinese privet mesophyll cells that lead to a bleached appearance of leaves and dieback of branch tips. L. hospita has five...

Source-sink interaction: a century old concept under the light of modern molecular systems biology.

Science.gov (United States)

Chang, Tian-Gen; Zhu, Xin-Guang; Raines, Christine

2017-07-20

Many approaches to engineer source strength have been proposed to enhance crop yield potential. However, a well-co-ordinated source-sink relationship is required finally to realize the promised increase in crop yield potential in the farmer's field. Source-sink interaction has been intensively studied for decades, and a vast amount of knowledge about the interaction in different crops and under different environments has been accumulated. In this review, we first introduce the basic concepts of source, sink and their interactions, then summarize current understanding of how source and sink can be manipulated through both environmental control and genetic manipulations. We show that the source-sink interaction underlies the diverse responses of crops to the same perturbations and argue that development of a molecular systems model of source-sink interaction is required towards a rational manipulation of the source-sink relationship for increased yield. We finally discuss both bottom-up and top-down routes to develop such a model and emphasize that a community effort is needed for development of this model. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Interactive robots in experimental biology.

Science.gov (United States)

Krause, Jens; Winfield, Alan F T; Deneubourg, Jean-Louis

2011-07-01

Interactive robots have the potential to revolutionise the study of social behaviour because they provide several methodological advances. In interactions with live animals, the behaviour of robots can be standardised, morphology and behaviour can be decoupled (so that different morphologies and behavioural strategies can be combined), behaviour can be manipulated in complex interaction sequences and models of behaviour can be embodied by the robot and thereby be tested. Furthermore, robots can be used as demonstrators in experiments on social learning. As we discuss here, the opportunities that robots create for new experimental approaches have far-reaching consequences for research in fields such as mate choice, cooperation, social learning, personality studies and collective behaviour. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

NARCIS (Netherlands)

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

2016-01-01

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

Hyperspherical effective interaction for nonlocal potentials

International Nuclear Information System (INIS)

Barnea, N.; Leidemann, W.; Orlandini, G.

2010-01-01

The effective interaction hyperspherical-harmonics method, formulated for local forces, is generalized to accommodate nonlocal interactions. As for local potentials this formulation retains the separation of the hyper-radial part leading solely to a hyperspherical effective interaction. By applying the method to study ground-state properties of 4 He with a modern effective-field-theory nucleon-nucleon potential model (Idaho-N3LO), one finds a substantial acceleration in the convergence rate of the hyperspherical-harmonics series. Also studied are the binding energies of the six-body nuclei 6 He and 6 Li with the JISP16 nuclear force. Again an excellent convergence is observed.

Separable expansions for local potentials with Coulomb interactions

International Nuclear Information System (INIS)

Adhikari, S.K.

1976-01-01

If two particles are interacting via a short range potential and a repulsive Coulomb potential the t matrix can be written as a sum of the Coulomb and the ''nuclear'' t matrices. In order to solve the three-nucleon problem with Coulomb interactions usually we need a separable representation of this ''nuclear'' t matrix. A recently proposed method for finding a separable expansion for local potentials is here extended to find a rapidly convergent separable expansion, with analytic form factors, for the ''nuclear'' part of the t matrix of a local potential, in the presence of Coulomb interactions. The method is illustrated for a two-term Malfliet-Tjon potential. In each rank the ''nuclear'' phase shift is close to the corresponding phase shift when the Coulomb interaction is switched off

Cell Biology of Astrocyte-Synapse Interactions.

Science.gov (United States)

Allen, Nicola J; Eroglu, Cagla

2017-11-01

Astrocytes, the most abundant glial cells in the mammalian brain, are critical regulators of brain development and physiology through dynamic and often bidirectional interactions with neuronal synapses. Despite the clear importance of astrocytes for the establishment and maintenance of proper synaptic connectivity, our understanding of their role in brain function is still in its infancy. We propose that this is at least in part due to large gaps in our knowledge of the cell biology of astrocytes and the mechanisms they use to interact with synapses. In this review, we summarize some of the seminal findings that yield important insight into the cellular and molecular basis of astrocyte-neuron communication, focusing on the role of astrocytes in the development and remodeling of synapses. Furthermore, we pose some pressing questions that need to be addressed to advance our mechanistic understanding of the role of astrocytes in regulating synaptic development. Copyright © 2017 Elsevier Inc. All rights reserved.

The fate of calcium carbonate nanoparticles administered by oral route: absorption and their interaction with biological matrices

Directory of Open Access Journals (Sweden)

Lee JA

2015-03-01

Full Text Available Jeong-A Lee,1,* Mi-Kyung Kim,1,* Hyoung-Mi Kim,2,* Jong Kwon Lee,3 Jayoung Jeong,4 Young-Rok Kim,5 Jae-Min Oh,2 Soo-Jin Choi1 1Department of Food Science and Technology, Seoul Women’s University, Seoul, Republic of Korea; 2Department of Chemistry and Medical Chemistry, College of Science and Technology, Yonsei University, Wonju, Republic of Korea; 3Hazard Substances Analysis Division, Gwangju Regional Food and Drug Administration, Ministry of Food and Drug Safety, Gwangju, Republic of Korea; 4Toxicological Research Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Chungcheongbuk-do, Republic of Korea; 5Department of Food Science and Biotechnology, Kyung Hee University, Yongin, Republic of Korea *These authors contributed equally to this work Background: Orally administered particles rapidly interact with biological fluids containing proteins, enzymes, electrolytes, and other biomolecules to eventually form particles covered by a corona, and this corona potentially affects particle uptake, fate, absorption, distribution, and elimination in vivo. This study explored relationships between the biological interactions of calcium carbonate particles and their biokinetics.Methods: We examined the effects of food grade calcium carbonates of different particle size (nano [N-Cal] and bulk [B-Cal]: specific surface areas of 15.8 and 0.83 m2/g, respectively on biological interactions in in vitro simulated physiological fluids, ex vivo biofluids, and in vivo in gastrointestinal fluid. Moreover, absorption and tissue distribution of calcium carbonates were evaluated following a single dose oral administration to rats.Results: N-Cal interacted more with biomatrices than bulk materials in vitro and ex vivo, as evidenced by high fluorescence quenching ratios, but it did not interact more actively with biomatrices in vivo. Analysis of coronas revealed that immunoglobulin, apolipoprotein, thrombin, and fibrinogen

Ionic interactions in biological and physical systems: a variational treatment.

Science.gov (United States)

Eisenberg, Bob

2013-01-01

Chemistry is about chemical reactions. Chemistry is about electrons changing their configurations as atoms and molecules react. Chemistry has for more than a century studied reactions as if they occurred in ideal conditions of infinitely dilute solutions. But most reactions occur in salt solutions that are not ideal. In those solutions everything (charged) interacts with everything else (charged) through the electric field, which is short and long range extending to the boundaries of the system. Mathematics has recently been developed to deal with interacting systems of this sort. The variational theory of complex fluids has spawned the theory of liquid crystals (or vice versa). In my view, ionic solutions should be viewed as complex fluids, particularly in the biological and engineering context. In both biology and electrochemistry ionic solutions are mixtures highly concentrated (to approximately 10 M) where they are most important, near electrodes, nucleic ids, proteins, active sites of enzymes, and ionic channels. Ca2+ is always involved in biological solutions because the concentration (really free energy per mole) of Ca2+ in a particular location is the signal that controls many biological functions. Such interacting systems are not simple fluids, and it is no wonder that analysis of interactions, such as the Hofmeister series, rooted in that tradition has not succeeded as one would hope. Here, we present a variational treatment of ard spheres in a frictional dielectric with the hope that such a treatment of an lectrolyte as a complex fluid will be productive. The theory automatically extends to spatially nonuniform boundary conditions and the nonequilibrium systems and flows they produce. The theory is unavoidably self-consistent since differential equations are derived (not assumed) from models of (Helmholtz free) nergy and dissipation of the electrolyte. The origin of the Hofmeister series is (in my view) an inverse problem that becomes well posed when

Potential application of SERS for arsenic speciation in biological matrices.

Science.gov (United States)

Yang, Mingwei; Matulis, Shannon; Boise, Lawrence H; McGoron, Anthony J; Cai, Yong

2017-08-01

Speciation of arsenic is usually carried out using chromatography-based methods coupled with spectroscopic determination; however, the inevitable procedures involving sample preparation and separation could potentially alter the integrity of the arsenic metabolites present in biological samples. Surface-enhanced Raman spectroscopy (SERS) could be a promising alternative for providing a reliable arsenic analysis under the influence of a cellular matrix. A method for arsenic speciation using SERS in cellular matrix was developed in this study and four arsenicals were selected, including arsenite (As III ), arsenate (As V ), monomethylarsonic acid (MMA V ) and dimethylarsinic acid (DMA V ). Silver nanoparticles in the form of colliodal suspension with different surface charges, i.e., coated with citrate (AgNPs-Citrate) and spermine (AgNPs-Spermine) were employed as SERS substrates. Adsorption of arsenicals on nanoparticles in colloidal suspensions and the cellular matrix and the pH, size, and zeta potential of the colloidal suspensions were investigated for a better understanding of the SERS signal response of arsenicals in the colloidal suspensions or under the influence of cellular matrix. Arsenicals showed substantially different SERS responses in the two colloidal suspensions, mainly because of the distinct difference in the interaction between the arsenicals and the nanoparticles. Arsenic speciation in cell lysate could be successfully carried out in AgNPs-Spermine suspension, while AgNPs-Citrate could not yield significant SERS signals under the experimental conditions. This study proved that AgNPs-Spermine colloidal suspension could be a promising SERS substrate for studying arsenic metabolism in a biological matrix, reducing the bias caused by traditional techniques that involve sample extraction and pretreatment.

Comparison of Leptospira interrogans and Leptospira biflexa genomes: analysis of potential leptospiral-host interactions.

Science.gov (United States)

Mehrotra, Prachi; Ramakrishnan, Gayatri; Dhandapani, Gunasekaran; Srinivasan, Narayanaswamy; Madanan, Madathiparambil G

2017-05-02

Leptospirosis, a potentially life-threatening disease, remains the most widespread zoonosis caused by pathogenic species of Leptospira. The pathogenic spirochaete, Leptospira interrogans, is characterized by its ability to permeate human host tissues rapidly and colonize multiple organs in the host. In spite of the efforts taken to comprehend the pathophysiology of the pathogen and the heterogeneity posed by L. interrogans, the current knowledge on the mechanism of pathogenesis is modest. In an attempt to contribute towards the same, we demonstrate the use of an established structure-based protocol coupled with information on subcellular localization of proteins and their tissue-specificity, in recognizing a set of 49 biologically feasible interactions potentially mediated by proteins of L. interrogans in humans. We have also presented means to adjudge the physicochemical viability of the predicted host-pathogen interactions, for selected cases, in terms of interaction energies and geometric shape complementarity of the interacting proteins. Comparative analyses of proteins of L. interrogans and the saprophytic spirochaete, Leptospira biflexa, and their predicted involvement in interactions with human hosts, aided in underpinning the functional relevance of leptospiral-host protein-protein interactions specific to L. interrogans as well as those specific to L. biflexa. Our study presents characteristics of the pathogenic L. interrogans that are predicted to facilitate its ability to persist in human hosts.

On singular interaction potentials in classical statistical mechanics

International Nuclear Information System (INIS)

Zagrebnov, V.A.; Pastur, L.A.

1978-01-01

A classical system of particles with stable two-body interaction potential is considered. It is shown that for a certain class of highly singular stable two-body potentials a cut-off procedure preserves the stability of the potential. The thermodynamical potentials (pressure and free energy density) and correlation functions are proved to have the property of asymptotic independence with respect to the continuation of the interaction potentials near singularity

A Synthetic Biology Project - Developing a single-molecule device for screening drug-target interactions.

Science.gov (United States)

Firman, Keith; Evans, Luke; Youell, James

2012-07-16

This review describes a European-funded project in the area of Synthetic Biology. The project seeks to demonstrate the application of engineering techniques and methodologies to the design and construction of a biosensor for detecting drug-target interactions at the single-molecule level. Production of the proteins required for the system followed the principle of previously described "bioparts" concepts (a system where a database of biological parts - promoters, genes, terminators, linking tags and cleavage sequences - is used to construct novel gene assemblies) and cassette-type assembly of gene expression systems (the concept of linking different "bioparts" to produce functional "cassettes"), but problems were quickly identified with these approaches. DNA substrates for the device were also constructed using a cassette-system. Finally, micro-engineering was used to build a magnetoresistive Magnetic Tweezer device for detection of single molecule DNA modifying enzymes (motors), while the possibility of constructing a Hall Effect version of this device was explored. The device is currently being used to study helicases from Plasmodium as potential targets for anti-malarial drugs, but we also suggest other potential uses for the device. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Identification of polycystic ovary syndrome potential drug targets based on pathobiological similarity in the protein-protein interaction network

OpenAIRE

Huang, Hao; He, Yuehan; Li, Wan; Wei, Wenqing; Li, Yiran; Xie, Ruiqiang; Guo, Shanshan; Wang, Yahui; Jiang, Jing; Chen, Binbin; Lv, Junjie; Zhang, Nana; Chen, Lina; He, Weiming

2016-01-01

Polycystic ovary syndrome (PCOS) is one of the most common endocrinological disorders in reproductive aged women. PCOS and Type 2 Diabetes (T2D) are closely linked in multiple levels and possess high pathobiological similarity. Here, we put forward a new computational approach based on the pathobiological similarity to identify PCOS potential drug target modules (PPDT-Modules) and PCOS potential drug targets in the protein-protein interaction network (PPIN). From the systems level and biologi...

Risk factors for potential drug interactions in general practice

DEFF Research Database (Denmark)

Bjerrum, Lars; Gonzalez Lopez-Valcarcel, Beatriz; Petersen, Gert

2008-01-01

interactions during 1 year. Patient factors associated with increased risk of potential drug interactions were high age, a high number of concurrently used drugs, and a high number of prescribers. Practice factors associated with potential drug interactions were a high percentage of elderly patients and a low......Objective: To identify patient- and practice-related factors associated with potential drug interactions. Methods: A register analysis study in general practices in the county of Funen, Denmark. Prescription data were retrieved from a population-based prescription database (Odense University......, depending on the severity of outcome and the quality of documentation. A two-level random coefficient logistic regression model was used to investigate factors related to potential drug interactions. Results: One-third of the population was exposed to polypharmacy, and 6% were exposed to potential drug...

Highlighting the nuances behind interaction of picosecond pulses with human skin: Relating distinct laser-tissue interactions to their potential in cutaneous interventions

Science.gov (United States)

Uzunbajakava, Natallia E.; Varghese, Babu; Botchkareva, Natalia V.; Verhagen, Rieko; Vogel, Alfred

2018-02-01

In recent years, several commercial systems relying on picosecond pulses have been introduced into the field of cutaneous interventions. In parallel with this development, a somewhat distinct research prototype also operating in the picosecond regime was described in literature. Albeit both market-available products and the investigational device employ laser beams of nearly the same pulse duration and were reported to cause laser-induced optical breakdown (LIOB), they are different in terms of wavelength, applied fluence, laser beam quality, optical architecture and related focusing optics, resulting in different histomorphological features (such as e.g. lesion size, location, expression of collagen). Understanding the differences between these systems in relation to implications for clinical results raises a need in highlighting the nuances behind interaction of picosecond pulses with biological tissue. To achieve this, we accentuate the interplay of irradiance levels of picosecond pulses in W/cm2 , absorption properties of a target tissue at a wavelength of a light source and resulting interaction mechanisms with biological object. We also relate these nuances to potential consequences for cutaneous interventions.

Interaction mechanisms and biological effects of static magnetic fields

Energy Technology Data Exchange (ETDEWEB)

Tenforde, T.S.

1994-06-01

Mechanisms through which static magnetic fields interact with living systems are described and illustrated by selected experimental observations. These mechanisms include electrodynamic interactions with moving, ionic charges (blood flow and nerve impulse conduction), magnetomechanical interactions (orientation and translation of molecules structures and magnetic particles), and interactions with electronic spin states in charge transfer reactions (photo-induced electron transfer in photosynthesis). A general summary is also presented of the biological effects of static magnetic fields. There is convincing experimental evidence for magnetoreception mechanisms in several classes of lower organisms, including bacteria and marine organisms. However, in more highly evolved species of animals, there is no evidence that the interactions of static magnetic fields with flux densities up to 2 Tesla (1 Tesla [T] = 10{sup 4} Gauss) produce either behavioral or physiolocical alterations. These results, based on controlled studies with laboratory animals, are consistent with the outcome of recent epidemiological surveys on human populations exposed occupationally to static magnetic fields.

Biclustering with Flexible Plaid Models to Unravel Interactions between Biological Processes.

Science.gov (United States)

Henriques, Rui; Madeira, Sara C

2015-01-01

Genes can participate in multiple biological processes at a time and thus their expression can be seen as a composition of the contributions from the active processes. Biclustering under a plaid assumption allows the modeling of interactions between transcriptional modules or biclusters (subsets of genes with coherence across subsets of conditions) by assuming an additive composition of contributions in their overlapping areas. Despite the biological interest of plaid models, few biclustering algorithms consider plaid effects and, when they do, they place restrictions on the allowed types and structures of biclusters, and suffer from robustness problems by seizing exact additive matchings. We propose BiP (Biclustering using Plaid models), a biclustering algorithm with relaxations to allow expression levels to change in overlapping areas according to biologically meaningful assumptions (weighted and noise-tolerant composition of contributions). BiP can be used over existing biclustering solutions (seizing their benefits) as it is able to recover excluded areas due to unaccounted plaid effects and detect noisy areas non-explained by a plaid assumption, thus producing an explanatory model of overlapping transcriptional activity. Experiments on synthetic data support BiP's efficiency and effectiveness. The learned models from expression data unravel meaningful and non-trivial functional interactions between biological processes associated with putative regulatory modules.

Biological interaction of living cells with COSAN-based synthetic vesicles.

Science.gov (United States)

Tarrés, Màrius; Canetta, Elisabetta; Paul, Eleanor; Forbes, Jordan; Azzouni, Karima; Viñas, Clara; Teixidor, Francesc; Harwood, Adrian J

2015-01-15

Cobaltabisdicarbollide (COSAN) [3,3'-Co(1,2-C2B9H11)2](-), is a complex boron-based anion that has the unusual property of self-assembly into membranes and vesicles. These membranes have similar dimensions to biological membranes found in cells, and previously COSAN has been shown to pass through synthetic lipid membranes and those of living cells without causing breakdown of membrane barrier properties. Here, we investigate the interaction of this inorganic membrane system with living cells. We show that COSAN has no immediate effect on cell viability, and cells fully recover when COSAN is removed following exposure for hours to days. COSAN elicits a range of cell biological effects, including altered cell morphology, inhibition of cell growth and, in some cases, apoptosis. These observations reveal a new biology at the interface between inorganic, synthetic COSAN membranes and naturally occurring biological membranes.

Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces.

Science.gov (United States)

Xia, Zheng; Wu, Ling-Yun; Zhou, Xiaobo; Wong, Stephen T C

2010-09-13

Predicting drug-protein interactions from heterogeneous biological data sources is a key step for in silico drug discovery. The difficulty of this prediction task lies in the rarity of known drug-protein interactions and myriad unknown interactions to be predicted. To meet this challenge, a manifold regularization semi-supervised learning method is presented to tackle this issue by using labeled and unlabeled information which often generates better results than using the labeled data alone. Furthermore, our semi-supervised learning method integrates known drug-protein interaction network information as well as chemical structure and genomic sequence data. Using the proposed method, we predicted certain drug-protein interactions on the enzyme, ion channel, GPCRs, and nuclear receptor data sets. Some of them are confirmed by the latest publicly available drug targets databases such as KEGG. We report encouraging results of using our method for drug-protein interaction network reconstruction which may shed light on the molecular interaction inference and new uses of marketed drugs.

Potential for widespread application of biological control of stored-product pests

DEFF Research Database (Denmark)

Hansen, Lise Stengaard

2007-01-01

Biological control of stored product pests has substantial potential in Europe". This is essentially the conclusion of the activities of a European working group funded by the COST system, an intergovernmental networking system. Working group 4 of COST action 842 (2000-2005) focussed on biologica...... for these situations will contribute to ensuring that stored food products are protected from insect and mite pests using techniques that are safe for consumers, workers and the environment.......Biological control of stored product pests has substantial potential in Europe". This is essentially the conclusion of the activities of a European working group funded by the COST system, an intergovernmental networking system. Working group 4 of COST action 842 (2000-2005) focussed on biological...

Low-level radiation: biological interactions, risks, and benefits. A bibliography

International Nuclear Information System (INIS)

1978-09-01

The bibliography contains 3294 references that were selected from the Department of Energy's data base (EDB). The subjects covered are lower-level radiation effects on man, environmental radiation, and other biological interactions of radiation that appear to be applicable to the low-level radiation problem

Metastable He (n=2) - Ne potential interaction calculation

International Nuclear Information System (INIS)

Rahal, H.

1983-10-01

Diabatic potential terms corresponding to He (2 1 S)-Ne and He (2 3 S)-Ne interactions are calculated. These potentials reproduce the experimental results thermal metastable atom elastic scattering on Ne target. A model which reduces the interaction to a one-electron problem is proposed: the He excited electron. Its interaction with the He + center is reproduced by a ''l'' dependent potential model with a 1/2 behaviour at short range. The electron interaction facing the Ne is described by a l-dependent pseudopotential reproducing with accuracy the electron elastic scattering on a Ne atom. The importance of the corrective term related to the Ne polarizations by the electron and the He + ion is showed in this work. In the modelling problems, the accuracy cannot be better than 0.1 MeV [fr

Low-level radiation: biological interactions, risks, and benefits. A bibliography

Energy Technology Data Exchange (ETDEWEB)

None

1978-09-01

The bibliography contains 3294 references that were selected from the Department of Energy's data base (EDB). The subjects covered are lower-level radiation effects on man, environmental radiation, and other biological interactions of radiation that appear to be applicable to the low-level radiation problem.

Electron spin interactions in chemistry and biology fundamentals, methods, reactions mechanisms, magnetic phenomena, structure investigation

CERN Document Server

Likhtenshtein, Gertz

2016-01-01

This book presents the versatile and pivotal role of electron spin interactions in nature. It provides the background, methodologies and tools for basic areas related to spin interactions, such as spin chemistry and biology, electron transfer, light energy conversion, photochemistry, radical reactions, magneto-chemistry and magneto-biology. The book also includes an overview of designing advanced magnetic materials, optical and spintronic devices and photo catalysts. This monograph appeals to scientists and graduate students working in the areas related to spin interactions physics, biophysics, chemistry and chemical engineering.

A generic framework for individual-based modelling and physical-biological interaction

DEFF Research Database (Denmark)

Christensen, Asbjørn; Mariani, Patrizio; Payne, Mark R.

2018-01-01

The increased availability of high-resolution ocean data globally has enabled more detailed analyses of physical-biological interactions and their consequences to the ecosystem. We present IBMlib, which is a versatile, portable and computationally effective framework for conducting Lagrangian...... scales. The open-source framework features a minimal robust interface to facilitate the coupling between individual-level biological models and oceanographic models, and we provide application examples including forward/backward simulations, habitat connectivity calculations, assessing ocean conditions...

Weak interaction potentials of nucleons in the Weinberg-Salam model

International Nuclear Information System (INIS)

Lobov, G.A.

1979-01-01

Weak interaction potentials of nucleons due to the nonet vector meson exchange are obtained in the Weinberg-Salam model using the vector-meson dominance. Contribution from the hadronic neutral currents to the weak interaction potential due to the charged pion exchange is obtained. The isotopic structure of the obtained potentials, that is unambiguous in the Weinberg-Salam model, is investigated. Enhancement of the nucleon weak interaction in nuclei resulting from the hadronic neutral currents is discussed. A nuclear one-particle weak interaction potential is presented that is a result of averaging of the two-particle potential over the states of the nuclear core. An approach to the nucleon weak interaction based on the quark model, is discussed. Effects of the nucleon weak interaction in the radiative capture of a thermal neutron by a proton, are considered

An integrated model for interaction of electromagnetic fields with biological systems

International Nuclear Information System (INIS)

Apollonio, F.; Liberti, M.; Cavagnaro, M.; D'Inzeo, G.; Tarricone, L.

1999-01-01

In this work is described a methodology for evaluation of interaction of high frequency electromagnetic field. Biological systems via connection of many macroscopic models. In particular the analysis of neuronal membrane exposed to electromagnetic fields [it

Regulation of drug-metabolizing enzymes in infectious and inflammatory disease: implications for biologics-small molecule drug interactions.

Science.gov (United States)

Mallick, Pankajini; Taneja, Guncha; Moorthy, Bhagavatula; Ghose, Romi

2017-06-01

Drug-metabolizing enzymes (DMEs) are primarily down-regulated during infectious and inflammatory diseases, leading to disruption in the metabolism of small molecule drugs (smds), which are increasingly being prescribed therapeutically in combination with biologics for a number of chronic diseases. The biologics may exert pro- or anti-inflammatory effect, which may in turn affect the expression/activity of DMEs. Thus, patients with infectious/inflammatory diseases undergoing biologic/smd treatment can have complex changes in DMEs due to combined effects of the disease and treatment. Areas covered: We will discuss clinical biologics-SMD interaction and regulation of DMEs during infection and inflammatory diseases. Mechanistic studies will be discussed and consequences on biologic-small molecule combination therapy on disease outcome due to changes in drug metabolism will be highlighted. Expert opinion: The involvement of immunomodulatory mediators in biologic-SMDs is well known. Regulatory guidelines recommend appropriate in vitro or in vivo assessments for possible interactions. The role of cytokines in biologic-SMDs has been documented. However, the mechanisms of drug-drug interactions is much more complex, and is probably multi-factorial. Studies aimed at understanding the mechanism by which biologics effect the DMEs during inflammation/infection are clinically important.

Predicting protein-protein interactions from multimodal biological data sources via nonnegative matrix tri-factorization.

Science.gov (United States)

Wang, Hua; Huang, Heng; Ding, Chris; Nie, Feiping

2013-04-01

Protein interactions are central to all the biological processes and structural scaffolds in living organisms, because they orchestrate a number of cellular processes such as metabolic pathways and immunological recognition. Several high-throughput methods, for example, yeast two-hybrid system and mass spectrometry method, can help determine protein interactions, which, however, suffer from high false-positive rates. Moreover, many protein interactions predicted by one method are not supported by another. Therefore, computational methods are necessary and crucial to complete the interactome expeditiously. In this work, we formulate the problem of predicting protein interactions from a new mathematical perspective--sparse matrix completion, and propose a novel nonnegative matrix factorization (NMF)-based matrix completion approach to predict new protein interactions from existing protein interaction networks. Through using manifold regularization, we further develop our method to integrate different biological data sources, such as protein sequences, gene expressions, protein structure information, etc. Extensive experimental results on four species, Saccharomyces cerevisiae, Drosophila melanogaster, Homo sapiens, and Caenorhabditis elegans, have shown that our new methods outperform related state-of-the-art protein interaction prediction methods.

Biologically controlled minerals as potential indicators of life

Science.gov (United States)

Schwartz, D. E.; Mancinelli, R. L.; Kaneshiro, E.

1991-01-01

Minerals can be produced and deposited either by abiotic or biologic means. Regardless of their origin, mineral crystals reflect the environment conditions (e.g., temperature, pressure, chemical composition, and redox potential) present during crystal formation. Biologically-produced mineral crystals are grown or reworked under the control of their host organism and reflect an environment different from the abiotic environment. In addition, minerals of either biologic or abiotic origin have great longevities. For these reasons, biologically produced minerals have been proposed as biomarkers. Biomarkers are key morphological, chemical, and isotopic signatures of living systems that can be used to determine if life processes have occurred. Studies of biologically controlled minerals produced by the protist, Paramecium tetraurelia, were initiated since techniques have already been developed to culture them and isolate their crystalline material, and methods are already in place to analyze this material. Two direct crystalline phases were identified. One phase, whose chemical composition is high in Mg, was identified as struvite. The second phase, whose chemical composition is high in Ca, has not been previously found occurring naturally and may be considered a newly discovered material. Analyses are underway to determine the characteristics of these minerals in order to compare them with characteristics of these minerals in order to compare them with characteristics of minerals formed abiotically, but with the same chemical composition.

Elucidating the Potential Biological Impact of Cellulose Nanocrystals

Directory of Open Access Journals (Sweden)

Sandra Camarero-Espinosa

2016-07-01

Full Text Available Cellulose nanocrystals exhibit an interesting combination of mechanical properties and physical characteristics, which make them potentially useful for a wide range of consumer applications. However, as the usage of these bio-based nanofibers increases, a greater understanding of human exposure addressing their potential health issues should be gained. The aim of this perspective is to highlight how knowledge obtained from studying the biological impact of other nanomaterials can provide a basis for future research strategies to deduce the possible human health risks posed by cellulose nanocrystals.

The potential for biological structure determination with pulsed neutrons

International Nuclear Information System (INIS)

Wilson, C.C.

1994-01-01

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

The potential for biological structure determination with pulsed neutrons

Energy Technology Data Exchange (ETDEWEB)

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

1994-12-31

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

ESL students learning biology: The role of language and social interactions

Science.gov (United States)

Jaipal, Kamini

This study explored three aspects related to ESL students in a mainstream grade 11 biology classroom: (1) the nature of students' participation in classroom activities, (2) the factors that enhanced or constrained ESL students' engagement in social interactions, and (3) the role of language in the learning of science. Ten ESL students were observed over an eight-month period in this biology classroom. Data were collected using qualitative research methods such as participant observation, audio-recordings of lessons, field notes, semi-structured interviews, short lesson recall interviews and students' written work. The study was framed within sociocultural perspectives, particularly the social constructivist perspectives of Vygotsky (1962, 1978) and Wertsch (1991). Data were analysed with respect to the three research aspects. Firstly, the findings showed that ESL students' preferred and exhibited a variety of participation practices that ranged from personal-individual to socio-interactive in nature. Both personal-individual and socio-interactive practices appeared to support science and language learning. Secondly, the findings indicated that ESL students' engagement in classroom social interactions was most likely influenced by the complex interactions between a number of competing factors at the individual, interpersonal and community/cultural levels (Rogoff, Radziszewska, & Masiello, 1995). In this study, six factors that appeared to enhance or constrain ESL students' engagement in classroom social interactions were identified. These factors were socio-cultural factors, prior classroom practice, teaching practices, affective factors, English language proficiency, and participation in the research project. Thirdly, the findings indicated that language played a significant mediational role in ESL students' learning of science. The data revealed that the learning of science terms and concepts can be explained by a functional model of language that includes: (1

Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach

Directory of Open Access Journals (Sweden)

Luan Yihui

2009-09-01

Full Text Available Abstract Background Many aspects of biological functions can be modeled by biological networks, such as protein interaction networks, metabolic networks, and gene coexpression networks. Studying the statistical properties of these networks in turn allows us to infer biological function. Complex statistical network models can potentially more accurately describe the networks, but it is not clear whether such complex models are better suited to find biologically meaningful subnetworks. Results Recent studies have shown that the degree distribution of the nodes is not an adequate statistic in many molecular networks. We sought to extend this statistic with 2nd and 3rd order degree correlations and developed a pseudo-likelihood approach to estimate the parameters. The approach was used to analyze the MIPS and BIOGRID yeast protein interaction networks, and two yeast coexpression networks. We showed that 2nd order degree correlation information gave better predictions of gene interactions in both protein interaction and gene coexpression networks. However, in the biologically important task of predicting functionally homogeneous modules, degree correlation information performs marginally better in the case of the MIPS and BIOGRID protein interaction networks, but worse in the case of gene coexpression networks. Conclusion Our use of dK models showed that incorporation of degree correlations could increase predictive power in some contexts, albeit sometimes marginally, but, in all contexts, the use of third-order degree correlations decreased accuracy. However, it is possible that other parameter estimation methods, such as maximum likelihood, will show the usefulness of incorporating 2nd and 3rd degree correlations in predicting functionally homogeneous modules.

Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach.

Science.gov (United States)

Wang, Wenhui; Nunez-Iglesias, Juan; Luan, Yihui; Sun, Fengzhu

2009-09-03

Many aspects of biological functions can be modeled by biological networks, such as protein interaction networks, metabolic networks, and gene coexpression networks. Studying the statistical properties of these networks in turn allows us to infer biological function. Complex statistical network models can potentially more accurately describe the networks, but it is not clear whether such complex models are better suited to find biologically meaningful subnetworks. Recent studies have shown that the degree distribution of the nodes is not an adequate statistic in many molecular networks. We sought to extend this statistic with 2nd and 3rd order degree correlations and developed a pseudo-likelihood approach to estimate the parameters. The approach was used to analyze the MIPS and BIOGRID yeast protein interaction networks, and two yeast coexpression networks. We showed that 2nd order degree correlation information gave better predictions of gene interactions in both protein interaction and gene coexpression networks. However, in the biologically important task of predicting functionally homogeneous modules, degree correlation information performs marginally better in the case of the MIPS and BIOGRID protein interaction networks, but worse in the case of gene coexpression networks. Our use of dK models showed that incorporation of degree correlations could increase predictive power in some contexts, albeit sometimes marginally, but, in all contexts, the use of third-order degree correlations decreased accuracy. However, it is possible that other parameter estimation methods, such as maximum likelihood, will show the usefulness of incorporating 2nd and 3rd degree correlations in predicting functionally homogeneous modules.

Mast cells: potential positive and negative roles in tumor biology.

Science.gov (United States)

Marichal, Thomas; Tsai, Mindy; Galli, Stephen J

2013-11-01

Mast cells are immune cells that reside in virtually all vascularized tissues. Upon activation by diverse mechanisms, mast cells can secrete a broad array of biologically active products that either are stored in the cytoplasmic granules of the cells (e.g., histamine, heparin, various proteases) or are produced de novo upon cell stimulation (e.g., prostaglandins, leukotrienes, cytokines, chemokines, and growth factors). Mast cells are best known for their effector functions during anaphylaxis and acute IgE-associated allergic reactions, but they also have been implicated in a wide variety of processes that maintain health or contribute to disease. There has been particular interest in the possible roles of mast cells in tumor biology. In vitro studies have shown that mast cells have the potential to influence many aspects of tumor biology, including tumor development, tumor-induced angiogenesis, and tissue remodeling, and the shaping of adaptive immune responses to tumors. Yet, the actual contributions of mast cells to tumor biology in vivo remain controversial. Here, we review some basic features of mast cell biology with a special emphasis on those relevant to their potential roles in tumors. We discuss how using in vivo tumor models in combination with models in which mast cell function can be modulated has implicated mast cells in the regulation of host responses to tumors. Finally, we summarize data from studies of human tumors that suggest either beneficial or detrimental roles for mast cells in tumors. ©2013 AACR.

Mechanisms of radiation interaction with DNA: Potential implications for radiation protection

International Nuclear Information System (INIS)

1988-01-01

The Office of Health and Environmental Research (OHER) of the US Department of Energy conducts a broad multidisciplinary research program which includes basic biophysics, biophysical chemistry, molecular and cellular biology as well as experimental animal studies and opportunistic human studies. This research is directed at understanding how low levels of radiation of various qualities produce the spectrum of biological effects that are seen for such exposures. This workshop was entitled ''Mechanisms of Radiation Interaction with DNA: Potential Implications for Radiation Protection.'' It ws jointly sponsored by the Department of Energy and the Commission of European Communities. The aim of the workshop was to review the base of knowledge in the area of mechanisms of radiation action at the DNA level, and to explore ways in which this information can be applied to the development of scientifically sound concepts and procedures for use in the field of radiation protection. The overview of research provided by this multidisciplinary group will be helpful to the Office in program planning. This report includes a summary of the presentations, extended abstracts, the meeting agenda, research recommendations, and a list of participants. Individual papers are processed separately for the data base

Mechanisms of radiation interaction with DNA: Potential implications for radiation protection

Energy Technology Data Exchange (ETDEWEB)

1988-01-01

The Office of Health and Environmental Research (OHER) of the US Department of Energy conducts a broad multidisciplinary research program which includes basic biophysics, biophysical chemistry, molecular and cellular biology as well as experimental animal studies and opportunistic human studies. This research is directed at understanding how low levels of radiation of various qualities produce the spectrum of biological effects that are seen for such exposures. This workshop was entitled ''Mechanisms of Radiation Interaction with DNA: Potential Implications for Radiation Protection.'' It ws jointly sponsored by the Department of Energy and the Commission of European Communities. The aim of the workshop was to review the base of knowledge in the area of mechanisms of radiation action at the DNA level, and to explore ways in which this information can be applied to the development of scientifically sound concepts and procedures for use in the field of radiation protection. The overview of research provided by this multidisciplinary group will be helpful to the Office in program planning. This report includes a summary of the presentations, extended abstracts, the meeting agenda, research recommendations, and a list of participants. Individual papers are processed separately for the data base.

Ion mobilities and ion-atom interaction potentials

International Nuclear Information System (INIS)

Gatland, I.R.

1982-01-01

The techniques for measuring the mobilities of ions in gases, relating interaction potentials to mobilities, and determining potentials from experimental mobilities are reviewed. Applications are presented for positive alkali ions and negative halogen ions in inert gases. (Auth.)

Potential intravenous drug interactions in intensive care

Directory of Open Access Journals (Sweden)

Maiara Benevides Moreira

Full Text Available Abstract OBJECTIVE To analyze potential intravenous drug interactions, and their level of severity associated with the administration of these drugs based on the prescriptions of an intensive care unit. METHOD Quantitative study, with aretrospective exploratory design, and descriptive statistical analysis of the ICU prescriptions of a teaching hospital from March to June 2014. RESULTS The sample consisted of 319 prescriptions and subsamples of 50 prescriptions. The mean number of drugs per patient was 9.3 records, and a higher probability of drug interaction inherent to polypharmacy was evidenced. The study identified severe drug interactions, such as concomitant administration of Tramadol with selective serotonin reuptake inhibitor drugs (e.g., Metoclopramide and Fluconazole, increasing the risk of seizures due to their epileptogenic actions, as well as the simultaneous use of Ranitidine-Fentanyl®, which can lead to respiratory depression. CONCLUSION A previous mapping of prescriptions enables the characterization of the drug therapy, contributing to prevent potential drug interactions and their clinical consequences.

Molecular mechanisms of nematode-nematophagous microbe interactions: basis for biological control of plant-parasitic nematodes.

Science.gov (United States)

Li, Juan; Zou, Chenggang; Xu, Jianping; Ji, Xinglai; Niu, Xuemei; Yang, Jinkui; Huang, Xiaowei; Zhang, Ke-Qin

2015-01-01

Plant-parasitic nematodes cause significant damage to a broad range of vegetables and agricultural crops throughout the world. As the natural enemies of nematodes, nematophagous microorganisms offer a promising approach to control the nematode pests. Some of these microorganisms produce traps to capture and kill the worms from the outside. Others act as internal parasites to produce toxins and virulence factors to kill the nematodes from within. Understanding the molecular basis of microbe-nematode interactions provides crucial insights for developing effective biological control agents against plant-parasitic nematodes. Here, we review recent advances in our understanding of the interactions between nematodes and nematophagous microorganisms, with a focus on the molecular mechanisms by which nematophagous microorganisms infect nematodes and on the nematode defense against pathogenic attacks. We conclude by discussing several key areas for future research and development, including potential approaches to apply our recent understandings to develop effective biocontrol strategies.

Localization of weakly interacting Bose gas in quasiperiodic potential

International Nuclear Information System (INIS)

Ray, Sayak; Pandey, Mohit; Ghosh, Anandamohan; Sinha, Subhasis

2016-01-01

We study the localization properties of weakly interacting Bose gas in a quasiperiodic potential. The Hamiltonian of the non-interacting system reduces to the well known ‘Aubry–André model’, which shows the localization transition at a critical strength of the potential. In the presence of repulsive interaction we observe multi-site localization and obtain a phase diagram of the dilute Bose gas by computing the superfluid fraction and the inverse participation ratio. We construct a low-dimensional classical Hamiltonian map and show that the onset of localization is manifested by the chaotic phase space dynamics. The level spacing statistics also identify the transition to localized states resembling a Poisson distribution that are ubiquitous for both non-interacting and interacting systems. We also study the quantum fluctuations within the Bogoliubov approximation and compute the quasiparticle energy spectrum. Enhanced quantum fluctuation and multi-site localization phenomenon of non-condensate density are observed above the critical coupling of the potential. We briefly discuss the effect of the trapping potential on the localization of matter wave. (paper)

Interaction of biological systems with static and ELF electric and magnetic fields

Energy Technology Data Exchange (ETDEWEB)

Anderson, L.E.; Kelman, B.J.; Weigel, R.J. (eds.)

1987-01-01

Although background levels of atmospheric electric and geomagnetic field levels are extremely low, over the past several decades, human beings and other life forms on this planet have been subjected to a dramatically changing electromagnetic milieu. An exponential increase in exposure to electromagnetic fields has occurred, largely because of such technological advances as the growth of electrical power generation and transmission systems, the increased use of wireless communications, and the use of radar. In addition, electromagnetic field generating devices have proliferated in industrial plants, office buildings, homes, public transportation systems, and elsewhere. Although significant increases have occurred in electromagnetic field strenghths spanning all frequency ranges, this symposium addresses only the impact of these fields at static and extremely low frequencies (ELF), primarily 50 and 60 Hz. This volume contains the proceedings of the symposium entitled /open quotes/Interaction of biological systems with static and ELF electric and magnetic fields/close quotes/. The purpose of the symposium was to provide a forum for discussions of all aspects of research on the interaction of static and ELF electromagnetic fields with biological systems. These systems include simple biophysical models, cell and organ preparations, whole animals, and man. Dosimetry, exposure system design, and artifacts in ELF bioeffects research were also addressed, along with current investigations that examine fundamental mechanisms of interactions between the fields and biological processes. Papers are indexed separately.

The Cytoskeleton: Mechanical, Physical, and Biological Interactions

Science.gov (United States)

1996-01-01

This workshop, entitled "The Cytoskeleton: Mechanical, Physical, and Biological Interactions," was sponsored by the Center for Advanced Studies in the Space Life Sciences at the Marine Biological Laboratory. This Center was established through a cooperative agreement between the MBL and the Life Sciences Division of the National Aeronautics and Space Administration. To achieve these goals, the Center sponsors a series of workshops on various topics in the life sciences. Elements of the cytoskeleton have been implicated in the effects of gravity on the growth of plants fungi. An intriguing finding in this regard is the report indicating that an integrin-like protein may be the gravireceptor in the internodal cells of Chara. Involvement of the cytoskeleton in cellular graviperception of the basidiomycete Flammulina velutipes has also been reported. Although the responses of mammalian cells to gravity are not well documented, it has been proposed that integrins can act as mechanochemical transducers in mammalian cells. Little is known about the integrated mechanical and physical properties of cytoplasm, this workshop would be the best place to begin developing interdisciplinary approaches to the effects of mechanical stresses on cells and their most likely responsive cytoplasmic elements- the fibrous proteins comprising the cytoskeleton.

Mathematical computer simulation of the process of ultrasound interaction with biological medium

International Nuclear Information System (INIS)

Yakovleva, T.; Nassiri, D.; Ciantar, D.

1996-01-01

The aim of the paper is to study theoretically the interaction of ultrasound irradiation with biological medium and the peculiarities of ultrasound scattering by inhomogeneities of biological tissue, which can be represented by fractal structures. This investigation has been used for the construction of the computer model of three-dimensional ultrasonic imaging system what gives the possibility to define more accurately the pathological changes in such a tissue by means of its image analysis. Poster 180. (author)

Interaction potential for two different atoms

International Nuclear Information System (INIS)

Kuzmichev, V.E.; Peresypkin, V.V.

1991-01-01

Using the rigorous approach to the nonrelativistic four Coulomb particle problem the interaction potentials between an ordinary hydrogen and muonic-hydrogen atoms at large: R>a e +a μ (1), and intermediate: a e >R>>a μ (2) distances, where a e and a μ are the Bohr radii, are calculated in the adiabatic approximation. The van der Waals potential constants in the region (1) and an explicit potential form in the region (2) taking into account both the polarization effects and the electron screening corrections are determined. 10 refs

Bioactive protein-based nanofibers interact with intestinal biological components resulting in transepithelial permeation of a therapeutic protein

DEFF Research Database (Denmark)

Boutrup Stephansen, Karen; García-Díaz, María; Jessen, Flemming

2015-01-01

Proteins originating from natural sources may constitute a novel type of material for use in drug delivery. However, thorough understanding of the behavior and effects of such a material when processed into a matrix together with a drug is crucial prior to further development into a drug product....... In the present study the potential of using bioactive electrospun fish sarcoplasmic proteins (FSP) as a carrier matrix for small therapeutic proteins was demonstrated in relation to the interactions with biological components of the intestinal tract. The inherent structural and chemical properties of FSP...... as a biomaterial facilitated interactions with cells and enzymes found in the gastrointestinal tract and displayed excellent biocompatibility. More specifically, insulin was efficiently encapsulated into FSP fibers maintaining its conformation, and subsequent controlled release was obtained in simulated intestinal...

Revealing complex function, process and pathway interactions with high-throughput expression and biological annotation data.

Science.gov (United States)

Singh, Nitesh Kumar; Ernst, Mathias; Liebscher, Volkmar; Fuellen, Georg; Taher, Leila

2016-10-20

The biological relationships both between and within the functions, processes and pathways that operate within complex biological systems are only poorly characterized, making the interpretation of large scale gene expression datasets extremely challenging. Here, we present an approach that integrates gene expression and biological annotation data to identify and describe the interactions between biological functions, processes and pathways that govern a phenotype of interest. The product is a global, interconnected network, not of genes but of functions, processes and pathways, that represents the biological relationships within the system. We validated our approach on two high-throughput expression datasets describing organismal and organ development. Our findings are well supported by the available literature, confirming that developmental processes and apoptosis play key roles in cell differentiation. Furthermore, our results suggest that processes related to pluripotency and lineage commitment, which are known to be critical for development, interact mainly indirectly, through genes implicated in more general biological processes. Moreover, we provide evidence that supports the relevance of cell spatial organization in the developing liver for proper liver function. Our strategy can be viewed as an abstraction that is useful to interpret high-throughput data and devise further experiments.

Biophysics of DNA-Protein Interactions From Single Molecules to Biological Systems

CERN Document Server

Williams, Mark C

2011-01-01

This book presents a concise overview of current research on the biophysics of DNA-protein interactions. A wide range of new and classical methods are presented by authors investigating physical mechanisms by which proteins interact with DNA. For example, several chapters address the mechanisms by which proteins search for and recognize specific binding sites on DNA, a process critical for cellular function. Single molecule methods such as force spectroscopy as well as fluorescence imaging and tracking are described in these chapters as well as other parts of the book that address the dynamics of protein-DNA interactions. Other important topics include the mechanisms by which proteins engage DNA sequences and/or alter DNA structure. These simple but important model interactions are then placed in the broader biological context with discussion of larger protein-DNA complexes . Topics include replication forks, recombination complexes, DNA repair interactions, and ultimately, methods to understand the chromatin...

Meta-analysis reveals complex marine biological responses to the interactive effects of ocean acidification and warming

Science.gov (United States)

Harvey, Ben P; Gwynn-Jones, Dylan; Moore, Pippa J

2013-01-01

Ocean acidification and warming are considered two of the greatest threats to marine biodiversity, yet the combined effect of these stressors on marine organisms remains largely unclear. Using a meta-analytical approach, we assessed the biological responses of marine organisms to the effects of ocean acidification and warming in isolation and combination. As expected biological responses varied across taxonomic groups, life-history stages, and trophic levels, but importantly, combining stressors generally exhibited a stronger biological (either positive or negative) effect. Using a subset of orthogonal studies, we show that four of five of the biological responses measured (calcification, photosynthesis, reproduction, and survival, but not growth) interacted synergistically when warming and acidification were combined. The observed synergisms between interacting stressors suggest that care must be made in making inferences from single-stressor studies. Our findings clearly have implications for the development of adaptive management strategies particularly given that the frequency of stressors interacting in marine systems will be likely to intensify in the future. There is now an urgent need to move toward more robust, holistic, and ecologically realistic climate change experiments that incorporate interactions. Without them accurate predictions about the likely deleterious impacts to marine biodiversity and ecosystem functioning over the next century will not be possible. PMID:23610641

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

Directory of Open Access Journals (Sweden)

Mihai V. Putz

2016-07-01

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

Gene-environment interaction and biological monitoring of occupational exposures

International Nuclear Information System (INIS)

Hirvonen, Ari

2005-01-01

Biological monitoring methods and biological limit values applied in occupational and environmental medicine have been traditionally developed on the assumption that individuals do not differ significantly in their biotransformation capacities. It has become clear, however, that this is not the case, but wide inter-individual differences exist in the metabolism of chemicals. Integration of the data on individual metabolic capacity in biological monitoring studies is therefore anticipated to represent a significant refinement of the currently used methods. We have recently conducted several biological monitoring studies on occupationally exposed subjects, which have included the determination of the workers' genotypes for the metabolic genes of potential importance for a given chemical exposure. The exposure levels have been measured by urine metabolites, adducts in blood macromolecules, and cytogenetic alterations in lymphocytes. Our studies indicate that genetic polymorphisms in metabolic genes may indeed be important modifiers of individual biological monitoring results of, e.g., carbon disulphide and styrene. The information is anticipated to be useful in insuring that the workplace is safe for everyone, including the most sensitive individuals. This knowledge could also be useful to occupational physicians, industrial hygienists, and regulatory bodies in charge of defining acceptable exposure limits for environmental and/or occupational pollutants

BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications.

Science.gov (United States)

Cui, Ya; Chen, Xiaowei; Luo, Huaxia; Fan, Zhen; Luo, Jianjun; He, Shunmin; Yue, Haiyan; Zhang, Peng; Chen, Runsheng

2016-06-01

We here present BioCircos.js, an interactive and lightweight JavaScript library especially for biological data interactive visualization. BioCircos.js facilitates the development of web-based applications for circular visualization of various biological data, such as genomic features, genetic variations, gene expression and biomolecular interactions. BioCircos.js and its manual are freely available online at http://bioinfo.ibp.ac.cn/biocircos/ rschen@ibp.ac.cn Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Potentials of single-cell biology in identification and validation of disease biomarkers.

Science.gov (United States)

Niu, Furong; Wang, Diane C; Lu, Jiapei; Wu, Wei; Wang, Xiangdong

2016-09-01

Single-cell biology is considered a new approach to identify and validate disease-specific biomarkers. However, the concern raised by clinicians is how to apply single-cell measurements for clinical practice, translate the message of single-cell systems biology into clinical phenotype or explain alterations of single-cell gene sequencing and function in patient response to therapies. This study is to address the importance and necessity of single-cell gene sequencing in the identification and development of disease-specific biomarkers, the definition and significance of single-cell biology and single-cell systems biology in the understanding of single-cell full picture, the development and establishment of whole-cell models in the validation of targeted biological function and the figure and meaning of single-molecule imaging in single cell to trace intra-single-cell molecule expression, signal, interaction and location. We headline the important role of single-cell biology in the discovery and development of disease-specific biomarkers with a special emphasis on understanding single-cell biological functions, e.g. mechanical phenotypes, single-cell biology, heterogeneity and organization of genome function. We have reason to believe that such multi-dimensional, multi-layer, multi-crossing and stereoscopic single-cell biology definitely benefits the discovery and development of disease-specific biomarkers. © 2016 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

Collaborative Research. Fundamental Science of Low Temperature Plasma-Biological Material Interactions

Energy Technology Data Exchange (ETDEWEB)

Graves, David Barry [Univ. California, Berkeley, CA (United States); Oehrlein, Gottlieb [Univ. of Maryland, College Park, MD (United States)

2014-09-01

Low temperature plasma (LTP) treatment of biological tissue is a promising path toward sterilization of bacteria due to its versatility and ability to operate under well-controlled and relatively mild conditions. The present collaborative research of an interdisciplinary team of investigators at University of Maryland, College Park (UMD), and University of California, Berkeley (UCB) focused on establishing our knowledge based with regard to low temperature plasma-induced chemical modifications in biomolecules that result in inactivation due to various plasma species, including ions, reactive radicals, and UV/VUV photons. The overall goals of the project were to identify and quantify the mechanisms by which low and atmospheric pressure plasma deactivates endotoxic biomolecules. Additionally, we wanted to understand the mechanism by which atmospheric pressure plasmas (APP) modify surfaces and how these modifications depend on the interaction of APP with the environment. Various low pressure plasma sources, a vacuum beam system and several atmospheric pressure plasma sources were used to accomplish this. In our work we elucidated for the first time the role of ions, VUV photons and radicals in biological deactivation of representative biomolecules, both in a UHV beam system and an inductively coupled, low pressure plasma system, and established the associated atomistic biomolecule changes. While we showed that both ions and VUV photons can be very efficient in deactivation of biomolecules, significant etching and/or deep modification (~200 nm) accompanied these biological effects. One of the most important findings in this work is the significant radical-induced deactivation and surface modification can occur with minimal etching. However, if radical fluxes and corresponding etch rates are relatively high, for example at atmospheric pressure, endotoxic biomolecule film inactivation may require near-complete removal of the film. These findings motivated further work at

Arsenic: A Review of the Element's Toxicity, Plant Interactions, and Potential Methods of Remediation.

Science.gov (United States)

Hettick, Bryan E; Cañas-Carrell, Jaclyn E; French, Amanda D; Klein, David M

2015-08-19

Arsenic is a naturally occurring element with a long history of toxicity. Sites of contamination are found worldwide as a result of both natural processes and anthropogenic activities. The broad scope of arsenic toxicity to humans and its unique interaction with the environment have led to extensive research into its physicochemical properties and toxic behavior in biological systems. The purpose of this review is to compile the results of recent studies concerning the metalloid and consider the chemical and physical properties of arsenic in the broad context of human toxicity and phytoremediation. Areas of focus include arsenic's mechanisms of human toxicity, interaction with plant systems, potential methods of remediation, and protocols for the determination of metals in experimentation. This assessment of the literature indicates that controlling contamination of water sources and plants through effective remediation and management is essential to successfully addressing the problems of arsenic toxicity and contamination.

Method and apparatus to image biological interactions in plants

Science.gov (United States)

Weisenberger, Andrew; Bonito, Gregory M.; Reid, Chantal D.; Smith, Mark Frederick

2015-12-22

A method to dynamically image the actual translocation of molecular compounds of interest in a plant root, root system, and rhizosphere without disturbing the root or the soil. The technique makes use of radioactive isotopes as tracers to label molecules of interest and to image their distribution in the plant and/or soil. The method allows for the study and imaging of various biological and biochemical interactions in the rhizosphere of a plant, including, but not limited to, mycorrhizal associations in such regions.

Synthetic Biology and Human Health: Potential Applications for Spaceflight

Science.gov (United States)

Karouia, Fathi; Carr, Christopher; Cai, Yizhi; Chen, Y.; Grenon, Marlene; Larios-Sanz, Maia; Jones, Jeffrey A.; Santos, Orlando

2011-01-01

Human space travelers experience a unique environment that affects homeostasis and physiologic adaptation. Spaceflight-related changes have been reported in the musculo-skeletal, cardiovascular, neurovestibular, endocrine, and immune systems. The spacecraft environment further subjects the traveler to noise and gravitational forces, as well as airborne chemical, microbiological contaminants, and radiation exposure. As humans prepare for longer duration missions effective countermeasures must be developed, verified, and implemented to ensure mission success. Over the past ten years, synthetic biology has opened new avenues for research and development in areas such as biological control, biomaterials, sustainable energy production, bioremediation, and biomedical therapies. The latter in particular is of great interest to the implementation of long-duration human spaceflight capabilities. This article discusses the effects of spaceflight on humans, and reviews current capabilities and potential needs associated with the health of the astronauts where synthetic biology could play an important role in the pursuit of space exploration.

Investigation of interactions in a biological membrane using structure factor/pair correlation function approach: a first communication on nerve myelin

International Nuclear Information System (INIS)

Gbordzoe, M.K.

1984-09-01

Interactions in biological and artificial membranes have been studied by applying mostly the methods of biochemical analysis and determination of thermodynamic parameters related to phase transition phenomena. Structure factor, obtained by measuring scattered intensity from small-angle X-ray or neutron scattering experiments, has been used mainly for determining electron density distribution. Drawing upon the experience of the theory of liquids, where Johnson and March (1963) and Johnson, Hutchinson and March (1964) first established the possibility of deriving interparticle potential from experimental measurement of structure factor, it is suggested that structure factor/distance correlation function approach, can be a useful method for studying interactions between various membrane components. Preliminary experimental data presented for nerve myelin are to demonstrate the possibility of studying interactions from the distance correlation function of a membrane pair. (author)

Systems biology approach to bioremediation

Energy Technology Data Exchange (ETDEWEB)

Chakraborty, Romy; Wu, Cindy H.; Hazen, Terry C.

2012-06-01

Bioremediation has historically been approached as a ‘black box’ in terms of our fundamental understanding. Thus it succeeds and fails, seldom without a complete understanding of why. Systems biology is an integrated research approach to study complex biological systems, by investigating interactions and networks at the molecular, cellular, community, and ecosystem level. The knowledge of these interactions within individual components is fundamental to understanding the dynamics of the ecosystem under investigation. Finally, understanding and modeling functional microbial community structure and stress responses in environments at all levels have tremendous implications for our fundamental understanding of hydrobiogeochemical processes and the potential for making bioremediation breakthroughs and illuminating the ‘black box’.

Trichoderma-plant-pathogen interactions: advances in genetics of biological control.

Science.gov (United States)

Mukherjee, Mala; Mukherjee, Prasun K; Horwitz, Benjamin A; Zachow, Christin; Berg, Gabriele; Zeilinger, Susanne

2012-12-01

Trichoderma spp. are widely used in agriculture as biofungicides. Induction of plant defense and mycoparasitism (killing of one fungus by another) are considered to be the most important mechanisms of Trichoderma-mediated biological control. Understanding these mechanisms at the molecular level would help in developing strains with superior biocontrol properties. In this article, we review our current understanding of the genetics of interactions of Trichoderma with plants and plant pathogens.

An attempt to understand glioma stem cell biology through centrality analysis of a protein interaction network.

Science.gov (United States)

Mallik, Mrinmay Kumar

2018-02-07

Biological networks can be analyzed using "Centrality Analysis" to identify the more influential nodes and interactions in the network. This study was undertaken to create and visualize a biological network comprising of protein-protein interactions (PPIs) amongst proteins which are preferentially over-expressed in glioma cancer stem cell component (GCSC) of glioblastomas as compared to the glioma non-stem cancer cell (GNSC) component and then to analyze this network through centrality analyses (CA) in order to identify the essential proteins in this network and their interactions. In addition, this study proposes a new centrality analysis method pertaining exclusively to transcription factors (TFs) and interactions amongst them. Moreover the relevant molecular functions, biological processes and biochemical pathways amongst these proteins were sought through enrichment analysis. A protein interaction network was created using a list of proteins which have been shown to be preferentially expressed or over-expressed in GCSCs isolated from glioblastomas as compared to the GNSCs. This list comprising of 38 proteins, created using manual literature mining, was submitted to the Reactome FIViz tool, a web based application integrated into Cytoscape, an open source software platform for visualizing and analyzing molecular interaction networks and biological pathways to produce the network. This network was subjected to centrality analyses utilizing ranked lists of six centrality measures using the FIViz application and (for the first time) a dedicated centrality analysis plug-in ; CytoNCA. The interactions exclusively amongst the transcription factors were nalyzed through a newly proposed centrality analysis method called "Gene Expression Associated Degree Centrality Analysis (GEADCA)". Enrichment analysis was performed using the "network function analysis" tool on Reactome. The CA was able to identify a small set of proteins with consistently high centrality ranks that

Nucleus-nucleus potential with repulsive core and elastic scattering. Part 1. Nucleus-nucleus interaction potential

International Nuclear Information System (INIS)

Davidovs'ka, O.Yi.; Denisov, V.Yu.; Nesterov, V.O.

2010-01-01

Various approaches for nucleus-nucleus interaction potential evaluation are discussed in details. It is shown that the antisymmetrization of nucleons belonging to different nuclei and the Pauli principle give the essential contribution into the nucleus-nucleus potential at distances, when nuclei are strongly overlapping, and lead to appearance of the repulsive core of nucleus nucleus interaction at small distances between nuclei.

Biological Interaction of Molybdenocene Dichloride with Bovine Serum Albumin Using Fluorescence Spectroscopy

Science.gov (United States)

Domínguez, Moralba; Cortes-Figueroa, Jose´ E.; Meléndez, Enrique

2018-01-01

Bioinorganic topics are ubiquitous in the inorganic chemistry curriculum; however, experiments to enhance understanding of related topics are scarce. In this proposed laboratory, upper undergraduate students assess the biological interaction of molybdenocene dichloride (Cp2MoCl2) with bovine serum albumin (BSA) by fluorescence spectroscopy.…

Neutron interactions with biological tissue. Final report

International Nuclear Information System (INIS)

1998-01-01

This program was aimed at creating a quantitative physical description, at the micrometer and nanometer levels, of the physical interactions of neutrons with tissue through the ejected secondary charged particles. The authors used theoretical calculations whose input includes neutron cross section data; range, stopping power, ion yield, and straggling information; and geometrical properties. Outputs are initial and slowing-down spectra of charged particles, kerma factors, average values of quality factors, microdosimetric spectra, and integral microdosimetric parameters such as bar y F , bar y D , y * . Since it has become apparent that nanometer site sizes are also relevant to radiobiological effects, the calculations of event size spectra and their parameters were extended to these smaller diameters. This information is basic to radiological physics, radiation biology, radiation protection of workers, and standards for neutron dose measurement

Magnetic nanoparticles as potential candidates for biomedical and biological applications.

Science.gov (United States)

Zeinali Sehrig, Fatemeh; Majidi, Sima; Nikzamir, Nasrin; Nikzamir, Nasim; Nikzamir, Mohammad; Akbarzadeh, Abolfazl

2016-05-01

Magnetic iron oxide nanoparticles have become the main candidates for biomedical and biological applications, and the application of small iron oxide nanoparticles in in vitro diagnostics has been practiced for about half a century. Magnetic nanoparticles (MNPs), in combination with an external magnetic field and/or magnetizable grafts, allow the delivery of particles to the chosen target area, fix them at the local site while the medication is released, and act locally. In this review, we focus mostly on the potential use of MNPs for biomedical and biotechnological applications, and the improvements made in using these nanoparticles (NPs) in biological applications.

Quantification of ultraviolet photon emission from interaction of charged particles in materials of interest in radiation biology research

Energy Technology Data Exchange (ETDEWEB)

Ahmad, Syed Bilal, E-mail: ahmadsb@mcmaster.ca [Department of Medical Physics and Applied Radiation Sciences, University of McMaster, Hamilton, ON (Canada); Department of Physics and Applied Mathematics, Pakistan Institute of Engineering and Applied Sciences, Islamabad (Pakistan); McNeill, Fiona E., E-mail: fmcneill@mcmaster.ca [Department of Medical Physics and Applied Radiation Sciences, University of McMaster, Hamilton, ON (Canada); Prestwich, William V., E-mail: prestwic@mcmaster.ca [Department of Medical Physics and Applied Radiation Sciences, University of McMaster, Hamilton, ON (Canada); Byun, Soo Hyun, E-mail: soohyun@mcmaster.ca [Department of Medical Physics and Applied Radiation Sciences, University of McMaster, Hamilton, ON (Canada); Seymour, Colin, E-mail: seymouc@mcmaster.ca [Department of Medical Physics and Applied Radiation Sciences, University of McMaster, Hamilton, ON (Canada); Mothersill, Carmel E., E-mail: mothers@mcmaster.ca [Department of Medical Physics and Applied Radiation Sciences, University of McMaster, Hamilton, ON (Canada)

2014-01-15

In radiation biology experiments often cells are irradiated using charged particles with the intention that only a specified number of cells are hit by the primary ion track. However, in doing so several other materials such as the cell container and the growth media etc. are also irradiated, and UV radiation emitted from these materials can potentially interact with the cells. We have hypothesized that some “bystander effects” that are thought to be chemically mediated, may be, in fact, a physical effect, where UV is interacting with non-targeted cells. Based upon our hypothesis we quantified the emission of UV from Polypropylene, Mylar, Teflon, and Cellophane which are all commonly used materials in radiation biology experiments. Additionally we measured the NIST standard materials of Oyster tissue and Citrus leaves as these powdered materials are derived from living cells. Protons accelerated up to an energy of 2.2 MeV, in a 3 MV Van de Graff accelerator, were used for irradiation. Beam current was kept to 10 nA, which corresponds to a proton fluence rate of 2.7 × 10{sup 10} protons mm{sup −2} s{sup −1}. All the materials were found to emit light at UV frequencies and intensities that were significant enough to conduct a further investigation for their biological consequences. Mylar and polypropylene are commonly used in radiation induced bystander effect studies and are considered to be non-fluorescent. However our study showed that this is not the case. Significant luminescence observed from the irradiated NIST standard reference materials for Oyster tissue and Citrus leaves verified that the luminescence emission is not restricted only to the polymeric materials that are used to contain cells. It can also occur from ion interactions within the cells as well.

Exploiting biological activities of brown seaweed Ecklonia cava for potential industrial applications: a review.

Science.gov (United States)

Wijesinghe, W A J P; Jeon, You-Jin

2012-03-01

Seaweeds are rich in vitamins, minerals, dietary fibres, proteins, polysaccharides and various functional polyphenols. Many researchers have focused on brown algae as a potential source of bioactive materials in the past few decades. Ecklonia cava is a brown seaweed that is abundant in the subtidal regions of Jeju Island in the Republic of Korea. This seaweed attracted extensive interest due to its multiple biological activities. E. cava has been identified as a potential producer of wide spectrum of natural substances such as carotenoids, fucoidans and phlorotannins showing different biological activities in vital industrial applications including pharmaceutical, nutraceutical, cosmeceutical and functional food. This review focuses on biological activities of the brown seaweed E. cava based on latest research results, including antioxidant, anticoagulative, antimicrobial, antihuman immunodeficiency virus, anti-inflammatory, immunomodulatory, antimutagenic, antitumour and anticancer effects. The facts summarized here may provide novel insights into the functions of E. cava and its derivatives and potentially enable their use as functional ingredients in potential industrial applications.

Interactive learning and action: realizing the promise of synthetic biology for global health

NARCIS (Netherlands)

Betten, A.W.; Roelofsen, A.; Broerse, J.E.W.

2013-01-01

The emerging field of synthetic biology has the potential to improve global health. For example, synthetic biology could contribute to efforts at vaccine development in a context in which vaccines and immunization have been identified by the international community as being crucial to international

Sialoglycoconjugates in Trypanosoma cruzi-host cell interaction: possible biological model - a review

Directory of Open Access Journals (Sweden)

Alane Beatriz Vermelho

1994-03-01

Full Text Available A number of glycoconjugates, including glycolipids and glycoproteins, participate in the process of host-cell invasion by Trypanosoma cruzi and one of the most important carbohydrates involved on this interaction is sialic acid. It is known that parasite trans-sialidase participates with sialic acid in a coordinated fashion in the initial stages of invasion. Given the importance of these sialogycoconjugates, this review sets out various possible biological models for the interaction between the parasite and mammalian cells that possess a sialylated receptor/ligand system.

Solitary wave exchange potential and nucleon-nucleon interaction

International Nuclear Information System (INIS)

Prema, K.; Raghavan, S.S.; Sekhar Raghavan

1986-11-01

Nucleon-nucleon interaction is studied using a phenomenological potential model called solitary wave exchange potential model. It is shown that this simple model reproduces the singlet and triplet scattering data and the deuteron parameters reasonably well. (author). 6 refs, 2 figs, 1 tab

Study of interaction in silica glass via model potential approach

Science.gov (United States)

Mann, Sarita; Rani, Pooja

2016-05-01

Silica is one of the most commonly encountered substances in daily life and in electronics industry. Crystalline SiO2 (in several forms: quartz, cristobalite, tridymite) is an important constituent of many minerals and gemstones, both in pure form and mixed with related oxides. Cohesive energy of amorphous SiO2 has been investigated via intermolecular potentials i.e weak Van der Waals interaction and Morse type short-range interaction. We suggest a simple atom-atom based Van der Waals as well as Morse potential to find cohesive energy of glass. It has been found that the study of silica structure using two different model potentials is significantly different. Van der Waals potential is too weak (P.E =0.142eV/molecule) to describe the interaction between silica molecules. Morse potential is a strong potential, earlier given for intramolecular bonding, but if applied for intermolecular bonding, it gives a value of P.E (=-21.92eV/molecule) to appropriately describe the structure of silica.

Potential disruption of protein-protein interactions by graphene oxide

International Nuclear Information System (INIS)

Feng, Mei; Kang, Hongsuk; Luan, Binquan; Yang, Zaixing; Zhou, Ruhong

2016-01-01

Graphene oxide (GO) is a promising novel nanomaterial with a wide range of potential biomedical applications due to its many intriguing properties. However, very little research has been conducted to study its possible adverse effects on protein-protein interactions (and thus subsequent toxicity to human). Here, the potential cytotoxicity of GO is investigated at molecular level using large-scale, all-atom molecular dynamics simulations to explore the interaction mechanism between a protein dimer and a GO nanosheet oxidized at different levels. Our theoretical results reveal that GO nanosheet could intercalate between the two monomers of HIV-1 integrase dimer, disrupting the protein-protein interactions and eventually lead to dimer disassociation as graphene does [B. Luan et al., ACS Nano 9(1), 663 (2015)], albeit its insertion process is slower when compared with graphene due to the additional steric and attractive interactions. This study helps to better understand the toxicity of GO to cell functions which could shed light on how to improve its biocompatibility and biosafety for its wide potential biomedical applications.

Potential disruption of protein-protein interactions by graphene oxide

Energy Technology Data Exchange (ETDEWEB)

Feng, Mei [Department of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou 310027 (China); Kang, Hongsuk; Luan, Binquan [Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598 (United States); Yang, Zaixing [Institute of Quantitative Biology and Medicine, SRMP and RAD-X, and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123 (China); Zhou, Ruhong, E-mail: ruhong@us.ibm.com [Department of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou 310027 (China); Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598 (United States); Department of Chemistry, Columbia University, New York, New York 10027 (United States)

2016-06-14

Graphene oxide (GO) is a promising novel nanomaterial with a wide range of potential biomedical applications due to its many intriguing properties. However, very little research has been conducted to study its possible adverse effects on protein-protein interactions (and thus subsequent toxicity to human). Here, the potential cytotoxicity of GO is investigated at molecular level using large-scale, all-atom molecular dynamics simulations to explore the interaction mechanism between a protein dimer and a GO nanosheet oxidized at different levels. Our theoretical results reveal that GO nanosheet could intercalate between the two monomers of HIV-1 integrase dimer, disrupting the protein-protein interactions and eventually lead to dimer disassociation as graphene does [B. Luan et al., ACS Nano 9(1), 663 (2015)], albeit its insertion process is slower when compared with graphene due to the additional steric and attractive interactions. This study helps to better understand the toxicity of GO to cell functions which could shed light on how to improve its biocompatibility and biosafety for its wide potential biomedical applications.

Diabatic interaction potential for nucleus-nucleus collisions

International Nuclear Information System (INIS)

Noerenberg, W.; Lukasiak, A.

1984-01-01

Within a refined method for the construction of diabatic states allowing for the treatment of the full spin-orbit coupling, characteristic features of the diabatic potential for nucleus-nucleus collisions are investigated. Approximately 90% of the strong repulsion results from diabatic particle-hole excitations, while only 10% is due to compression. The diabatic interaction potential describes a physical situation intermediate between adiabatic and sudden approximations. (orig.)

Binaural interaction in auditory evoked potentials: Brainstem, middle- and long-latency components

OpenAIRE

McPherson, DL; Starr, A

1993-01-01

Binaural interaction occurs in the auditory evoked potentials when the sum of the monaural auditory evoked potentials are not equivalent to the binaural evoked auditory potentials. Binaural interaction of the early- (0-10 ms), middle- (10-50 ms) and long-latency (50-200 ms) auditory evoked potentials was studied in 17 normal young adults. For the early components, binaural interaction was maximal at 7.35 ms accounting for a reduction of 21% of the amplitude of the binaural evoked potentials. ...

Creating biological nanomaterials using synthetic biology

International Nuclear Information System (INIS)

Rice, MaryJoe K; Ruder, Warren C

2014-01-01

Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems. (review)

Creating biological nanomaterials using synthetic biology.

Science.gov (United States)

Rice, MaryJoe K; Ruder, Warren C

2014-02-01

Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems.

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

A knowledge-driven interaction analysis reveals potential neurodegenerative mechanism of multiple sclerosis susceptibility.

Science.gov (United States)

Bush, W S; McCauley, J L; DeJager, P L; Dudek, S M; Hafler, D A; Gibson, R A; Matthews, P M; Kappos, L; Naegelin, Y; Polman, C H; Hauser, S L; Oksenberg, J; Haines, J L; Ritchie, M D

2011-07-01

Gene-gene interactions are proposed as an important component of the genetic architecture of complex diseases, and are just beginning to be evaluated in the context of genome-wide association studies (GWAS). In addition to detecting epistasis, a benefit to interaction analysis is that it also increases power to detect weak main effects. We conducted a knowledge-driven interaction analysis of a GWAS of 931 multiple sclerosis (MS) trios to discover gene-gene interactions within established biological contexts. We identify heterogeneous signals, including a gene-gene interaction between CHRM3 (muscarinic cholinergic receptor 3) and MYLK (myosin light-chain kinase) (joint P=0.0002), an interaction between two phospholipase C-β isoforms, PLCβ1 and PLCβ4 (joint P=0.0098), and a modest interaction between ACTN1 (actinin alpha 1) and MYH9 (myosin heavy chain 9) (joint P=0.0326), all localized to calcium-signaled cytoskeletal regulation. Furthermore, we discover a main effect (joint P=5.2E-5) previously unidentified by single-locus analysis within another related gene, SCIN (scinderin), a calcium-binding cytoskeleton regulatory protein. This work illustrates that knowledge-driven interaction analysis of GWAS data is a feasible approach to identify new genetic effects. The results of this study are among the first gene-gene interactions and non-immune susceptibility loci for MS. Further, the implicated genes cluster within inter-related biological mechanisms that suggest a neurodegenerative component to MS.

Experimental evidence of biological interactions among different isolates of Trypanosoma cruzi from the Chaco Region.

Directory of Open Access Journals (Sweden)

Paula G Ragone

Full Text Available Many infectious diseases arise from co-infections or re-infections with more than one genotype of the same pathogen. These mixed infections could alter host fitness, the severity of symptoms, success in pathogen transmission and the epidemiology of the disease. Trypanosoma cruzi, the etiological agent of Chagas disease, exhibits a high biological variability often correlated with its genetic diversity. Here, we developed an experimental approach in order to evaluate biological interaction between three T. cruzi isolates belonging to different Discrete Typing Units (DTUs TcIII, TcV and TcVI. These isolates were obtained from a restricted geographical area in the Chaco Region. Different mixed infections involving combinations of two isolates (TcIII + TcV, TcIII + TcVI and TcV + TcVI were studied in a mouse model. The parameters evaluated were number of parasites circulating in peripheral blood, histopathology and genetic characterization of each DTU in different tissues by DNA hybridization probes. We found a predominance of TcVI isolate in blood and tissues respect to TcIII and TcV; and a decrease of the inflammatory response in heart when the damage of mice infected with TcVI and TcIII + TcVI mixture were compared. In addition, simultaneous presence of two isolates in the same tissue was not detected. Our results show that biological interactions between isolates with different biological behaviors lead to changes in their biological properties. The occurrence of interactions among different genotypes of T. cruzi observed in our mouse model suggests that these phenomena could also occur in natural cycles in the Chaco Region.

Do field-free electromagnetic potentials play a role in biology?

Science.gov (United States)

Szasz, A; Vincze, G; Andocs, G; Szasz, O

2009-01-01

All bio-systems are imperfect dielectrics. Their general properties however cannot be described by conventional simple electrodynamics; the system is more complex. A central question in our present paper is centered on a controversial debate of the possible effect of the zero fields (only potentials exist). We show that the identical use of the "field-free," "curl-free," and "force-free" terminologies is incorrect, there have definitely different meanings. It is shown that the effective electro-dynamical parameters that describe and modify living systems are the potentials and not the fields. We discuss how the potentials have a role in biological processes even in field-free cases.

Study of interaction in silica glass via model potential approach

Energy Technology Data Exchange (ETDEWEB)

Mann, Sarita, E-mail: saritaiitr2003@gmail.com [Department of Physics, Panjab University, Chandigarh-160014 (India); Rani, Pooja [D.A.V. College, Sec-10, Chandigarh-160010 (India)

2016-05-06

Silica is one of the most commonly encountered substances in daily life and in electronics industry. Crystalline SiO{sub 2} (in several forms: quartz, cristobalite, tridymite) is an important constituent of many minerals and gemstones, both in pure form and mixed with related oxides. Cohesive energy of amorphous SiO{sub 2} has been investigated via intermolecular potentials i.e weak Van der Waals interaction and Morse type short-range interaction. We suggest a simple atom-atom based Van der Waals as well as Morse potential to find cohesive energy of glass. It has been found that the study of silica structure using two different model potentials is significantly different. Van der Waals potential is too weak (P.E =0.142eV/molecule) to describe the interaction between silica molecules. Morse potential is a strong potential, earlier given for intramolecular bonding, but if applied for intermolecular bonding, it gives a value of P.E (=−21.92eV/molecule) to appropriately describe the structure of silica.

Biological potential of Stillingia oppositifolia

Directory of Open Access Journals (Sweden)

Betania Barros Cota

2011-02-01

Full Text Available Organic extracts from leaves and stems of Stillingia oppositifolia Baill. ex Müll. Arg., Euphorbiaceae, were screened for antifungal and cytotoxic properties. The extracts presented Minimum Inhibitory Concentration values around 250 µg.mL-1 against Candida krusei and Candida tropicalis, and around 63 µg.mL-1 for Paracoccidioides brasiliensis. They were tested on three human cell lines (UACC-62, MCF-7, and TK-10, disclosing GI50 values, (concentration able to inhibit 50% of the cell growth ranging from 50 to 100 µg.mL-1. Organic extract from stems furnished hexanic, dichloromethanic and aqueous phases after partition. Chromatographic fractionation of the hexanic soluble phase of the stems yielded aleuritolic acid 3-acetate, β-sitosterol, 3-epi-β-amyrin, β-amyrone and palmitic acid. These compounds showed antifungal and cytotoxic activities in the same range as the organic crude extract and low toxic effect against mononuclear cells obtained from human peripheral blood. This is the first report on chemical and biological potential of S. oppositifolia.

Microorganisms in potential host rocks for geological disposal of nuclear waste and their interactions with radionuclides

Energy Technology Data Exchange (ETDEWEB)

Cherkouk, A.; Liebe, M.; Luetke, L.; Moll, H.; Stumpf, T. [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Inst. of Resource Ecology

2015-07-01

The long-term safety of nuclear waste in a deep geological repository is an important issue in our society. Microorganisms indigenous to potential host rocks are able to influence the oxidation state, speciation and therefore the mobility of radionuclides as well as gas generation or canister corrosion. Therefore, for the safety assessment of such a repository it is necessary to know which microorganisms are present in the potential host rocks (e.g. clay, salt) and if these microorganisms can influence the performance of a repository. Microbial diversity in potential host rocks for geological disposal of nuclear waste was analyzed by culture-independent molecular biological methods (e.g. 16S rRNA gene retrieval) as well as enrichment and isolation of indigenous microbes. Among other isolates, a Paenibacillus strain, as a representative of Firmicutes, was recovered in R2A media under anaerobic conditions from Opalinus clay from the Mont Terri in Switzerland. Accumulation experiments and potentiometric titrations showed a strong interaction of Paenibacillus sp. cells with U(VI) within a broad pH range (3-7). Additionally, the interactions of the halophilic archaeal strain Halobacterium noricense DSM 15987, a salt rock representative reference strain, with U(VI) at high ionic strength was investigated. After 48 h the cells were still alive at uranium concentrations up to 60 μM, which demonstrates that Halobacterium noricense can tolerate uranium concentrations up to this level. The formed uranium sorption species were examined with time-resolved laser-induced fluorescence spectroscopy (TRLFS). The results about the microbial communities present in potential host rocks for nuclear waste repositories and their interactions with radionuclides contribute to the safety assessment of a prospective nuclear waste repository.

Microorganisms in potential host rocks for geological disposal of nuclear waste and their interactions with radionuclides

International Nuclear Information System (INIS)

Cherkouk, A.; Liebe, M.; Luetke, L.; Moll, H.; Stumpf, T.

2015-01-01

The long-term safety of nuclear waste in a deep geological repository is an important issue in our society. Microorganisms indigenous to potential host rocks are able to influence the oxidation state, speciation and therefore the mobility of radionuclides as well as gas generation or canister corrosion. Therefore, for the safety assessment of such a repository it is necessary to know which microorganisms are present in the potential host rocks (e.g. clay, salt) and if these microorganisms can influence the performance of a repository. Microbial diversity in potential host rocks for geological disposal of nuclear waste was analyzed by culture-independent molecular biological methods (e.g. 16S rRNA gene retrieval) as well as enrichment and isolation of indigenous microbes. Among other isolates, a Paenibacillus strain, as a representative of Firmicutes, was recovered in R2A media under anaerobic conditions from Opalinus clay from the Mont Terri in Switzerland. Accumulation experiments and potentiometric titrations showed a strong interaction of Paenibacillus sp. cells with U(VI) within a broad pH range (3-7). Additionally, the interactions of the halophilic archaeal strain Halobacterium noricense DSM 15987, a salt rock representative reference strain, with U(VI) at high ionic strength was investigated. After 48 h the cells were still alive at uranium concentrations up to 60 μM, which demonstrates that Halobacterium noricense can tolerate uranium concentrations up to this level. The formed uranium sorption species were examined with time-resolved laser-induced fluorescence spectroscopy (TRLFS). The results about the microbial communities present in potential host rocks for nuclear waste repositories and their interactions with radionuclides contribute to the safety assessment of a prospective nuclear waste repository.

Using novel descriptor accounting for ligand-receptor interactions to define and visually explore biologically relevant chemical space.

Science.gov (United States)

Rabal, Obdulia; Oyarzabal, Julen

2012-05-25

The definition and pragmatic implementation of biologically relevant chemical space is critical in addressing navigation strategies in the overlapping regions where chemistry and therapeutically relevant targets reside and, therefore, also key to performing an efficient drug discovery project. Here, we describe the development and implementation of a simple and robust method for representing biologically relevant chemical space as a general reference according to current knowledge, independently of any reference space, and analyzing chemical structures accordingly. Underlying our method is the generation of a novel descriptor (LiRIf) that converts structural information into a one-dimensional string accounting for the plausible ligand-receptor interactions as well as for topological information. Capitalizing on ligand-receptor interactions as a descriptor enables the clustering, profiling, and comparison of libraries of compounds from a chemical biology and medicinal chemistry perspective. In addition, as a case study, R-groups analysis is performed to identify the most populated ligand-receptor interactions according to different target families (GPCR, kinases, etc.), as well as to evaluate the coverage of biologically relevant chemical space by structures annotated in different databases (ChEMBL, Glida, etc.).

Using consumption rate to assess potential predators for biological control of white perch

Directory of Open Access Journals (Sweden)

Gosch N.J.C.

2011-08-01

Full Text Available Control of undesirable fishes is important in aquatic systems, and using predation as a tool for biological control is an attractive option to fishery biologists. However, determining the appropriate predators for biological control is critical for success. The objective of this study was to evaluate the utility of consumption rate as an index to determine the most effective predators for biological control of an invasive fish. Consumption rate values were calculated for nine potential predators that prey on white perch Morone americana in Branched Oak and Pawnee reservoirs, Nebraska. The consumption rate index provided a unique and insightful means of determining the potential effectiveness of each predator species in controlling white perch. Cumulative frequency distributions facilitated interpretation by providing a graphical presentation of consumption rates by all individuals within each predator species. Largemouth bass Micropterus salmoides, walleye Sander vitreus and sauger S. canadensis were the most efficient white perch predators in both reservoirs; however, previous attempts to increase biomass of these predators have failed suggesting that successful biological control is unlikely using existing predator species in these Nebraska reservoirs.

Stability of stationary states of non-local equations with singular interaction potentials

KAUST Repository

Fellner, Klemens

2011-04-01

We study the large-time behaviour of a non-local evolution equation for the density of particles or individuals subject to an external and an interaction potential. In particular, we consider interaction potentials which are singular in the sense that their first derivative is discontinuous at the origin.For locally attractive singular interaction potentials we prove under a linear stability condition local non-linear stability of stationary states consisting of a finite sum of Dirac masses. For singular repulsive interaction potentials we show the stability of stationary states of uniformly bounded solutions under a convexity condition.Finally, we present numerical simulations to illustrate our results. © 2010 Elsevier Ltd.

Co-culture systems and technologies: taking synthetic biology to the next level.

Science.gov (United States)

Goers, Lisa; Freemont, Paul; Polizzi, Karen M

2014-07-06

Co-culture techniques find myriad applications in biology for studying natural or synthetic interactions between cell populations. Such techniques are of great importance in synthetic biology, as multi-species cell consortia and other natural or synthetic ecology systems are widely seen to hold enormous potential for foundational research as well as novel industrial, medical and environmental applications with many proof-of-principle studies in recent years. What is needed for co-cultures to fulfil their potential? Cell-cell interactions in co-cultures are strongly influenced by the extracellular environment, which is determined by the experimental set-up, which therefore needs to be given careful consideration. An overview of existing experimental and theoretical co-culture set-ups in synthetic biology and adjacent fields is given here, and challenges and opportunities involved in such experiments are discussed. Greater focus on foundational technology developments for co-cultures is needed for many synthetic biology systems to realize their potential in both applications and answering biological questions. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

Science.gov (United States)

Sorokin, Anatoly; Le Novère, Nicolas; Luna, Augustin; Czauderna, Tobias; Demir, Emek; Haw, Robin; Mi, Huaiyu; Moodie, Stuart; Schreiber, Falk; Villéger, Alice

2015-09-04

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Entity Relationship language (ER) represents biological entities and their interactions and relationships within a network. SBGN ER focuses on all potential relationships between entities without considering temporal aspects. The nodes (elements) describe biological entities, such as proteins and complexes. The edges (connections) provide descriptions of interactions and relationships (or influences), e.g., complex formation, stimulation and inhibition. Among all three languages of SBGN, ER is the closest to protein interaction networks in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

3D-printed biological organs: medical potential and patenting opportunity.

Science.gov (United States)

Yoo, Seung-Schik

2015-05-01

Three-dimensional (3D) bioprinting has emerged as a new disruptive technology that may address the ever-increasing demand for organ transplants. 3D bioprinting offers many technical features that allow for building functional biological tissue constructs by dispensing the individual or group of cells into specific locations along with various types of bio-scaffold materials and extracellular matrices, and thus, may provide flexibility needed for on-demand individualized construction of biological organs. Several key classes of 3D bioprinting techniques are reviewed, including potential medical and industrial applications. Several unanswered engineering components for the ultimate creation of printed biological organs are also discussed. The complicated nature of the human organs, in addition to the legal and ethical requirements for safe implantation into the human body, would require significant research and development to produce marketable bioprinted organs. This also suggests the possibility for further patenting and licensing opportunities from different sectors of the economy.

Physical mechanisms of biological molecular motors

International Nuclear Information System (INIS)

Miller, John H. Jr.; Vajrala, Vijayanand; Infante, Hans L.; Claycomb, James R.; Palanisami, Akilan; Fang Jie; Mercier, George T.

2009-01-01

Biological motors generally fall into two categories: (1) those that convert chemical into mechanical energy via hydrolysis of a nucleoside triphosphate, usually adenosine triphosphate, regarded as life's chemical currency of energy and (2) membrane bound motors driven directly by an ion gradient and/or membrane potential. Here we argue that electrostatic interactions play a vital role for both types of motors and, therefore, the tools of physics can greatly contribute to understanding biological motors

Construction of analytically solvable models for interacting species. [biological species competition

Science.gov (United States)

Rosen, G.

1976-01-01

The basic form of a model representation for systems of n interacting biological species is a set of essentially nonlinear autonomous ordinary differential equations. A generic canonical expression for the rate functions in the equations is reported which permits the analytical general solution to be obtained by elementary computation. It is shown that a general analytical solution is directly obtainable for models where the rate functions are prescribed by the generic canonical expression from the outset. Some illustrative examples are given which demonstrate that the generic canonical expression can be used to construct analytically solvable models for two interacting species with limit-cycle dynamics as well as for a three-species interdependence.

MicroRNAs and potential target interactions in psoriasis

DEFF Research Database (Denmark)

Zibert, John Robert; Løvendorf, Marianne B.; Litman, Thomas

2010-01-01

BACKGROUND: Psoriasis is a chronic inflammatory skin disease often seen in patients with a genetic susceptibility. MicroRNAs (miRNA) are endogenous, short RNA molecules that can bind to parts of mRNA target genes, thus inhibiting their translation and causing accelerated turnover or transcript...... degradation. MicroRNAs are important in the pathogenesis of human diseases such as immunological disorders, as they regulate a broad range of biological processes. OBJECTIVE: We investigated miRNA-mRNA interactions in involved (PP) and non-involved (PN) psoriatic skin compared with healthy skin (NN). METHODS...

Detecting Biological Motion for Human–Robot Interaction: A Link between Perception and Action

Directory of Open Access Journals (Sweden)

Alessia Vignolo

2017-06-01

Full Text Available One of the fundamental skills supporting safe and comfortable interaction between humans is their capability to understand intuitively each other’s actions and intentions. At the basis of this ability is a special-purpose visual processing that human brain has developed to comprehend human motion. Among the first “building blocks” enabling the bootstrapping of such visual processing is the ability to detect movements performed by biological agents in the scene, a skill mastered by human babies in the first days of their life. In this paper, we present a computational model based on the assumption that such visual ability must be based on local low-level visual motion features, which are independent of shape, such as the configuration of the body and perspective. Moreover, we implement it on the humanoid robot iCub, embedding it into a software architecture that leverages the regularities of biological motion also to control robot attention and oculomotor behaviors. In essence, we put forth a model in which the regularities of biological motion link perception and action enabling a robotic agent to follow a human-inspired sensory-motor behavior. We posit that this choice facilitates mutual understanding and goal prediction during collaboration, increasing the pleasantness and safety of the interaction.

Calculation of Rydberg interaction potentials

DEFF Research Database (Denmark)

Weber, Sebastian; Tresp, Christoph; Menke, Henri

2017-01-01

for calculating the required electric multipole moments and the inclusion of electromagnetic fields with arbitrary direction. We focus specifically on symmetry arguments and selection rules, which greatly reduce the size of the Hamiltonian matrix, enabling the direct diagonalization of the Hamiltonian up...... to higher multipole orders on a desktop computer. Finally, we present example calculations showing the relevance of the full interaction calculation to current experiments. Our software for calculating Rydberg potentials including all features discussed in this tutorial is available as open source....

Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes.

Science.gov (United States)

Farré, Jean-Claude; Kramer, Michael; Ideker, Trey; Subramani, Suresh

2017-07-03

Increasingly, various 'omics data are contributing significantly to our understanding of novel biological processes, but it has not been possible to iteratively elucidate hierarchical functions in complex phenomena. We describe a general systems biology approach called Active Interaction Mapping (AI-MAP), which elucidates the hierarchy of functions for any biological process. Existing and new 'omics data sets can be iteratively added to create and improve hierarchical models which enhance our understanding of particular biological processes. The best datatypes to further improve an AI-MAP model are predicted computationally. We applied this approach to our understanding of general and selective autophagy, which are conserved in most eukaryotes, setting the stage for the broader application to other cellular processes of interest. In the particular application to autophagy-related processes, we uncovered and validated new autophagy and autophagy-related processes, expanded known autophagy processes with new components, integrated known non-autophagic processes with autophagy and predict other unexplored connections.

Reactions of copper macrocycles with antioxidants and HOCl: potential for biological redox sensing.

Science.gov (United States)

Sowden, Rebecca J; Trotter, Katherine D; Dunbar, Lynsey; Craig, Gemma; Erdemli, Omer; Spickett, Corinne M; Reglinski, John

2013-02-01

A series of simple copper N(2)S(2) macrocycles were examined for their potential as biological redox sensors, following previous characterization of their redox potentials and crystal structures. The divalent species were reduced by glutathione or ascorbate at a biologically relevant pH in aqueous buffer. A less efficient reduction was also achieved by vitamin E in DMSO. Oxidation of the corresponding univalent copper species by sodium hypochlorite resulted in only partial (~65 %) recovery of the divalent form. This was concluded to be due to competition between metal oxidation and ligand oxidation, which is believed to contribute to macrocycle demetallation. Electrospray mass spectrometry confirmed that ligand oxidation had occurred. Moreover, the macrocyclic complexes could be demetallated by incubation with EDTA and bovine serum albumin, demonstrating that they would be inappropriate for use in biological systems. The susceptibility to oxidation and demetallation was hypothesized to be due to oxidation of the secondary amines. Consequently these were modified to incorporate additional oxygen donor atoms. This modification led to greater resistance to demetallation and ligand oxidation, providing a better platform for further development of copper macrocycles as redox sensors for use in biological systems.

Potential drug-drug interactions on in-patient medication ...

African Journals Online (AJOL)

Potential drug-drug interactions on in-patient medication prescriptions at Mbarara Regional Referral Hospital (MRRH) in western Uganda: prevalence, clinical importance and associated factors. SJ Lubinga, E Uwiduhaye ...

Physical mechanisms of biological molecular motors

Energy Technology Data Exchange (ETDEWEB)

Miller, John H. Jr. [Department of Physics and Texas Center for Superconductivity, University of Houston, 4800 Calhoun Road, Ste. 617 SR1 Houston, TX 77204-5005 (United States)], E-mail: jhmiller@uh.edu; Vajrala, Vijayanand; Infante, Hans L. [Department of Physics and Texas Center for Superconductivity, University of Houston, 4800 Calhoun Road, Ste. 617 SR1 Houston, TX 77204-5005 (United States); Claycomb, James R. [Department of Physics and Texas Center for Superconductivity, University of Houston, 4800 Calhoun Road, Ste. 617 SR1 Houston, TX 77204-5005 (United States); Department of Mathematics and Physics, Houston Baptist University, 7502 Fondren Road, Houston, TX 77074-3298 (United States); Palanisami, Akilan; Fang Jie; Mercier, George T. [Department of Physics and Texas Center for Superconductivity, University of Houston, 4800 Calhoun Road, Ste. 617 SR1 Houston, TX 77204-5005 (United States)

2009-03-01

Biological motors generally fall into two categories: (1) those that convert chemical into mechanical energy via hydrolysis of a nucleoside triphosphate, usually adenosine triphosphate, regarded as life's chemical currency of energy and (2) membrane bound motors driven directly by an ion gradient and/or membrane potential. Here we argue that electrostatic interactions play a vital role for both types of motors and, therefore, the tools of physics can greatly contribute to understanding biological motors.

Biological agents with potential for misuse: a historical perspective and defensive measures

International Nuclear Information System (INIS)

Bhalla, Deepak K.; Warheit, David B.

2004-01-01

Biological and chemical agents capable of producing serious illness or mortality have been used in biowarfare from ancient times. Use of these agents has progressed from crude forms in early and middle ages, when snakes and infected cadavers were used as weapons in battles, to sophisticated preparations for use during and after the second World War. Cults and terrorist organizations have attempted the use of biological agents with an aim to immobilize populations or cause serious harm. The reasons for interest in these agents by individuals and organizations include relative ease of acquisition, potential for causing mass casualty or panic, modest financing requirement, availability of technology, and relative ease of delivery. The Centers for Disease Control and Prevention has classified Critical Biological Agents into three major categories. This classification was based on several criteria, which include severity of impact on human health, potential for delivery in a weapon, capacity to cause panic and special needs for development, and stockpiling of medication. Agents that could cause the greatest harm following deliberate use were placed in category A. Category B included agents capable of producing serious harm and significant mortality but of lower magnitude than category A agents. Category C included emerging pathogens that could be developed for mass dispersion in future and their potential as a major health threat. A brief description of the category A bioagents is included and the pathophysiology of two particularly prominent agents, namely anthrax and smallpox, is discussed in detail. The potential danger from biological agents and their ever increasing threat to human populations have created a need for developing technologies for their early detection, for developing treatment strategies, and for refinement of procedures to ensure survival of affected individuals so as to attain the ultimate goal of eliminating the threat from intentional use of

Biological agents with potential for misuse: a historical perspective and defensive measures.

Science.gov (United States)

Bhalla, Deepak K; Warheit, David B

2004-08-15

Biological and chemical agents capable of producing serious illness or mortality have been used in biowarfare from ancient times. Use of these agents has progressed from crude forms in early and middle ages, when snakes and infected cadavers were used as weapons in battles, to sophisticated preparations for use during and after the second World War. Cults and terrorist organizations have attempted the use of biological agents with an aim to immobilize populations or cause serious harm. The reasons for interest in these agents by individuals and organizations include relative ease of acquisition, potential for causing mass casualty or panic, modest financing requirement, availability of technology, and relative ease of delivery. The Centers for Disease Control and Prevention has classified Critical Biological Agents into three major categories. This classification was based on several criteria, which include severity of impact on human health, potential for delivery in a weapon, capacity to cause panic and special needs for development, and stockpiling of medication. Agents that could cause the greatest harm following deliberate use were placed in category A. Category B included agents capable of producing serious harm and significant mortality but of lower magnitude than category A agents. Category C included emerging pathogens that could be developed for mass dispersion in future and their potential as a major health threat. A brief description of the category A bioagents is included and the pathophysiology of two particularly prominent agents, namely anthrax and smallpox, is discussed in detail. The potential danger from biological agents and their ever increasing threat to human populations have created a need for developing technologies for their early detection, for developing treatment strategies, and for refinement of procedures to ensure survival of affected individuals so as to attain the ultimate goal of eliminating the threat from intentional use of

An appraisal of biological responses and network of environmental interactions in non-mining and mining impacted coastal waters

Digital Repository Service at National Institute of Oceanography (India)

Fernandes, C.E.G.; Malik, A; Jineesh, V.K.; Fernandes, S.O.; Das, A; Pandey, S.S.; Kanolkar, G.; Sujith, P.P.; Velip, D.; Shaikh, S.; Helekar, S.; Gonsalves, M.J.B.D.; Nair, S.; LokaBharathi, P.A

iron brought from the hinterlands. We hypothesize that there could be a shift in biological response along with changes in network of interactions between environmental and biological variables in these mining and non-mining impacted regions, lying 160...

Analytical local electron-electron interaction model potentials for atoms

International Nuclear Information System (INIS)

Neugebauer, Johannes; Reiher, Markus; Hinze, Juergen

2002-01-01

Analytical local potentials for modeling the electron-electron interaction in an atom reduce significantly the computational effort in electronic structure calculations. The development of such potentials has a long history, but some promising ideas have not yet been taken into account for further improvements. We determine a local electron-electron interaction potential akin to those suggested by Green et al. [Phys. Rev. 184, 1 (1969)], which are widely used in atom-ion scattering calculations, electron-capture processes, and electronic structure calculations. Generalized Yukawa-type model potentials are introduced. This leads, however, to shell-dependent local potentials, because the origin behavior of such potentials is different for different shells as has been explicated analytically [J. Neugebauer, M. Reiher, and J. Hinze, Phys. Rev. A 65, 032518 (2002)]. It is found that the parameters that characterize these local potentials can be interpolated and extrapolated reliably for different nuclear charges and different numbers of electrons. The analytical behavior of the corresponding localized Hartree-Fock potentials at the origin and at long distances is utilized in order to reduce the number of fit parameters. It turns out that the shell-dependent form of Green's potential, which we also derive, yields results of comparable accuracy using only one shell-dependent parameter

On the mechanisms of interaction of low-intensity millimeter waves with biological objects

Energy Technology Data Exchange (ETDEWEB)

Betskii, O.V.

1994-07-01

The interaction of low-intensity millimeter-band electromagnetic waves with biological objects is examined. These waves are widely used in medical practice as a means of physiotherapy for the treatment of various human disorders. Principal attention is given to the mechanisms through which millimeter waves act on the human organism.

Market potential for interactive audio-visual media

NARCIS (Netherlands)

Leurdijk, A.; Limonard, S.

2005-01-01

NM2 (New Media for a New Millennium) develops tools for interactive, personalised and non-linear audio-visual content that will be tested in seven pilot productions. This paper looks at the market potential for these productions from a technological, a business and a users' perspective. It shows

Diagnostics of plasma-biological surface interactions in low pressure and atmospheric pressure plasmas

International Nuclear Information System (INIS)

Ishikawa, Kenji; Hori, Masaru

2014-01-01

Mechanisms of plasma-surface interaction are required to understand in order to control the reactions precisely. Recent progress in atmospheric pressure plasma provides to apply as a tool of sterilization of contaminated foodstuffs. To use the plasma with safety and optimization, the real time in situ detection of free radicals - in particular dangling bonds by using the electron-spin-resonance (ESR) technique has been developed because the free radical plays important roles for dominantly biological reactions. First, the kinetic analysis of free radicals on biological specimens such as fungal spores of Penicillium digitatum interacted with atomic oxygen generated plasma electric discharge. We have obtained information that the in situ real time ESR signal from the spores was observed and assignable to semiquinone radical with a g-value of around 2.004 and a line width of approximately 5G. The decay of the signal was correlated with a link to the inactivation of the fungal spore. Second, we have studied to detect chemical modification of edible meat after the irradiation. Using matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy (MALDI-TOF-MS) and ESR, signals give qualification results for chemical changes on edible liver meat. The in situ real-time measurements have proven to be a useful method to elucidate plasma-induced surface reactions on biological specimens. (author)

The potential of protein-nanomaterial interaction for advanced drug delivery.

Science.gov (United States)

Peng, Qiang; Mu, Huiling

2016-03-10

Nanomaterials, like nanoparticles, micelles, nano-sheets, nanotubes and quantum dots, have great potentials in biomedical fields. However, their delivery is highly limited by the formation of protein corona upon interaction with endogenous proteins. This new identity, instead of nanomaterial itself, would be the real substance the organs and cells firstly encounter. Consequently, the behavior of nanomaterials in vivo is uncontrollable and some undesired effects may occur, like rapid clearance from blood stream; risk of capillary blockage; loss of targeting capacity; and potential toxicity. Therefore, protein-nanomaterial interaction is a great challenge for nanomaterial systems and should be inhibited. However, this interaction can also be used to functionalize nanomaterials by forming a selected protein corona. Unlike other decoration using exogenous molecules, nanomaterials functionalized by selected protein corona using endogenous proteins would have greater promise for clinical use. In this review, we aim to provide a comprehensive understanding of protein-nanomaterial interaction. Importantly, a discussion about how to use such interaction is launched and some possible applications of such interaction for advanced drug delivery are presented. Copyright © 2016 Elsevier B.V. All rights reserved.

Triactome: neuro-immune-adipose interactions. Implication in vascular biology

Directory of Open Access Journals (Sweden)

George Nikov Chaldakov

2014-04-01

Full Text Available Understanding how the precise interactions of nerves, immune cells and adipose tissue account for cardiovascular and metabolic biology is a central aim of biomedical research at present. A long standing paradigm holds that the vascular wall is composed of three concentric tissue coats (tunicae: intima, media, and adventitia. However, large- and medium-sized arteries, where usually atherosclerotic lesions develop, are consistently surrounded by periadventitial adipose tissue, we recently designated tunica adiposa (in brief, adiposa like intima, media, adventitia. According to present paradigm, atherosclerosis is an immune-mediated inflammatory disease featured by endothelial dysfunction/intimal thickening, medial atrophy and adventitial lesions associated with adipose dysfunction, whereas hypertension is characterized by hyperinnervation-associated medial thickening due to smooth muscle cell hypertrophy/hyperplasia. Periadventitial adipose tissue expansion is associated with increased infiltration of immune cells, both adipocytes and immunocytes secreting pro-inflammatory and anti-inflammatory (metabotrophic signaling proteins collectively dubbed adipokines. However, the role of perivascular nerves and their interactions with immune cells and paracrine adipose tissue is not yet evaluated in such an integrated way. The present review attempts to briefly highlight the findings in basic and translational sciences in this area focusing on neuro-immune-adipose interactions, herein referred to as triactome. Triactome-targeted pharmacology may provide a novel therapeutic approach in cardiovascular disease.

Plasma membrane--cortical cytoskeleton interactions: a cell biology approach with biophysical considerations.

Science.gov (United States)

Kapus, András; Janmey, Paul

2013-07-01

From a biophysical standpoint, the interface between the cell membrane and the cytoskeleton is an intriguing site where a "two-dimensional fluid" interacts with an exceedingly complex three-dimensional protein meshwork. The membrane is a key regulator of the cytoskeleton, which not only provides docking sites for cytoskeletal elements through transmembrane proteins, lipid binding-based, and electrostatic interactions, but also serves as the source of the signaling events and molecules that control cytoskeletal organization and remolding. Conversely, the cytoskeleton is a key determinant of the biophysical and biochemical properties of the membrane, including its shape, tension, movement, composition, as well as the mobility, partitioning, and recycling of its constituents. From a cell biological standpoint, the membrane-cytoskeleton interplay underlies--as a central executor and/or regulator--a multitude of complex processes including chemical and mechanical signal transduction, motility/migration, endo-/exo-/phagocytosis, and other forms of membrane traffic, cell-cell, and cell-matrix adhesion. The aim of this article is to provide an overview of the tight structural and functional coupling between the membrane and the cytoskeleton. As biophysical approaches, both theoretical and experimental, proved to be instrumental for our understanding of the membrane/cytoskeleton interplay, this review will "oscillate" between the cell biological phenomena and the corresponding biophysical principles and considerations. After describing the types of connections between the membrane and the cytoskeleton, we will focus on a few key physical parameters and processes (force generation, curvature, tension, and surface charge) and will discuss how these contribute to a variety of fundamental cell biological functions. © 2013 American Physiological Society.

Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

Science.gov (United States)

Chen, Bor-Sen; Wu, Chia-Chou

2013-01-01

Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875

Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

Directory of Open Access Journals (Sweden)

Bor-Sen Chen

2013-10-01

Full Text Available Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

Omics/systems biology and cancer cachexia.

Science.gov (United States)

Gallagher, Iain J; Jacobi, Carsten; Tardif, Nicolas; Rooyackers, Olav; Fearon, Kenneth

2016-06-01

Cancer cachexia is a complex syndrome generated by interaction between the host and tumour cells with a background of treatment effects and toxicity. The complexity of the physiological pathways likely involved in cancer cachexia necessitates a holistic view of the relevant biology. Emergent properties are characteristic of complex systems with the result that the end result is more than the sum of its parts. Recognition of the importance of emergent properties in biology led to the concept of systems biology wherein a holistic approach is taken to the biology at hand. Systems biology approaches will therefore play an important role in work to uncover key mechanisms with therapeutic potential in cancer cachexia. The 'omics' technologies provide a global view of biological systems. Genomics, transcriptomics, proteomics, lipidomics and metabolomics approaches all have application in the study of cancer cachexia to generate systems level models of the behaviour of this syndrome. The current work reviews recent applications of these technologies to muscle atrophy in general and cancer cachexia in particular with a view to progress towards integration of these approaches to better understand the pathology and potential treatment pathways in cancer cachexia. Copyright © 2016. Published by Elsevier Ltd.

Water reuse potential in truck wash using a Rotating Biological Contactor

OpenAIRE

Eduardo Lucas Subtil; José Carlos Mierzwa; Ivanildo Hespanhol; Raphael Rodrigues

2016-01-01

This study evaluated the water reuse potential for truck washing using the effluent treated by a Rotating Biological Contactor (RBC) operated in full scale. In order to evaluate the reuse potential, a mass balance was performed for the reuse system taking into account the concentration of Total Dissolved Solids as the critical contaminant. The treatment system produced an effluent with average concentration of color, turbidity, TDS and BOD5 of 45 ± 14 uC, 15 ± 6.0 NTU, 244 ± 99 mg TDS / L and...

Visual event-related potentials to biological motion stimuli in autism spectrum disorders

Science.gov (United States)

Bletsch, Anke; Krick, Christoph; Siniatchkin, Michael; Jarczok, Tomasz A.; Freitag, Christine M.; Bender, Stephan

2014-01-01

Atypical visual processing of biological motion contributes to social impairments in autism spectrum disorders (ASD). However, the exact temporal sequence of deficits of cortical biological motion processing in ASD has not been studied to date. We used 64-channel electroencephalography to study event-related potentials associated with human motion perception in 17 children and adolescents with ASD and 21 typical controls. A spatio-temporal source analysis was performed to assess the brain structures involved in these processes. We expected altered activity already during early stimulus processing and reduced activity during subsequent biological motion specific processes in ASD. In response to both, random and biological motion, the P100 amplitude was decreased suggesting unspecific deficits in visual processing, and the occipito-temporal N200 showed atypical lateralization in ASD suggesting altered hemispheric specialization. A slow positive deflection after 400 ms, reflecting top-down processes, and human motion-specific dipole activation differed slightly between groups, with reduced and more diffuse activation in the ASD-group. The latter could be an indicator of a disrupted neuronal network for biological motion processing in ADS. Furthermore, early visual processing (P100) seems to be correlated to biological motion-specific activation. This emphasizes the relevance of early sensory processing for higher order processing deficits in ASD. PMID:23887808

Defining the Synthetic Biology Supply Chain

Energy Technology Data Exchange (ETDEWEB)

Frazar, Sarah L.; Hund, Gretchen E.; Bonheyo, George T.; Diggans, James; Bartholomew, Rachel A.; Gehrig, Lindsey; Greaves, Mark

2017-08-01

In this article, a team of experts in synthetic biology, data analytics, and national security describe the overall supply chain surrounding synthetic biology. The team analyzes selected interactions within that network to better understand the risks raised by synthetic biology and identifies opportunities for risk mitigation. To introduce the concept, the article will briefly describe how an understanding of supply chains has been important in promoting nuclear nonproliferation objectives. The article concludes by assessing the structure and networks identified in the supply chains to reveal potential opportunities for future biodefense research and development; options for additional information exchange; and means to interdict, detect, or deter suspicious activity.

Chemical warfare agent and biological toxin-induced pulmonary toxicity: could stem cells provide potential therapies?

Science.gov (United States)

Angelini, Daniel J; Dorsey, Russell M; Willis, Kristen L; Hong, Charles; Moyer, Robert A; Oyler, Jonathan; Jensen, Neil S; Salem, Harry

2013-01-01

Chemical warfare agents (CWAs) as well as biological toxins present a significant inhalation injury risk to both deployed warfighters and civilian targets of terrorist attacks. Inhalation of many CWAs and biological toxins can induce severe pulmonary toxicity leading to the development of acute lung injury (ALI) as well as acute respiratory distress syndrome (ARDS). The therapeutic options currently used to treat these conditions are very limited and mortality rates remain high. Recent evidence suggests that human stem cells may provide significant therapeutic options for ALI and ARDS in the near future. The threat posed by CWAs and biological toxins for both civilian populations and military personnel is growing, thus understanding the mechanisms of toxicity and potential therapies is critical. This review will outline the pulmonary toxic effects of some of the most common CWAs and biological toxins as well as the potential role of stem cells in treating these types of toxic lung injuries.

How Genetic and Other Biological Factors Interact with Smoking Decisions.

Science.gov (United States)

Bierut, Laura; Cesarini, David

2015-09-01

Despite clear links between genes and smoking, effective public policy requires far richer measurement of the feedback between biological, behavioral, and environmental factors. The Kavli HUMAN Project (KHP) plans to exploit the plummeting costs of data gathering and to make creative use of new technologies to construct a longitudinal panel data set that would compare favorably to existing longitudinal surveys, both in terms of the richness of the behavioral measures and the cost-effectiveness of the data collection. By developing a more comprehensive approach to characterizing behavior than traditional methods, KHP will allow researchers to paint a much richer picture of an individual's life-cycle trajectory of smoking, alcohol, and drug use, and interactions with other choices and environmental factors. The longitudinal nature of KHP will be particularly valuable in light of the increasing evidence for how smoking behavior affects physiology and health. The KHP could have a transformative impact on the understanding of the biology of addictive behaviors such as smoking, and of a rich range of prevention and amelioration policies.

Strong Ligand-Protein Interactions Derived from Diffuse Ligand Interactions with Loose Binding Sites.

Science.gov (United States)

Marsh, Lorraine

2015-01-01

Many systems in biology rely on binding of ligands to target proteins in a single high-affinity conformation with a favorable ΔG. Alternatively, interactions of ligands with protein regions that allow diffuse binding, distributed over multiple sites and conformations, can exhibit favorable ΔG because of their higher entropy. Diffuse binding may be biologically important for multidrug transporters and carrier proteins. A fine-grained computational method for numerical integration of total binding ΔG arising from diffuse regional interaction of a ligand in multiple conformations using a Markov Chain Monte Carlo (MCMC) approach is presented. This method yields a metric that quantifies the influence on overall ligand affinity of ligand binding to multiple, distinct sites within a protein binding region. This metric is essentially a measure of dispersion in equilibrium ligand binding and depends on both the number of potential sites of interaction and the distribution of their individual predicted affinities. Analysis of test cases indicates that, for some ligand/protein pairs involving transporters and carrier proteins, diffuse binding contributes greatly to total affinity, whereas in other cases the influence is modest. This approach may be useful for studying situations where "nonspecific" interactions contribute to biological function.

Potential drug interactions in patients given antiretroviral therapy.

Science.gov (United States)

Santos, Wendel Mombaque Dos; Secoli, Silvia Regina; Padoin, Stela Maris de Mello

2016-11-21

to investigate potential drug-drug interactions (PDDI) in patients with HIV infection on antiretroviral therapy. a cross-sectional study was conducted on 161 adults with HIV infection. Clinical, socio demographic, and antiretroviral treatment data were collected. To analyze the potential drug interactions, we used the software Micromedex(r). Statistical analysis was performed by binary logistic regression, with a p-value of ≤0.05 considered statistically significant. of the participants, 52.2% were exposed to potential drug-drug interactions. In total, there were 218 potential drug-drug interactions, of which 79.8% occurred between drugs used for antiretroviral therapy. There was an association between the use of five or more medications and potential drug-drug interactions (p = 0.000) and between the time period of antiretroviral therapy being over six years and potential drug-drug interactions (p central nervous and cardiovascular systems, but also can interfere in tests used for detection of HIV resistance to antiretroviral drugs. investigar potenciais interações droga-droga (PDDI) em pacientes infectados com HIV em terapia de antirretroviral. um estudo de corte transversal foi conduzido em 161 pessoas infectadas com o HIV. Dados de tratamentos clínicos, sociodemográficos e antirretrovirais foram coletados. Para analisar a possível interação medicamentosa, nós usamos o software Micromedex(r). A análise estatística foi feita por regressão logística binária, com um valor P de ≤0.05, considerado estatisticamente significativo. dos participantes, 52.2% foram expostos a potenciais interações droga-droga. No total, houve 218 interações droga-droga, das quais 79.8% ocorreram entre drogas usadas para a terapia antirretroviral. Houve uma associação entre o uso de cinco ou mais medicamentos e possíveis interações droga-droga (p = 0.000), e entre o período de tempo de terapia antirretroviral acima de seis anos e possíveis interações droga

Viral induced oxidative and inflammatory response in Alzheimer's disease pathogenesis with identification of potential drug candidates: A systematic review using systems biology approach.

Science.gov (United States)

Talwar, Puneet; Gupta, Renu; Kushwaha, Suman; Agarwal, Rachna; Saso, Luciano; Kukreti, Shrikant; Kukreti, Ritushree

2018-04-19

Alzheimer's disease (AD) is genetically complex with multifactorial etiology. Here, we aim to identify the potential viral pathogens leading to aberrant inflammatory and oxidative stress response in AD along with potential drug candidates using systems biology approach. We retrieved protein interactions of amyloid precursor protein (APP) and tau protein (MAPT) from NCBI and genes for oxidative stress from NetAge, for inflammation from NetAge and InnateDB databases. Genes implicated in aging were retrieved from GenAge database and two GEO expression datasets. These genes were individually used to create protein-protein interaction network using STRING database (score≥0.7). The interactions of candidate genes with known viruses were mapped using virhostnet v2.0 database. Drug molecules targeting candidate genes were retrieved using the Drug-Gene Interaction Database (DGIdb). Data mining resulted in 2095 APP, 116 MAPT, 214 oxidative stress, 1269 inflammatory genes. After STRING PPIN analysis, 404 APP, 109 MAPT, 204 oxidative stress and 1014 inflammation related high confidence proteins were identified. The overlap among all datasets yielded eight common markers (AKT1, GSK3B, APP, APOE, EGFR, PIN1, CASP8 and SNCA). These genes showed association with hepatitis C virus (HCV), Epstein-Barr virus (EBV), human herpes virus 8 and Human papillomavirus (HPV). Further, screening of drugs targeting candidate genes, and possessing anti-inflammatory property, antiviral activity along with suggested role in AD pathophysiology yielded 12 potential drug candidates. Our study demonstrated the role of viral etiology in AD pathogenesis by elucidating interaction of oxidative stress and inflammation causing candidate genes with common viruses along with the identification of potential AD drug candidates. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Repulsive baryonic interactions and lattice QCD observables at imaginary chemical potential

Directory of Open Access Journals (Sweden)

Volodymyr Vovchenko

2017-12-01

Full Text Available The first principle lattice QCD methods allow to calculate the thermodynamic observables at finite temperature and imaginary chemical potential. These can be compared to the predictions of various phenomenological models. We argue that Fourier coefficients with respect to imaginary baryochemical potential are sensitive to modeling of baryonic interactions. As a first application of this sensitivity, we consider the hadron resonance gas (HRG model with repulsive baryonic interactions, which are modeled by means of the excluded volume correction. The Fourier coefficients of the imaginary part of the net-baryon density at imaginary baryochemical potential – corresponding to the fugacity or virial expansion at real chemical potential – are calculated within this model, and compared with the Nt=12 lattice data. The lattice QCD behavior of the first four Fourier coefficients up to T≃185 MeV is described fairly well by an interacting HRG with a single baryon–baryon eigenvolume interaction parameter b≃1 fm3, while the available lattice data on the difference χ2B−χ4B of baryon number susceptibilities is reproduced up to T≃175 MeV. Keywords: Hadron resonance gas, Excluded volume, Imaginary chemical potential

Interaction potentials and their effect on crystal nucleation and symmetry

International Nuclear Information System (INIS)

Hsu, C.S.; Rahman, A.

1979-01-01

Molecular dynamics technique has been used to study the effect of the interaction potential on crystal nucleation and the symmetry of the nucleated phase. Four systems, namely rubidium, Lennard-Jones, rubidium-truncated, and Lennard-Jones-truncated, have been studied each at reduced density 0.95. Two types of calculations were performed. Firstly, starting from a liquid state, each system was quenched rapidly to a reduced temperature of approx.0.1. The nucleation process for these systems was monitored by studying the time dependence of temperature and the pair correlation function, and the resulting crystalline structure analyzed using among other properties the Voronoi polyhedra. Only in the case of rubidium was a b.c.c. structure nucleated. In the other three cases we obtained a f.c.c. ordering. Secondly, we have studied the effect of changing the interaction potential in a system which has already achieved an ordered state under the action of some other potential. After establishing a b.c.c. structure in a rubidium system, the change in the symmetry of the system was studied when the pair potential was modified to one of the other three forms. The results from both types of calculations are consistent: the rubidium potential leads to a b.c.c. structure while the other three potentials give an f.c.c. structure. Metastable disordered structures were not obtained in any of the calculations. However, the time elapse between the moment when the system is quick-quenched and the moment when nucleation occurs appears to depend upon the potential of interaction

The potential of standards-based agriculture biology as an alternative to traditional biology in California

Science.gov (United States)

Sellu, George Sahr

schools. Thoron & Meyer (2011) suggested that research into the contribution of integrated science courses toward higher test scores yielded mixed results. This finding may have been due in part to the fact that integrated science courses only incorporate select topics into agriculture education courses. In California, however, agriculture educators have developed standards-based courses such as Agriculture Biology (AgBio) that cover the same content standards as core traditional courses such as traditional biology. Students in both AgBio and traditional biology take the same standardized biology test. This is the first time there has been an opportunity for a fair comparison and a uniform metric for an agriscience course such as AgBio to be directly compared to traditional biology. This study will examine whether there are differences between AgBio and traditional biology with regard to standardized test scores in biology. Furthermore, the study examines differences in perception between teachers and students regarding teaching and learning activities associated with higher achievement in science. The findings of the study could provide a basis for presenting AgBio as a potential alternative to traditional biology. The findings of this study suggest that there are no differences between AgBio and traditional biology students with regard to standardized biology test scores. Additionally, the findings indicate that co-curricular activities in AgBio could contribute higher student achievement in biology. However, further research is required to identify specific activities in AgBio that contribute to higher achievement in science.

The Isolation of DNA by Polycharged Magnetic Particles: An Analysis of the Interaction by Zeta Potential and Particle Size.

Science.gov (United States)

Haddad, Yazan; Xhaxhiu, Kledi; Kopel, Pavel; Hynek, David; Zitka, Ondrej; Adam, Vojtech

2016-04-20

Magnetic isolation of biological targets is in major demand in the biotechnology industry today. This study considers the interaction of four surface-modified magnetic micro- and nanoparticles with selected DNA fragments. Different surface modifications of nanomaghemite precursors were investigated: MAN37 (silica-coated), MAN127 (polyvinylpyrrolidone-coated), MAN158 (phosphate-coated), and MAN164 (tripolyphosphate-coated). All particles were positive polycharged agglomerated monodispersed systems. Mean particle sizes were 0.48, 2.97, 2.93, and 3.67 μm for MAN37, MAN127, MAN164, and MAN158, respectively. DNA fragments exhibited negative zeta potential of -0.22 mV under binding conditions (high ionic strength, low pH, and dehydration). A decrease in zeta potential of particles upon exposure to DNA was observed with exception of MAN158 particles. The measured particle size of MAN164 particles increased by nearly twofold upon exposure to DNA. Quantitative PCR isolation of DNA with a high retrieval rate was observed by magnetic particles MAN127 and MAN164. Interaction between polycharged magnetic particles and DNA is mediated by various binding mechanisms such as hydrophobic and electrostatic interactions. Future development of DNA isolation technology requires an understanding of the physical and biochemical conditions of this process.

The potential of text mining in data integration and network biology for plant research: a case study on Arabidopsis.

Science.gov (United States)

Van Landeghem, Sofie; De Bodt, Stefanie; Drebert, Zuzanna J; Inzé, Dirk; Van de Peer, Yves

2013-03-01

Despite the availability of various data repositories for plant research, a wealth of information currently remains hidden within the biomolecular literature. Text mining provides the necessary means to retrieve these data through automated processing of texts. However, only recently has advanced text mining methodology been implemented with sufficient computational power to process texts at a large scale. In this study, we assess the potential of large-scale text mining for plant biology research in general and for network biology in particular using a state-of-the-art text mining system applied to all PubMed abstracts and PubMed Central full texts. We present extensive evaluation of the textual data for Arabidopsis thaliana, assessing the overall accuracy of this new resource for usage in plant network analyses. Furthermore, we combine text mining information with both protein-protein and regulatory interactions from experimental databases. Clusters of tightly connected genes are delineated from the resulting network, illustrating how such an integrative approach is essential to grasp the current knowledge available for Arabidopsis and to uncover gene information through guilt by association. All large-scale data sets, as well as the manually curated textual data, are made publicly available, hereby stimulating the application of text mining data in future plant biology studies.

Female versus male biological identities of nanoparticles determine the interaction with immune cells in fish

DEFF Research Database (Denmark)

Hayashi, Yuya; Miclaus, Teodora; Murugadoss, Sivakumar

2017-01-01

Biomolecule decoration of nanoparticles provides a corona that modulates how the nanoparticles interact with biological milieus. The corona composition has proved to reflect the differences in the repertoire of proteins to which the nanoparticles are exposed, and as a result the same nanoparticles...... and myeloid populations of the blood cells preferentially accumulated the nanoparticles with a female biological identity, irrespective of the sex of the fish from which the cells were obtained. The concept of repertoire differences in the corona proteome therefore deserves further attention, as various...

Biological activities and biomedical potential of sea cucumber (Stichopus japonicus: a review

Directory of Open Access Journals (Sweden)

Gun-Woo Oh

2017-11-01

Full Text Available Abstract Members of the phylum Echinodermata, commonly known as echinoderms, are exclusively marine invertebrates. Among the Echinodermata, sea cucumber belongs to the family Holothuroidea. The sea cucumber Stichopus (Apostichous japonicus (Selenka is an invertebrate animal inhabiting the coastal sea around Korean, Japan, China, and Russia. Sea cucumber has a significant commercial value, because it contains valuable nutrients such as vitamins and minerals. They possess a number of distinctive biologically and pharmacologically important compounds. In particular, the body wall of sea cucumber is a major edible part. It consists of peptide, collagen, gelatin, polysaccharide, and saponin, which possess several biological activities such as anti-cancer, anti-coagulation, anti-oxidation, and anti-osteoclastogenesis. Furthermore, the regenerative capacity of sea cucumber makes it a medically important organism. This review presents the various biological activities and biomedical potential of sea cucumber S. japonicus.

The Promise of Systems Biology Approaches for Revealing Host Pathogen Interactions in Malaria

Directory of Open Access Journals (Sweden)

Meghan Zuck

2017-11-01

Full Text Available Despite global eradication efforts over the past century, malaria remains a devastating public health burden, causing almost half a million deaths annually (WHO, 2016. A detailed understanding of the mechanisms that control malaria infection has been hindered by technical challenges of studying a complex parasite life cycle in multiple hosts. While many interventions targeting the parasite have been implemented, the complex biology of Plasmodium poses a major challenge, and must be addressed to enable eradication. New approaches for elucidating key host-parasite interactions, and predicting how the parasite will respond in a variety of biological settings, could dramatically enhance the efficacy and longevity of intervention strategies. The field of systems biology has developed methodologies and principles that are well poised to meet these challenges. In this review, we focus our attention on the Liver Stage of the Plasmodium lifecycle and issue a “call to arms” for using systems biology approaches to forge a new era in malaria research. These approaches will reveal insights into the complex interplay between host and pathogen, and could ultimately lead to novel intervention strategies that contribute to malaria eradication.

[Potential antimicrobial drug interactions in clinical practice: consequences of polypharmacy and multidrug resistance].

Science.gov (United States)

Martínez-Múgica, Cristina

2015-12-01

Polypharmacy is a growing problem nowadays, which can increase the risk of potential drug interactions, and result in a loss of effectiveness. This is particularly relevant to the anti-infective therapy, especially when infection is produced by resistant bacteria, because therapeutic options are limited and interactions can cause treatment failure. All antimicrobial prescriptions were retrospectively reviewed during a week in the Pharmacy Department, in order to detect potential drug-interactions and analysing their clinical significance. A total of 314 antimicrobial prescriptions from 151 patients were checked. There was at least one potential interaction detected in 40% of patients, being more frequent and severe in those infected with multidrug-resistant microorganisms. Drugs most commonly involved were quinolones, azoles, linezolid and vancomycin. Potential drug interactions with antimicrobial agents are a frequent problem that can result in a loss of effectiveness. This is why they should be detected and avoided when possible, in order to optimize antimicrobial therapy, especially in case of multidrug resistant infections.

The Chemical Potential of Plasma Membrane Cholesterol: Implications for Cell Biology.

Science.gov (United States)

Ayuyan, Artem G; Cohen, Fredric S

2018-02-27

Cholesterol is abundant in plasma membranes and exhibits a variety of interactions throughout the membrane. Chemical potential accounts for thermodynamic consequences of molecular interactions, and quantifies the effective concentration (i.e., activity) of any substance participating in a process. We have developed, to our knowledge, the first method to measure cholesterol chemical potential in plasma membranes. This was accomplished by complexing methyl-β-cyclodextrin with cholesterol in an aqueous solution and equilibrating it with an organic solvent containing dissolved cholesterol. The chemical potential of cholesterol was thereby equalized in the two phases. Because cholesterol is dilute in the organic phase, here activity and concentration were equivalent. This equivalence allowed the amount of cholesterol bound to methyl-β-cyclodextrin to be converted to cholesterol chemical potential. Our method was used to determine the chemical potential of cholesterol in erythrocytes and in plasma membranes of nucleated cells in culture. For erythrocytes, the chemical potential did not vary when the concentration was below a critical value. Above this value, the chemical potential progressively increased with concentration. We used standard cancer lines to characterize cholesterol chemical potential in plasma membranes of nucleated cells. This chemical potential was significantly greater for highly metastatic breast cancer cells than for nonmetastatic breast cancer cells. Chemical potential depended on density of the cancer cells. A method to alter and fix the cholesterol chemical potential to any value (i.e., a cholesterol chemical potential clamp) was also developed. Cholesterol content did not change when cells were clamped for 24-48 h. It was found that the level of activation of the transcription factor STAT3 increased with increasing cholesterol chemical potential. The cholesterol chemical potential may regulate signaling pathways. Copyright © 2018. Published by

Potential games and interactive decisions with multiple criteria

NARCIS (Netherlands)

Voorneveld, M.

1999-01-01

Game theory is a mathematical theory for analyzing strategic interaction between decision makers. This thesis covers two game-theoretic topics. The first part of this thesis deals with potential games: noncooperative games in which the information about the goals of the separate players that is

The potential of protein-nanomaterial interaction for advanced drug delivery

DEFF Research Database (Denmark)

Peng, Qiang; Mu, Huiling

2016-01-01

Nanomaterials, like nanoparticles, micelles, nano-sheets, nanotubes and quantum dots, have great potentials in biomedical fields. However, their delivery is highly limited by the formation of protein corona upon interaction with endogenous proteins. This new identity, instead of nanomaterial itself...... of such interaction for advanced drug delivery are presented........ Therefore, protein-nanomaterial interaction is a great challenge for nanomaterial systems and should be inhibited. However, this interaction can also be used to functionalize nanomaterials by forming a selected protein corona. Unlike other decoration using exogenous molecules, nanomaterials functionalized...

Identification of polycystic ovary syndrome potential drug targets based on pathobiological similarity in the protein-protein interaction network

Science.gov (United States)

Li, Wan; Wei, Wenqing; Li, Yiran; Xie, Ruiqiang; Guo, Shanshan; Wang, Yahui; Jiang, Jing; Chen, Binbin; Lv, Junjie; Zhang, Nana; Chen, Lina; He, Weiming

2016-01-01

Polycystic ovary syndrome (PCOS) is one of the most common endocrinological disorders in reproductive aged women. PCOS and Type 2 Diabetes (T2D) are closely linked in multiple levels and possess high pathobiological similarity. Here, we put forward a new computational approach based on the pathobiological similarity to identify PCOS potential drug target modules (PPDT-Modules) and PCOS potential drug targets in the protein-protein interaction network (PPIN). From the systems level and biological background, 1 PPDT-Module and 22 PCOS potential drug targets were identified, 21 of which were verified by literatures to be associated with the pathogenesis of PCOS. 42 drugs targeting to 13 PCOS potential drug targets were investigated experimentally or clinically for PCOS. Evaluated by independent datasets, the whole PPDT-Module and 22 PCOS potential drug targets could not only reveal the drug response, but also distinguish the statuses between normal and disease. Our identified PPDT-Module and PCOS potential drug targets would shed light on the treatment of PCOS. And our approach would provide valuable insights to research on the pathogenesis and drug response of other diseases. PMID:27191267

Information needs for making clinical recommendations about potential drug-drug interactions: a synthesis of literature review and interviews.

Science.gov (United States)

Romagnoli, Katrina M; Nelson, Scott D; Hines, Lisa; Empey, Philip; Boyce, Richard D; Hochheiser, Harry

2017-02-22

Drug information compendia and drug-drug interaction information databases are critical resources for clinicians and pharmacists working to avoid adverse events due to exposure to potential drug-drug interactions (PDDIs). Our goal is to develop information models, annotated data, and search tools that will facilitate the interpretation of PDDI information. To better understand the information needs and work practices of specialists who search and synthesize PDDI evidence for drug information resources, we conducted an inquiry that combined a thematic analysis of published literature with unstructured interviews. Starting from an initial set of relevant articles, we developed search terms and conducted a literature search. Two reviewers conducted a thematic analysis of included articles. Unstructured interviews with drug information experts were conducted and similarly coded. Information needs, work processes, and indicators of potential strengths and weaknesses of information systems were identified. Review of 92 papers and 10 interviews identified 56 categories of information needs related to the interpretation of PDDI information including drug and interaction information; study design; evidence including clinical details, quality and content of reports, and consequences; and potential recommendations. We also identified strengths/weaknesses of PDDI information systems. We identified the kinds of information that might be most effective for summarizing PDDIs. The drug information experts we interviewed had differing goals, suggesting a need for detailed information models and flexible presentations. Several information needs not discussed in previous work were identified, including temporal overlaps in drug administration, biological plausibility of interactions, and assessment of the quality and content of reports. Richly structured depictions of PDDI information may help drug information experts more effectively interpret data and develop recommendations

A reactive empirical bond order (REBO) potential for hydrocarbon-oxygen interactions

International Nuclear Information System (INIS)

Ni, Boris; Lee, Ki-Ho; Sinnott, Susan B

2004-01-01

The expansion of the second-generation reactive empirical bond order (REBO) potential for hydrocarbons, as parametrized by Brenner and co-workers, to include oxygen is presented. This involves the explicit inclusion of C-O, H-O, and O-O interactions to the existing C-C, C-H, and H-H interactions in the REBO potential. The details of the expansion, including all parameters, are given. The new, expanded potential is then applied to the study of the structure and chemical stability of several molecules and polymer chains, and to modelling chemical reactions among a series of molecules, within classical molecular dynamics simulations

Dynamically analyzing cell interactions in biological environments using multiagent social learning framework.

Science.gov (United States)

Zhang, Chengwei; Li, Xiaohong; Li, Shuxin; Feng, Zhiyong

2017-09-20

Biological environment is uncertain and its dynamic is similar to the multiagent environment, thus the research results of the multiagent system area can provide valuable insights to the understanding of biology and are of great significance for the study of biology. Learning in a multiagent environment is highly dynamic since the environment is not stationary anymore and each agent's behavior changes adaptively in response to other coexisting learners, and vice versa. The dynamics becomes more unpredictable when we move from fixed-agent interaction environments to multiagent social learning framework. Analytical understanding of the underlying dynamics is important and challenging. In this work, we present a social learning framework with homogeneous learners (e.g., Policy Hill Climbing (PHC) learners), and model the behavior of players in the social learning framework as a hybrid dynamical system. By analyzing the dynamical system, we obtain some conditions about convergence or non-convergence. We experimentally verify the predictive power of our model using a number of representative games. Experimental results confirm the theoretical analysis. Under multiagent social learning framework, we modeled the behavior of agent in biologic environment, and theoretically analyzed the dynamics of the model. We present some sufficient conditions about convergence or non-convergence and prove them theoretically. It can be used to predict the convergence of the system.

Interactions of C+(2PJ) with rare gas atoms: incipient chemical interactions, potentials and transport coefficients

Science.gov (United States)

Tuttle, William D.; Thorington, Rebecca L.; Viehland, Larry A.; Breckenridge, W. H.; Wright, Timothy G.

2018-03-01

Accurate interatomic potentials were calculated for the interaction of a singly charged carbon cation, C+, with a single rare gas atom, RG (RG = Ne-Xe). The RCCSD(T) method and basis sets of quadruple-ζ and quintuple-ζ quality were employed; each interaction energy was counterpoise corrected and extrapolated to the basis set limit. The lowest C+(2P) electronic term of the carbon cation was considered, and the interatomic potentials calculated for the diatomic terms that arise from these: 2Π and 2Σ+. Additionally, the interatomic potentials for the respective spin-orbit levels were calculated, and the effect on the spectroscopic parameters was examined. In doing this, anomalously large spin-orbit splittings for RG = Ar-Xe were found, and this was investigated using multi-reference configuration interaction calculations. The latter indicated a small amount of RG → C+ electron transfer and this was used to rationalize the observations. This is taken as evidence of an incipient chemical interaction, which was also examined via contour plots, Birge-Sponer plots and various population analyses across the C+-RG series (RG = He-Xe), with the latter showing unexpected results. Trends in several spectroscopic parameters were examined as a function of the increasing atomic number of the RG atom. Finally, each set of RCCSD(T) potentials was employed, including spin-orbit coupling to calculate the transport coefficients for C+ in RG, and the results were compared with the limited available data. This article is part of the theme issue `Modern theoretical chemistry'.

Systems Biology for Organotypic Cell Cultures

Energy Technology Data Exchange (ETDEWEB)

Grego, Sonia [RTI International, Research Triangle Park, NC (United States); Dougherty, Edward R. [Texas A & M Univ., College Station, TX (United States); Alexander, Francis J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Auerbach, Scott S. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Berridge, Brian R. [GlaxoSmithKline, Research Triangle Park, NC (United States); Bittner, Michael L. [Translational Genomics Research Inst., Phoenix, AZ (United States); Casey, Warren [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Cooley, Philip C. [RTI International, Research Triangle Park, NC (United States); Dash, Ajit [HemoShear Therapeutics, Charlottesville, VA (United States); Ferguson, Stephen S. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Fennell, Timothy R. [RTI International, Research Triangle Park, NC (United States); Hawkins, Brian T. [RTI International, Research Triangle Park, NC (United States); Hickey, Anthony J. [RTI International, Research Triangle Park, NC (United States); Kleensang, Andre [Johns Hopkins Univ., Baltimore, MD (United States). Center for Alternatives to Animal Testing; Liebman, Michael N. [IPQ Analytics, Kennett Square, PA (United States); Martin, Florian [Phillip Morris International, Neuchatel (Switzerland); Maull, Elizabeth A. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Paragas, Jason [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Qiao, Guilin [Defense Threat Reduction Agency, Ft. Belvoir, VA (United States); Ramaiahgari, Sreenivasa [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Sumner, Susan J. [RTI International, Research Triangle Park, NC (United States); Yoon, Miyoung [The Hamner Inst. for Health Sciences, Research Triangle Park, NC (United States); ScitoVation, Research Triangle Park, NC (United States)

2016-08-04

Translating in vitro biological data into actionable information related to human health holds the potential to improve disease treatment and risk assessment of chemical exposures. While genomics has identified regulatory pathways at the cellular level, translation to the organism level requires a multiscale approach accounting for intra-cellular regulation, inter-cellular interaction, and tissue/organ-level effects. Tissue-level effects can now be probed in vitro thanks to recently developed systems of three-dimensional (3D), multicellular, “organotypic” cell cultures, which mimic functional responses of living tissue. However, there remains a knowledge gap regarding interactions across different biological scales, complicating accurate prediction of health outcomes from molecular/genomic data and tissue responses. Systems biology aims at mathematical modeling of complex, non-linear biological systems. We propose to apply a systems biology approach to achieve a computational representation of tissue-level physiological responses by integrating empirical data derived from organotypic culture systems with computational models of intracellular pathways to better predict human responses. Successful implementation of this integrated approach will provide a powerful tool for faster, more accurate and cost-effective screening of potential toxicants and therapeutics. On September 11, 2015, an interdisciplinary group of scientists, engineers, and clinicians gathered for a workshop in Research Triangle Park, North Carolina, to discuss this ambitious goal. Participants represented laboratory-based and computational modeling approaches to pharmacology and toxicology, as well as the pharmaceutical industry, government, non-profits, and academia. Discussions focused on identifying critical system perturbations to model, the computational tools required, and the experimental approaches best suited to generating key data. This consensus report summarizes the discussions held.

[Cell signaling pathways interaction in cellular proliferation: Potential target for therapeutic interventionism].

Science.gov (United States)

Valdespino-Gómez, Víctor Manuel; Valdespino-Castillo, Patricia Margarita; Valdespino-Castillo, Víctor Edmundo

2015-01-01

Nowadays, cellular physiology is best understood by analysing their interacting molecular components. Proteins are the major components of the cells. Different proteins are organised in the form of functional clusters, pathways or networks. These molecules are ordered in clusters of receptor molecules of extracellular signals, transducers, sensors and biological response effectors. The identification of these intracellular signaling pathways in different cellular types has required a long journey of experimental work. More than 300 intracellular signaling pathways have been identified in human cells. They participate in cell homeostasis processes for structural and functional maintenance. Some of them participate simultaneously or in a nearly-consecutive progression to generate a cellular phenotypic change. In this review, an analysis is performed on the main intracellular signaling pathways that take part in the cellular proliferation process, and the potential use of some components of these pathways as target for therapeutic interventionism are also underlined. Copyright © 2015 Academia Mexicana de Cirugía A.C. Published by Masson Doyma México S.A. All rights reserved.

Intracellular antibody capture: A molecular biology approach to inhibitors of protein-protein interactions.

Science.gov (United States)

Zhang, Jing; Rabbitts, Terence H

2014-11-01

Many proteins of interest in basic biology, translational research studies and for clinical targeting in diseases reside inside the cell and function by interacting with other macromolecules. Protein complexes control basic processes such as development and cell division but also abnormal cell growth when mutations occur such as found in cancer. Interfering with protein-protein interactions is an important aspiration in both basic and disease biology but small molecule inhibitors have been difficult and expensive to isolate. Recently, we have adapted molecular biology techniques to develop a simple set of protocols for isolation of high affinity antibody fragments (in the form of single VH domains) that function within the reducing environment of higher organism cells and can bind to their target molecules. The method called Intracellular Antibody Capture (IAC) has been used to develop inhibitory anti-RAS and anti-LMO2 single domains that have been used for target validation of these antigens in pre-clinical cancer models and illustrate the efficacy of the IAC approach to generation of drug surrogates. Future use of inhibitory VH antibody fragments as drugs in their own right (we term these macrodrugs to distinguish them from small molecule drugs) requires their delivery to target cells in vivo but they can also be templates for small molecule drug development that emulate the binding sites of the antibody fragments. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody. Copyright © 2014 Elsevier B.V. All rights reserved.

Improved Interaction Potentials for Charged Residues in Proteins

DEFF Research Database (Denmark)

Kepp, Kasper Planeta

2008-01-01

Electrostatic interactions dominate the structure and free energy of biomolecules. To obtain accurate free energies involving charged groups from molecular simulations, OPLS-AA parameters have been reoptimized using Monte Carlo free energy perturbation. New parameters fit a self-consistent, exper......Electrostatic interactions dominate the structure and free energy of biomolecules. To obtain accurate free energies involving charged groups from molecular simulations, OPLS-AA parameters have been reoptimized using Monte Carlo free energy perturbation. New parameters fit a self......, TIP4P or TIP3P; i.e., each water model requires specific water-charged molecule interaction potentials. New models (models 1 and 3) are thus described for both water models. Uncertainties in relative free energies of charged residues are ~2 kcal/mol with the new parameters, due to variations in system...

Double folded Yukawa interaction potential between two heavy ions

International Nuclear Information System (INIS)

Bulgac, A.; Carstoiu, F.; Dumitrescu, O.

1980-02-01

A simple semi-analytical formula for the heavy ion interaction potential within the double-folding model approximation is obtained. The folded interaction is assumed to be expressed in Yukawa terms or the derivatives of them. The densities used can be both experimental or theoretical (of simple ''step-wise'', ''Fermi-Saxon-Woods'' or complicated ''shell model'' structure) densities. A way of inserting the exchange terms is discussed. Numerical calculations for some colliding partners are reported. (author)

Interaction of Herbal Compounds with Biological Targets: A Case Study with Berberine

Directory of Open Access Journals (Sweden)

Xiao-Wu Chen

2012-01-01

Full Text Available Berberine is one of the main alkaloids found in the Chinese herb Huang lian (Rhizoma Coptidis, which has been reported to have multiple pharmacological activities. This study aimed to analyze the molecular targets of berberine based on literature data followed by a pathway analysis using the PANTHER program. PANTHER analysis of berberine targets showed that the most classes of molecular functions include receptor binding, kinase activity, protein binding, transcription activity, DNA binding, and kinase regulator activity. Based on the biological process classification of in vitro berberine targets, those targets related to signal transduction, intracellular signalling cascade, cell surface receptor-linked signal transduction, cell motion, cell cycle control, immunity system process, and protein metabolic process are most frequently involved. In addition, berberine was found to interact with a mixture of biological pathways, such as Alzheimer’s disease-presenilin and -secretase pathways, angiogenesis, apoptosis signalling pathway, FAS signalling pathway, Hungtington disease, inflammation mediated by chemokine and cytokine signalling pathways, interleukin signalling pathway, and p53 pathways. We also explored the possible mechanism of action for the anti-diabetic effect of berberine. Further studies are warranted to elucidate the mechanisms of action of berberine using systems biology approach.

Clinically relevant potential drug-drug interactions among outpatients: A nationwide database study.

Science.gov (United States)

Jazbar, Janja; Locatelli, Igor; Horvat, Nejc; Kos, Mitja

2018-06-01

Adverse drug events due to drug-drug interactions (DDIs) represent a considerable public health burden, also in Slovenia. A better understanding of the most frequently occurring potential DDIs may enable safer pharmacotherapy and minimize drug-related problems. The aim of this study was to evaluate the prevalence and predictors of potential DDIs among outpatients in Slovenia. An analysis of potential DDIs was performed using health claims data on prescription drugs from a nationwide database. The Lexi-Interact Module was used as the reference source of interactions. The influence of patient-specific predictors on the risk of potential clinically relevant DDIs was evaluated using logistic regression model. The study population included 1,179,803 outpatients who received 15,811,979 prescriptions. The total number of potential DDI cases identified was 3,974,994, of which 15.6% were potentially clinically relevant. Altogether, 9.3% (N = 191,213) of the total population in Slovenia is exposed to clinically relevant potential DDIs, and the proportion is higher among women and the elderly. After adjustment for cofactors, higher number of medications and older age are associated with higher odds of clinically relevant potential DDIs. The burden of DDIs is highest with drug combinations that increase risk of bleeding, enhance CNS depression or anticholinergic effects or cause cardiovascular complications. The current study revealed that 1 in 10 individuals in the total Slovenian population is exposed to clinically relevant potential DDIs yearly. Taking into account the literature based conservative estimate that approximately 1% of potential DDIs result in negative health outcomes, roughly 1800 individuals in Slovenia experience an adverse health outcome each year as a result of clinically relevant potential interactions alone. Copyright © 2017 Elsevier Inc. All rights reserved.

Estimating the Effects of Habitat and Biological Interactions in an Avian Community.

Directory of Open Access Journals (Sweden)

Robert M Dorazio

Full Text Available We used repeated sightings of individual birds encountered in community-level surveys to investigate the relative roles of habitat and biological interactions in determining the distribution and abundance of each species. To analyze these data, we developed a multispecies N-mixture model that allowed estimation of both positive and negative correlations between abundances of different species while also estimating the effects of habitat and the effects of errors in detection of each species. Using a combination of single- and multispecies N-mixture modeling, we examined for each species whether our measures of habitat were sufficient to account for the variation in encounter histories of individual birds or whether other habitat variables or interactions with other species needed to be considered. In the community that we studied, habitat appeared to be more influential than biological interactions in determining the distribution and abundance of most avian species. Our results lend support to the hypothesis that abundances of forest specialists are negatively affected by forest fragmentation. Our results also suggest that many species were associated with particular types of vegetation as measured by structural attributes of the forests. The abundances of 6 of the 73 species observed in our study were strongly correlated. These species included large birds (American Crow (Corvus brachyrhynchos and Red-winged Blackbird (Agelaius phoeniceus that forage on the ground in open habitats and small birds (Red-eyed Vireo (Vireo olivaceus, House Wren (Troglodytes aedon, Hooded Warbler (Setophaga citrina, and Prairie Warbler (Setophaga discolor that are associated with dense shrub cover. Species abundances were positively correlated within each size group and negatively correlated between groups. Except for the American Crow, which preys on eggs and nestlings of small song birds, none of the other 5 species is known to display direct interactions, so we

Potential drug–drug interactions in Alzheimer patients with behavioral symptoms

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Pasqualetti G

2015-09-01

Full Text Available Giuseppe Pasqualetti, Sara Tognini, Valeria Calsolaro, Antonio Polini, Fabio Monzani Geriatrics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy Abstract: The use of multi drug regimens among the elderly population has increased tremendously over the last decade although the benefits of medications are always accompanied by potential harm, even when prescribed at recommended doses. The elderly populations are particularly at an increased risk of adverse drug reactions considering comorbidity, poly-therapy, physiological changes affecting the pharmacokinetics and pharmacodynamics of many drugs and, in some cases, poor compliance due to cognitive impairment and/or depression. In this setting, drug–drug interaction may represent a serious and even life-threatening clinical condition. Moreover, the inability to distinguish drug-induced symptoms from a definitive medical diagnosis often results in addition of yet another drug to treat the symptoms, which in turn increases drug–drug interactions. Cognitive enhancers, including acetylcholinesterase inhibitors and memantine, are the most widely prescribed agents for Alzheimer’s disease (AD patients. Behavioral and psychological symptoms of dementia, including psychotic symptoms and behavioral disorders, represent noncognitive disturbances frequently observed in AD patients. Antipsychotic drugs are at high risk of adverse events, even at modest doses, and may interfere with the progression of cognitive impairment and interact with several drugs including anti-arrhythmics and acetylcholinesterase inhibitors. Other medications often used in AD patients are represented by anxiolytic, like benzodiazepine, or antidepressant agents. These agents also might interfere with other concomitant drugs through both pharmacokinetic and pharmacodynamic mechanisms. In this review we focus on the most frequent drug–drug interactions, potentially harmful, in AD patients with

Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations

DEFF Research Database (Denmark)

Aziz, Ramy K.; Monk, Jonathan M.; Lewis, R. M.

2015-01-01

Mathematical models of metabolism from bacterial systems biology have proven their utility across multiple fields, for example metabolic engineering, growth phenotype simulation, and biological discovery. The usefulness of the models stems from their ability to compute a link between genotype...... of metabolic models, and highlight one potential application of systems biology to drug discovery and translational medicine....

A comparison of student reactions to biology instruction by interactive videodisc or conventional laboratory

Science.gov (United States)

Leonard, William H.

This study was designed to learn if students perceived an interactive computer/videodisc learning system to represent a viable alternative to (or extension of) the conventional laboratory for learning biology skills and concepts normally taught under classroom laboratory conditions. Data were collected by questionnaire for introductory biology classes at a large midwestern university where students were randomly assigned to two interactive videodisc/computer lessons titled Respiration and Climate and Life or traditional laboratory investigation with the same titles and concepts. The interactive videodisc system consisted of a TRS-80 Model III microcomputer interfaced to a Pioneer laser-disc player and a color TV monitor. Students indicated an overall level satisfaction with this strategy very similar to that of conventional laboratory instruction. Students frequently remarked that videodisc instruction gave them more experimental and procedural options and more efficient use of instructional time than did the conventional laboratory mode. These two results are consistent with past CAI research. Students also had a strong perception that the images on the videodisc were not real and this factor was perceived as having both advantages and disadvantages. Students found the two approaches to be equivalent to conventional laboratory instruction in the areas of general interest, understanding of basic principles, help on examinations, and attitude toward science. The student-opinion data in this study do not suggest that interactive videodisc technology serve as a substitute to the wet laboratory experience, but that this medium may enrich the spectrum of educational experiences usually not possible in typical classroom settings.

Expanding Interaction Potentials within Virtual Environments: Investigating the Usability of Speech and Manual Input Modes for Decoupled Interaction

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Alex Stedmon

2011-01-01

Full Text Available Distributed technologies and ubiquitous computing now support users who may be detached or decoupled from traditional interactions. In order to investigate the potential usability of speech and manual input devices, an evaluation of speech input across different user groups and a usability assessment of independent-user and collaborative-user interactions was conducted. Whilst the primary focus was on a formative usability evaluation, the user group evaluation provided a formal basis to underpin the academic rigor of the exercise. The results illustrate that using a speech interface is important in understanding user acceptance of such technologies. From the usability assessment it was possible to translate interactions and make them compatible with innovative input devices. This approach to interaction is still at an early stage of development, and the potential or validity of this interfacing concept is still under evaluation; however, as a concept demonstrator, the results of these initial evaluations demonstrate the potential usability issues of both input devices as well as highlighting their suitability for advanced virtual applications.

Measuring RNA-Ligand Interactions with Microscale Thermophoresis.

Science.gov (United States)

Moon, Michelle H; Hilimire, Thomas A; Sanders, Allix M; Schneekloth, John S

2018-01-31

In recent years, there has been dramatic growth in the study of RNA. RNA has gone from being known as an intermediate in the central dogma of molecular biology to a molecule with a large diversity of structure and function that is involved in all aspects of biology. As new functions are rapidly discovered, it has become clear that there is a need for RNA-targeting small molecule probes to investigate RNA biology and clarify the potential for therapeutics based on RNA-small molecule interactions. While a host of techniques exist to measure RNA-small molecule interactions, many of these have drawbacks that make them intractable for routine use and are often not broadly applicable. A newer technology called microscale thermophoresis (MST), which measures the directed migration of a molecule and/or molecule-ligand complex along a temperature gradient, can be used to measure binding affinities using very small amounts of sample. The high sensitivity of this technique enables measurement of affinity constants in the nanomolar and micromolar range. Here, we demonstrate how MST can be used to study a range of biologically relevant RNA interactions, including peptide-RNA interactions, RNA-small molecule interactions, and displacement of an RNA-bound peptide by a small molecule.

Potential biological hazard of importance for HACCP plans in fresh fish processing

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Baltić Milan Ž.

2009-01-01

Full Text Available The Hazard Analysis and Critical Control Point (HACCP system is scientifically based and focused on problem prevention in order to assure the produced food products are safe to consume. Prerequisite programs such as GMP (Good Manufacturing Practices, GHP (Good Hygienic Practices are an essential foundation for the development and implementation of successful HACCP plans. One of the preliminary tasks in the development of HACCP plan is to conduct a hazard analysis. The process of conducting a hazard analysis involves two stages. The first is hazard identification and the second stage is the HACCP team decision which potential hazards must be addressed in the HACCP plan. By definition, the HACCP concept covers all types of potential food safety hazards: biological, chemical and physical, whether they are naturally occurring in the food, contributed by the environment or generated by a mistake in the manufacturing process. In raw fish processing, potential significant biological hazards which are reasonably likely to cause illness of humans are parasites (Trematodae, Nematodae, Cestodae, bacteria (Salmonella, E. coli, Vibrio parahemolyticus, Vibrio vulnificus, Listeria monocytogenes, Clostridium botulinum, Staphyloccocus aureus, viruses (Norwalk virus, Entero virusesi, Hepatitis A, Rotovirus and bio-toxins. Upon completion of hazard analysis, any measure(s that are used to control the hazard(s should be described.

Biologic interactions between HSV-2 and HIV-1 and possible implications for HSV vaccine development.

Science.gov (United States)

Schiffer, Joshua T; Gottlieb, Sami L

2017-09-25

Development of a safe and effective vaccine against herpes simplex virus type 2 (HSV-2) has the potential to limit the global burden of HSV-2 infection and disease, including genital ulcer disease and neonatal herpes, and is a global sexual and reproductive health priority. Another important potential benefit of an HSV-2 vaccine would be to decrease HIV infections, as HSV-2 increases the risk of HIV-1 acquisition several-fold. Acute and chronic HSV-2 infection creates ulcerations and draws dendritic cells and activated CD4+ T cells into genital mucosa. These cells are targets for HIV entry and replication. Prophylactic HSV-2 vaccines (to prevent infection) and therapeutic vaccines (to modify or treat existing infections) are currently under development. By preventing or modifying infection, an effective HSV-2 vaccine could limit HSV-associated genital mucosal inflammation and thus HIV risk. However, a vaccine might have competing effects on HIV risk depending on its mechanism of action and cell populations generated in the genital mucosa. In this article, we review biologic interactions between HSV-2 and HIV-1, consider HSV-2 vaccine development in the context of HIV risk, and discuss implications and research needs for future HSV vaccine development. Copyright © 2017 Elsevier Ltd. All rights reserved.

Anopheline Reproductive Biology: Impacts on Vectorial Capacity and Potential Avenues for Malaria Control.

Science.gov (United States)

Mitchell, Sara N; Catteruccia, Flaminia

2017-12-01

Vectorial capacity is a mathematical approximation of the efficiency of vector-borne disease transmission, measured as the number of new infections disseminated per case per day by an insect vector. Multiple elements of mosquito biology govern their vectorial capacity, including survival, population densities, feeding preferences, and vector competence. Intriguingly, biological pathways essential to mosquito reproductive fitness directly or indirectly influence a number of these elements. Here, we explore this complex interaction, focusing on how the interplay between mating and blood feeding in female Anopheles not only shapes their reproductive success but also influences their ability to sustain Plasmodium parasite development. Central to malaria transmission, mosquito reproductive biology has recently become the focus of research strategies aimed at malaria control, and we discuss promising new methods based on the manipulation of key reproductive steps. In light of widespread resistance to all public health-approved insecticides targeting mosquito reproduction may prove crucial to the success of malaria-eradication campaigns. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Molecular Insights into the Potential Toxicological Interaction of 2-Mercaptothiazoline with the Antioxidant Enzyme—Catalase

Science.gov (United States)

Huang, Zhenxing; Huang, Ming; Mi, Chenyu; Wang, Tao; Chen, Dong; Teng, Yue

2016-01-01

2-mercaptothiazoline (2-MT) is widely used in many industrial fields, but its residue is potentially harmful to the environment. In this study, to evaluate the biological toxicity of 2-MT at protein level, the interaction between 2-MT and the pivotal antioxidant enzyme—catalase (CAT) was investigated using multiple spectroscopic techniques and molecular modeling. The results indicated that the CAT fluorescence quenching caused by 2-MT should be dominated by a static quenching mechanism through formation of a 2-MT/CAT complex. Furthermore, the identifications of the binding constant, binding forces, and the number of binding sites demonstrated that 2-MT could spontaneously interact with CAT at one binding site mainly via Van der Waals’ forces and hydrogen bonding. Based on the molecular docking simulation and conformation dynamic characterization, it was found that 2-MT could bind into the junctional region of CAT subdomains and that the binding site was close to enzyme active sites, which induced secondary structural and micro-environmental changes in CAT. The experiments on 2-MT toxicity verified that 2-MT significantly inhibited CAT activity via its molecular interaction, where 2-MT concentration and exposure time both affected the inhibitory action. Therefore, the present investigation provides useful information for understanding the toxicological mechanism of 2-MT at the molecular level. PMID:27537873

Biological productivity and potential resources of the exclusive economic zone (EEZ) of India

Digital Repository Service at National Institute of Oceanography (India)

Goswami, S.C.

An assessment of the biological production and the potential fishery resources has been made based on the data collected over a period of 15 years (1976-1991). The entire Exclusive Economic Zone (EEZ), measuring 2.02 million km sup(2) was divided...

Statistical analysis of simulation calculation of sputtering for two interaction potentials

International Nuclear Information System (INIS)

Shao Qiyun

1992-01-01

The effects of the interaction potentials (Moliere potential and Universal potential) are presented on computer simulation results of sputtering via Monte Carlo simulation based on the binary collision approximation. By means of Wilcoxon two-Sample paired sign rank test, the statistically significant difference for the above results is obtained

Organization A Comprehensive System Of Insurance Coverage In The Potential Chemical And Biological Contamination Zone In Regions

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Nina Vladimirovna Zaytseva

2014-12-01

Full Text Available The article provides a scientific rationale for an integrated approach to the provision of insurance coverage in the potential chemical and biological contamination zone. The following modern forms of chemical safety in the Russian Federation were considered: state reserve’s system, target program financing, state social insurance. The separate issue tackles the obligatory civil liability insurance for owners of dangerous objects. For improvement of the existing insurance protection system against emergency situations, risks were analyzed (shared on exogenous and endogenous. Among the exogenous risks including natural and climatic conditions of a region, its geographical arrangement, economic specialization, the seismic and terrorist risks were chosen and approaches to its solution were suggested. In endogenous risks’ group, the special focus is on wear and tear and obsolescence of hazardous chemical and biological object’s fixed assets. In case of high risk of an incident, it is suggested to increase in extent of insurance protection through self-insurance, a mutual insurance in the form of the organization of societies of a mutual insurance or the self-regulating organizations, and also development of voluntary insurance of a civil liability, both the owner of hazardous object, and regions of the Russian Federation and municipalities. The model of insurance coverage in the potential chemical and biological contamination zone is based on a differentiated approach to the danger level of the area. A matrix of adequate forms and types of insurance (required for insurance coverage of the population in the potential chemical and biological contamination zone was constructed. Proposed health risk management toolkit in the potential chemical and biological contamination zone will allow to use financial resources for chemical and biological safety in the regions more efficiently.

Choice of single-particle potential and the convergence of the effective interaction

International Nuclear Information System (INIS)

Hjorth-Jensen, M.; Osnes, E.; Muether, H.; Schmid, K.W.

1990-02-01

The convergence of the expansion for the effective interaction is studied considering as example the shell model for the nuclei 18 O and 18 F. In this work the effective interaction is computed through third order in the Brueckner G matrix, using both a harmonic-oscillator (HO) basis and a Brueckner-Hartree-Fock (BHF) basis. The significant differences in the convergence behavior of the effective interaction in these two cases are reported. The results indicate that the choice of the BHF single-particle potential facilitates the convergence of the effective interaction in low-orders of the expansion, whereas the HO results exhibit a non-convergent behavior. The implications for the HO approach are discussed. All calculations have been performed considering a modern version of the Bonn one-boson-exchange potential for the nucleon-nucleon interaction. 23 refs., 4 figs., 2 tabs

Systems biology of fungal infection

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Fabian eHorn

2012-04-01

Full Text Available Elucidation of pathogenicity mechanisms of the most important human pathogenic fungi, Aspergillus fumigatus and Candida albicans, has gained great interest in the light of the steadily increasing number of cases of invasive fungal infections.A key feature of these infections is the interaction of the different fungal morphotypes with epithelial and immune effector cells in the human host. Because of the high level of complexity, it is necessary to describe and understand invasive fungal infection by taking a systems biological approach, i.e., by a comprehensive quantitative analysis of the non-linear and selective interactions of a large number of functionally diverse, and frequently multifunctional, sets of elements, e.g., genes, proteins, metabolites, which produce coherent and emergent behaviours in time and space. The recent advances in systems biology will now make it possible to uncover the structure and dynamics of molecular and cellular cause-effect relationships within these pathogenic interactions.We review current efforts to integrate omics and image-based data of host-pathogen interactions into network and spatio-temporal models. The modelling will help to elucidate pathogenicity mechanisms and to identify diagnostic biomarkers and potential drug targets for therapy and could thus pave the way for novel intervention strategies based on novel antifungal drugs and cell therapy.

Changes of antioxidant potential of pasta fortified with parsley (Petroselinum Crispum mill.) leaves in the light of protein-phenolics interactions.

Science.gov (United States)

Sęczyk, Łukasz; Świeca, Michał; Gawlik-Dziki, Urszula

2015-01-01

Pasta is considered as an effective carrier of prohealth ingredients in food fortification. The aim of this study was to examine the changes of antioxidant potential of wheat pasta affected by fortification with powdered parsley leaves. A special attention was paid to effectiveness of fortification in the light of proteinphenolic interactions. To improve antioxidant activity of pasta, part of wheat flour was replaced with powdered parsley leaves from 1% to 4% (w/w). The total phenolics content was determined with Folin-Ciocalteau reagent. Antioxidant capacity was evaluated using in vitro assays - abilities to scavenge free radicals (ABTS) and to reduce iron (III) (FRAP). Predicted phenolic contents and antioxidant activity were calculated. To determine the protein-phenolics interactions SE-HPLC and SDS-PAGE techniques were used. Fortification of pasta had a positive effect on its phenolic contents and antioxidant properties. The highest phenolics level and antioxidant activity of pasta were obtained by supplementation with 4% of parsley leaves. However, in most cases experimental values were significantly lower than those predicted. The protein profiles obtained after SDS-PAGE differed significantly among control and enriched pasta. Furthermore, the addition of parsley leaves to pasta resulted in increase of peaks areas obtained by SE-HPLC. Results indicate the occurrence of the protein-phenolics interactions in fortified pasta. Overall, the effectiveness of fortification and consequently biological effect is limited by many factors including interactions between phenolics and pasta proteins. In the light of this results the study of potential interaction of bioactive supplements with food matrix should be taken into account during designing new functional food products.

The Respon of IKIP BUDI UTOMO Students Toward The Instructional Book of Cell Biology Subject Aided by Interactive Multimedia

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Tri Asih Wahyu Hartati

2017-07-01

Full Text Available The development of Science and Technology (Science and Technology takes place very rapidly. The development of science and technology will impact on graduate competency changes desired by the industry. This change of course will be followed by updating the curriculum, learning resources and teaching materials are used, one of them teaching materials on the subjects of Cell Biology. In the course of Cell Biology, the students only take textbooks without the support of interactive multimedia. Good teaching materials is the teaching materials arranged in a systematic, according to the needs and character of students, as well as validated by the teaching materials. The purpose of this study was to determine response students Biology Education IKIP Budi Utomo against Cell Biology course textbook aided interactive multimedia. The development method used is the 4D model consisting of stages define, design, develop, and disseminate. This study is limited to the stages develop. Legibility test results showed that students responded well teaching materials and provide proper assessment of the teaching materials.

Do biological-based strategies hold promise to biofouling control in MBRs?

KAUST Repository

Malaeb, Lilian; Le-Clech, Pierre; Vrouwenvelder, Johannes S.; Ayoub, George M.; Saikaly, Pascal

2013-01-01

. The reason for the slow advancement in successful control of biofouling is largely attributed to the complex interactions of involved biological compounds and the lack of representative-for-practice experimental approaches to evaluate potential effective

The role of antioxidant-protein interactions in biological membrane

International Nuclear Information System (INIS)

McGillivray, Duncan J; Singh, Rachna; Melton, Laurence D.; Worcester, David L.; Gilbert, Elliot P.

2009-01-01

Full text: Oxidative damage of cellular membranes has been linked to a variety of disease pathologies, including cardiac disease, Alzheimer's and complications due to diabetes. The oxidation of unsaturated and polyunsaturated fatty acid chains found in cellular membranes leads to significant alteration in membrane physical properties, including lipid orientation and membrane permeability, which ultimately affect biological function. Polyphenols are naturally occurring phytochemicals present in a number of fruit and vegetables that are of interest for their anti-oxidative powers. These polyphenols inhibit lipid oxidation in cellular membrane surfaces, although the mechanism of this inhibition is not entirely clear. Moreover, the polyphenols have significant binding affinity for proteins, which can lead to the formation of soluble and insoluble protein-polyphenol complexes Significantly, in the presence of casein proteins the oxidation inhibition the polyphenols in the membrane is significantly enhanced (as assessed by Lipid Peroxidation Inhibition Capacity assays). Thus the antioxidant pathway appears to involve these protein/polyphenol complexes, as well as direct antioxidant action by the polyphenol. Here we discuss neutron and x-ray scattering results from phospholipid membranes, looking at the positioning of two examples of polyphenolic antioxidants in phospholipid membranes, quercetin and phloretin, the antioxidants' impact on the membrane organisation, and the interaction between antioxidant and extra-membranous protein. This information sheds light on the mechanism of antioxidant protection in these systems, which may be used to understand biological responses to oxidative stress.

Linking neuroethology to the chemical biology of natural products

DEFF Research Database (Denmark)

Olivera, Baldomero M.; Raghuraman, Shrinivasan; Schmidt, Eric W.

2017-01-01

From a biological perspective, a natural product can be defined as a compound evolved by an organism for chemical interactions with another organism including prey, predator, competitor, pathogen, symbiont or host. Natural products hold tremendous potential as drug leads and have been extensively...... a better understanding of the evolution, biology and biochemistry of natural products will facilitate both neuroscience and the potential for drug leads. The larger goal is to establish a new sub-discipline in the broader field of neuroethology that we refer to as “Chemical Neuroethology”, linking...... the substantial work carried out by chemists on natural products with accelerating advances in neuroethology....

Biosocial Conservation: Integrating Biological and Ethnographic Methods to Study Human-Primate Interactions.

Science.gov (United States)

Setchell, Joanna M; Fairet, Emilie; Shutt, Kathryn; Waters, Siân; Bell, Sandra

2017-01-01

Biodiversity conservation is one of the grand challenges facing society. Many people interested in biodiversity conservation have a background in wildlife biology. However, the diverse social, cultural, political, and historical factors that influence the lives of people and wildlife can be investigated fully only by incorporating social science methods, ideally within an interdisciplinary framework. Cultural hierarchies of knowledge and the hegemony of the natural sciences create a barrier to interdisciplinary understandings. Here, we review three different projects that confront this difficulty, integrating biological and ethnographic methods to study conservation problems. The first project involved wildlife foraging on crops around a newly established national park in Gabon. Biological methods revealed the extent of crop loss, the species responsible, and an effect of field isolation, while ethnography revealed institutional and social vulnerability to foraging wildlife. The second project concerned great ape tourism in the Central African Republic. Biological methods revealed that gorilla tourism poses risks to gorillas, while ethnography revealed why people seek close proximity to gorillas. The third project focused on humans and other primates living alongside one another in Morocco. Incorporating shepherds in the coproduction of ecological knowledge about primates built trust and altered attitudes to the primates. These three case studies demonstrate how the integration of biological and social methods can help us to understand the sustainability of human-wildlife interactions, and thus promote coexistence. In each case, an integrated biosocial approach incorporating ethnographic data produced results that would not otherwise have come to light. Research that transcends conventional academic boundaries requires the openness and flexibility to move beyond one's comfort zone to understand and acknowledge the legitimacy of "other" kinds of knowledge. It is

Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions

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Cheryl-Emiliane Tien Chow

2015-04-01

Full Text Available Viral diversity and virus-host interactions in oxygen-starved regions of the ocean, also known as oxygen minimum zones (OMZs, remain relatively unexplored. Microbial community metabolism in OMZs alters nutrient and energy flow through marine food webs, resulting in biological nitrogen loss and greenhouse gas production. Thus, viruses infecting OMZ microbes have the potential to modulate community metabolism with resulting feedback on ecosystem function. Here, we describe viral communities inhabiting oxic surface (10m and oxygen-starved basin (200m waters of Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia using viral metagenomics and complete viral fosmid sequencing on samples collected between April 2007 and April 2010. Of 6459 open reading frames (ORFs predicted across all 34 viral fosmids, 77.6% (n=5010 had no homology to reference viral genomes. These fosmids recruited a higher proportion of viral metagenomic sequences from Saanich Inlet than from nearby northeastern subarctic Pacific Ocean (Line P waters, indicating differences in the viral communities between coastal and open ocean locations. While functional annotations of fosmid ORFs were limited, recruitment to NCBI’s non-redundant ‘nr’ database and publicly available single-cell genomes identified putative viruses infecting marine thaumarchaeal and SUP05 proteobacteria to provide potential host linkages with relevance to coupled biogeochemical cycling processes in OMZ waters. Taken together, these results highlight the power of coupled analyses of multiple sequence data types, such as viral metagenomic and fosmid sequence data with prokaryotic single cell genomes, to chart viral diversity, elucidate genomic and ecological contexts for previously unclassifiable viral sequences, and identify novel host interactions in natural and engineered ecosystems.

Dendrimer-protein interactions versus dendrimer-based nanomedicine.

Science.gov (United States)

Shcharbin, Dzmitry; Shcharbina, Natallia; Dzmitruk, Volha; Pedziwiatr-Werbicka, Elzbieta; Ionov, Maksim; Mignani, Serge; de la Mata, F Javier; Gómez, Rafael; Muñoz-Fernández, Maria Angeles; Majoral, Jean-Pierre; Bryszewska, Maria

2017-04-01

Dendrimers are hyperbranched polymers belonging to the huge class of nanomedical devices. Their wide application in biology and medicine requires understanding of the fundamental mechanisms of their interactions with biological systems. Summarizing, electrostatic force plays the predominant role in dendrimer-protein interactions, especially with charged dendrimers. Other kinds of interactions have been proven, such as H-bonding, van der Waals forces, and even hydrophobic interactions. These interactions depend on the characteristics of both participants: flexibility and surface charge of a dendrimer, rigidity of protein structure and the localization of charged amino acids at its surface. pH and ionic strength of solutions can significantly modulate interactions. Ligands and cofactors attached to a protein can also change dendrimer-protein interactions. Binding of dendrimers to a protein can change its secondary structure, conformation, intramolecular mobility and functional activity. However, this strongly depends on rigidity versus flexibility of a protein's structure. In addition, the potential applications of dendrimers to nanomedicine are reviwed related to dendrimer-protein interactions. Copyright © 2017 Elsevier B.V. All rights reserved.

On modelling adiabatic N-soliton interactions and perturbations. Effects of external potentials

International Nuclear Information System (INIS)

Gerdjikov, V.; Baizakov, B.

2005-01-01

We analyze several perturbed versions of the complex Toda chain (CTC) in an attempt to describe the adiabatic N-soliton train interactions of the perturbed nonlinear Schrodinger equation (NLS). Particular types of perturbations, including quadratic and periodic external potentials are treated by both analytical and numerical means. We show that the perturbed CTC model provides a good description for the N-soliton interactions in the presence of a weak external potential. (authors)

The Potential of Text Mining in Data Integration and Network Biology for Plant Research: A Case Study on Arabidopsis[C][W

Science.gov (United States)

Van Landeghem, Sofie; De Bodt, Stefanie; Drebert, Zuzanna J.; Inzé, Dirk; Van de Peer, Yves

2013-01-01

Despite the availability of various data repositories for plant research, a wealth of information currently remains hidden within the biomolecular literature. Text mining provides the necessary means to retrieve these data through automated processing of texts. However, only recently has advanced text mining methodology been implemented with sufficient computational power to process texts at a large scale. In this study, we assess the potential of large-scale text mining for plant biology research in general and for network biology in particular using a state-of-the-art text mining system applied to all PubMed abstracts and PubMed Central full texts. We present extensive evaluation of the textual data for Arabidopsis thaliana, assessing the overall accuracy of this new resource for usage in plant network analyses. Furthermore, we combine text mining information with both protein–protein and regulatory interactions from experimental databases. Clusters of tightly connected genes are delineated from the resulting network, illustrating how such an integrative approach is essential to grasp the current knowledge available for Arabidopsis and to uncover gene information through guilt by association. All large-scale data sets, as well as the manually curated textual data, are made publicly available, hereby stimulating the application of text mining data in future plant biology studies. PMID:23532071

Informing biological design by integration of systems and synthetic biology.

Science.gov (United States)

Smolke, Christina D; Silver, Pamela A

2011-03-18

Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. Copyright © 2011 Elsevier Inc. All rights reserved.

Biological efficiency of interaction between various radiation and chemicals

International Nuclear Information System (INIS)

Kim, Jin Kyu; Yu, Dong Han; Lee, Byoung Hun; Petin, Vladislav G.; Geras'kin, Stanislav A.; Cebulska-Wasilewska, Antonina; Panek, Agnieszka; Wiechec, Anna

2004-06-01

This research project has been carried out jointly with INP (Poland) to develop technologies to assess the biological efficiency of interaction between radiation and chemicals. Through the cooperative project, KAERI and INP have established wide variety of bioassay techniques applicable to radiation bioscience, human monitoring, molecular epidemiology and environmental science. The joint experiment, in special, made it possible to utilize the merits of both institutes and to upgrade and verify KAERI's current technology level. All results of the cooperative research will be jointly published in high standard scientific journals listed in the Science Citation Index (SCI), which can make the role of fundamental basis for improving relationship between Korea and Poland. Research skills such as Trad-MCN assay, SCGE assay, immunohistochemical assay and molecular assay developed through joint research will be further elaborated and will be continuously used for the collaboration between two institutes

Nucleon-nucleon interaction with quark exchanges and prediction to colour van der Waals potential

International Nuclear Information System (INIS)

Osman, A.

1985-11-01

The nucleon-nucleon interaction is considered by including the colour nucleon clusters. The nucleon-nucleon system is treated as a six-quark system. The obtained local potentials reduce the short-range repulsion. The resulted nucleon-nucleon potential by using a quark-quark potential well agrees with the central-force potentials. The phase shifts calculated by using these local potentials are in good agreement with those obtained from other methods. Introducing the quark-quark potential in the nucleon-nucleon interaction, leads to a colour van der Waals potential very strong compared with that predicted by experiments. (author)

Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy

Directory of Open Access Journals (Sweden)

Oyang Yen-Jen

2010-10-01

Full Text Available Abstract Background Molecular networks represent the backbone of molecular activity within cells and provide opportunities for understanding the mechanism of diseases. While protein-protein interaction data constitute static network maps, integration of condition-specific co-expression information provides clues to the dynamic features of these networks. Dilated cardiomyopathy is a leading cause of heart failure. Although previous studies have identified putative biomarkers or therapeutic targets for heart failure, the underlying molecular mechanism of dilated cardiomyopathy remains unclear. Results We developed a network-based comparative analysis approach that integrates protein-protein interactions with gene expression profiles and biological function annotations to reveal dynamic functional modules under different biological states. We found that hub proteins in condition-specific co-expressed protein interaction networks tended to be differentially expressed between biological states. Applying this method to a cohort of heart failure patients, we identified two functional modules that significantly emerged from the interaction networks. The dynamics of these modules between normal and disease states further suggest a potential molecular model of dilated cardiomyopathy. Conclusions We propose a novel framework to analyze the interaction networks in different biological states. It successfully reveals network modules closely related to heart failure; more importantly, these network dynamics provide new insights into the cause of dilated cardiomyopathy. The revealed molecular modules might be used as potential drug targets and provide new directions for heart failure therapy.

The sensor on the principle of ionization chamber for the measurement of biological objects and of their mutual interactions

International Nuclear Information System (INIS)

Komarek, K.; Chrapan, J.; Herec, I.; Bucka, P.

2012-01-01

In the contribution the sensor for measuring biological objects 'Auro-Graph' is described, which was suggested and designed for measuring the expressions of human's aura. From the physical point of view the aura is a field with electrical charge in the surroundings of biological as well as non-biological object, whose expressions are measured by known interactions of electrical and magnetically field. It is a field with electrical field in the human's surrounding, where atoms of surroundings are being excited by operation of biopotential (authors)

Interaction Potential between Parabolic Rotator and an Outside Particle

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Dan Wang

2014-01-01

Full Text Available At micro/nanoscale, the interaction potential between parabolic rotator and a particle located outside the rotator is studied on the basis of the negative exponential pair potential 1/Rn between particles. Similar to two-dimensional curved surfaces, we confirm that the potential of the three-dimensional parabolic rotator and outside particle can also be expressed as a unified form of curvatures; that is, it can be written as the function of curvatures. Furthermore, we verify that the driving forces acting on the particle may be induced by the highly curved micro/nano-parabolic rotator. Curvatures and the gradient of curvatures are the essential elements forming the driving forces. Through the idealized numerical experiments, the accuracy of the curvature-based potential is preliminarily proved.

Kinetic Behaviour of Nanoparticles Across the Biological Physiology

Energy Technology Data Exchange (ETDEWEB)

Emond, Claude, E-mail: claude.emond@biosmc.com [BioSimulation Consulting Inc., 220E. Delaware Avenue 1182, Newark, DE, 19711 (United States)

2011-07-06

Nanotoxicokinetics is a subsection of the toxicology field that involves the study of kinetic displacement of nanoparticles (NPs) in an organism. Four different steps, namely absorption, distribution, metabolism and elimination (ADME), are involved in nanotoxicokinetics. However, only ADE will be covert in this mini review. Because of their size, NPs react differently than particulate matter larger than the nanometre unit in diameter. In the organism, a closer interaction between NPs and biological matrices, called nanotoxicodynamics, might increase the health effects. (Animals are usually in studies to evaluate the global interaction of NPs and biological matrices and to control and reduce the bias.) Understanding the different steps of kinetics is very important to increase the confidence of the amount of NP delivery in the target organ and to assess the level of risk. The objective of this work was to review the behaviour of the NPs interacting with the biological kinetic steps of the ADME and their limitations and constraints. Specifically, it was reviewed the impact of each of the four steps of nanotoxicokinetics, from exposure to elimination in the organism. Recent publications have provided some information on this issue, allowing for a better understanding on how the NPs behave across physiology; however, information is still lacking. We also systematically reviewed the ADME process, and supported our review with examples from the literature. We reviewed the two major factors that influence the absorption of NPs: enumerated biotransformation and elimination limitations. One of the focuses of this study was the interaction between NPs and biological matrices because the morphology and chemical properties may drive the potential for exposure. This paper present different examples of interactions find from literature. To study these interactions, we used a classical pharmacokinetic approach employed in the pharmaceutical industry and compared it to a dynamic

Short range part of the NN interaction: Equivalent local potentials from quark exchange kernels

International Nuclear Information System (INIS)

Suzuk, Y.; Hecht, K.T.

1983-01-01

To focus on the nature of the short range part of the NN interaction, the intrinsically nonlocal interaction among the quark constituents of colorless nucleons is converted to an equivalent local potential using resonating group kernels which can be evaluated in analytic form. The WKB approximation based on the Wigner transform of the nonlocal kernels has been used to construct the equivalent potentials without recourse to the long range part of the NN interaction. The relative importance of the various components of the exchange kernels can be examined: The results indicate the importance of the color magnetic part of the exchange kernel for the repulsive part in the (ST) = (10), (01) channels, in particular since the energy dependence of the effective local potentials seems to be set by this term. Large cancellations of color Coulombic and quark confining contributions, together with the kinetic energy and norm exchange terms, indicate that the exact nature of the equivalent local potential may be sensitive to the details of the parametrization of the underlying quark-quark interaction. The equivalent local potentials show some of the characteristics of the phenomenological short range terms of the Paris potential

Natural enemy-mediated indirect interactions among prey species: potential for enhancing biocontrol services in agroecosystems

NARCIS (Netherlands)

Chailleux, A.; Mohl, E.K.; Teixeira Alves, M.; Messelink, G.J.; Desneux, N.

2014-01-01

Understanding how arthropod pests and their natural enemies interact in complex agroecosystems is essential for pest management programmes. Theory predicts that prey sharing a predator, such as a biological control agent, can indirectly reduce each other's density at equilibrium (apparent

Biological effects of radiation

International Nuclear Information System (INIS)

2013-01-01

This fourth chapter presents: cell structure and metabolism; radiation interaction with biological tissues; steps of the production of biological effect of radiation; radiosensitivity of tissues; classification of biological effects; reversibility, transmissivity and influence factors; pre-natal biological effects; biological effects in therapy and syndrome of acute irradiation

Pannus growth regulators as potential targets for biological therapy in rheumatoid arthritis

Directory of Open Access Journals (Sweden)

A. S. Mikhaylova

2018-01-01

Full Text Available The main goal of treatment for rheumatoid arthritis (RA is to suppress inflammation using basic and symptomatic therapies. At the same time, the above strategy does not significantly stop joint  destruction that leads to disability in patients. The review analyzes  publications dealing with a search for intercellular interaction  regulators among the main effector cells in the pannus – fibroblast- like synoviocytes (FLSs. It assesses the influence of FLS aggression  factors on invasive pannus behavior, the possibility of their targeted deactivation during biological therapy, and the preliminary  results of similar treatment by the examples of animal models. It is  shown that the most promising targets for biological therapy may be FLS adhesion molecules, such as transmembrane receptor cadherin  11, integrins α5/β1, and VCAM1, ICAM1, which actively participate in the attachment of FLSs to the cartilage surface and activate their production of cytokines, growth factors and aggression factors.

Novel nonlinear knowledge-based mean force potentials based on machine learning.

Science.gov (United States)

Dong, Qiwen; Zhou, Shuigeng

2011-01-01

The prediction of 3D structures of proteins from amino acid sequences is one of the most challenging problems in molecular biology. An essential task for solving this problem with coarse-grained models is to deduce effective interaction potentials. The development and evaluation of new energy functions is critical to accurately modeling the properties of biological macromolecules. Knowledge-based mean force potentials are derived from statistical analysis of proteins of known structures. Current knowledge-based potentials are almost in the form of weighted linear sum of interaction pairs. In this study, a class of novel nonlinear knowledge-based mean force potentials is presented. The potential parameters are obtained by nonlinear classifiers, instead of relative frequencies of interaction pairs against a reference state or linear classifiers. The support vector machine is used to derive the potential parameters on data sets that contain both native structures and decoy structures. Five knowledge-based mean force Boltzmann-based or linear potentials are introduced and their corresponding nonlinear potentials are implemented. They are the DIH potential (single-body residue-level Boltzmann-based potential), the DFIRE-SCM potential (two-body residue-level Boltzmann-based potential), the FS potential (two-body atom-level Boltzmann-based potential), the HR potential (two-body residue-level linear potential), and the T32S3 potential (two-body atom-level linear potential). Experiments are performed on well-established decoy sets, including the LKF data set, the CASP7 data set, and the Decoys “R”Us data set. The evaluation metrics include the energy Z score and the ability of each potential to discriminate native structures from a set of decoy structures. Experimental results show that all nonlinear potentials significantly outperform the corresponding Boltzmann-based or linear potentials, and the proposed discriminative framework is effective in developing knowledge

Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

Directory of Open Access Journals (Sweden)

Peter B McGarvey

2009-09-01

Full Text Available The NIAID (National Institute for Allergy and Infectious Diseases Biodefense Proteomics program aims to identify targets for potential vaccines, therapeutics, and diagnostics for agents of concern in bioterrorism, including bacterial, parasitic, and viral pathogens. The program includes seven Proteomics Research Centers, generating diverse types of pathogen-host data, including mass spectrometry, microarray transcriptional profiles, protein interactions, protein structures and biological reagents. The Biodefense Resource Center (www.proteomicsresource.org has developed a bioinformatics framework, employing a protein-centric approach to integrate and support mining and analysis of the large and heterogeneous data. Underlying this approach is a data warehouse with comprehensive protein + gene identifier and name mappings and annotations extracted from over 100 molecular databases. Value-added annotations are provided for key proteins from experimental findings using controlled vocabulary. The availability of pathogen and host omics data in an integrated framework allows global analysis of the data and comparisons across different experiments and organisms, as illustrated in several case studies presented here. (1 The identification of a hypothetical protein with differential gene and protein expressions in two host systems (mouse macrophage and human HeLa cells infected by different bacterial (Bacillus anthracis and Salmonella typhimurium and viral (orthopox pathogens suggesting that this protein can be prioritized for additional analysis and functional characterization. (2 The analysis of a vaccinia-human protein interaction network supplemented with protein accumulation levels led to the identification of human Keratin, type II cytoskeletal 4 protein as a potential therapeutic target. (3 Comparison of complete genomes from pathogenic variants coupled with experimental information on complete proteomes allowed the identification and

Resonant long-range interactions between polar macromolecules

International Nuclear Information System (INIS)

Preto, Jordane; Pettini, Marco

2013-01-01

Motivated by its prospective biological relevance, the issue of resonant long-range interactions between two molecules displaying oscillating dipole moments is reinvestigated within the framework of classical electrodynamics. In particular, our findings shed new light on Fröhlich's theory of selective long-range interactions between biomolecules. First, terms of a very long-range kind – which have never been reported so far – are found in the interaction potential, due to field retardation. Second, at variance with a long-standing belief, it is shown that sizable resonant long-range interactions may exist only if the interacting system is out of thermal equilibrium.

Collisional effects on interaction potential in complex plasma in presence of magnetic field

International Nuclear Information System (INIS)

Bezbaruah, Pratikshya; Das, Nilakshi

2016-01-01

Interaction potential in complex plasma with streaming ions is derived analytically in presence of ion-neutral collision and magnetic field. The linear dielectric response function obtained describes the behavior of charged micron sized dust particles in strong collisional limit. A new type of repulsive potential is found to be operative among the dust grains apart from the normal Debye–Hückel potential. The amplitude and shielding length involved in the potential are substantially affected by the parameters describing ion cyclotron frequency, collision frequency among ions and neutrals, and ion streaming. It is also observed that the usual mechanism of ion focusing surrounding the grain is inhibited due to collision. As a result, the attractive wake potential structure is destroyed in the ion flow direction. The horizontal interaction involves only Debye–Hückel potential.

Collisional effects on interaction potential in complex plasma in presence of magnetic field

Energy Technology Data Exchange (ETDEWEB)

Bezbaruah, Pratikshya, E-mail: pratphd@tezu.ernet.in; Das, Nilakshi [Department of Physics, Tezpur University, Tezpur, Assam 784028 (India)

2016-04-15

Interaction potential in complex plasma with streaming ions is derived analytically in presence of ion-neutral collision and magnetic field. The linear dielectric response function obtained describes the behavior of charged micron sized dust particles in strong collisional limit. A new type of repulsive potential is found to be operative among the dust grains apart from the normal Debye–Hückel potential. The amplitude and shielding length involved in the potential are substantially affected by the parameters describing ion cyclotron frequency, collision frequency among ions and neutrals, and ion streaming. It is also observed that the usual mechanism of ion focusing surrounding the grain is inhibited due to collision. As a result, the attractive wake potential structure is destroyed in the ion flow direction. The horizontal interaction involves only Debye–Hückel potential.

Biological intrusion of low-level-waste trench covers

Science.gov (United States)

Hakonson, T. E.; Gladney, E. S.

The long-term integrity of low-level waste shallow land burialsites is dependent on the interaction of physical, chemical, and biological factors that modify the waste containment system. The need to consider biological processes as being potentially important in reducing the integrity of waste burial site cover treatment is demonstrated. One approach to limiting biological intrusion through the waste cover is to apply a barrier within the profile to limit root and animal penetration with depth. Experiments in the Los Alamos Experimental Engineered Test Facility were initiated to develop and evaluate biological barriers that are effective in minimizing intrusion into waste trenches. The experiments that are described employ four different candidate barrier materials of geologic origin. Experimental variables that will be evaluated, in addition to barrier type, are barrier depth and sil overburden depth.

Association of COMT and COMT-DRD2 interaction with creative potential

Directory of Open Access Journals (Sweden)

Shun eZhang

2014-04-01

Full Text Available Several lines of evidence suggest that genes involved in dopamine (DA transmission may contribute to creativity. Among these genes, the catechol-O-methyltransferase gene (COMT and the dopamine D2 receptor gene (DRD2 are the most promising candidates. Our previous study has revealed evidence for the involvement of DRD2 in creative potential. The present study extended our previous study by systematically exploring the association of COMT with creative potential as well as the interaction between COMT and DRD2. Twelve single nucleotide polymorphisms (SNPs covering COMT were genotyped in 543 healthy Chinese college students whose creative potentials were assessed by divergent thinking tests. Single SNP analysis showed that rs174697 was nominally associated with verbal originality, two SNPs (rs737865 and rs5993883 were nominally associated with figural fluency, and two SNPs (rs737865 and rs4680 were nominally associated with figural originality. Haplotype analysis showed that, the TCT and CCT haplotype (rs737865-rs174675-rs5993882 were nominally associated with figural originality, and the TATGCAG and CGCGGGA haplotype (rs4646312-rs6269-rs4633-rs6267-rs4818-rs4680-rs769224 were nominally associated with figural originality and verbal flexibility, respectively. However, none of these nominal findings survived correction for multiple testing. Gene-gene interaction analysis identified one significant four-way interaction of rs174675 (COMT, rs174697 (COMT, rs1076560 (DRD2 and rs4436578 (DRD2 on verbal fluency, one significant four-way interaction of rs174675 (COMT, rs4818 (COMT, rs1076560 (DRD2 and rs4648317 (DRD2 on verbal flexibility, and one significant three-way interaction of rs5993883 (COMT, rs4648319 (DRD2 and rs4648317 (DRD2 on figural flexibility. In conclusion, the present study provides nominal evidence for the involvement of COMT in creative potential and suggests that DA related genes may act in coordination to contribute to creativity.

Potential biological control agents for management of cogongrass (Cyperales: Poaceae) in the southeastern USA

Science.gov (United States)

Cogongrass, Imperata cylindrica (L.) Palisot de Beauvois (Cyperales: Poaceae), is a noxious invasive weed in the southeastern USA. Surveys for potential biological control agents of cogongrass were conducted in Asia and East Africa from 2013 to 2016. Several insect herbivores were found that may hav...

Mining Functional Modules in Heterogeneous Biological Networks Using Multiplex PageRank Approach.

Science.gov (United States)

Li, Jun; Zhao, Patrick X

2016-01-01

Identification of functional modules/sub-networks in large-scale biological networks is one of the important research challenges in current bioinformatics and systems biology. Approaches have been developed to identify functional modules in single-class biological networks; however, methods for systematically and interactively mining multiple classes of heterogeneous biological networks are lacking. In this paper, we present a novel algorithm (called mPageRank) that utilizes the Multiplex PageRank approach to mine functional modules from two classes of biological networks. We demonstrate the capabilities of our approach by successfully mining functional biological modules through integrating expression-based gene-gene association networks and protein-protein interaction networks. We first compared the performance of our method with that of other methods using simulated data. We then applied our method to identify the cell division cycle related functional module and plant signaling defense-related functional module in the model plant Arabidopsis thaliana. Our results demonstrated that the mPageRank method is effective for mining sub-networks in both expression-based gene-gene association networks and protein-protein interaction networks, and has the potential to be adapted for the discovery of functional modules/sub-networks in other heterogeneous biological networks. The mPageRank executable program, source code, the datasets and results of the presented two case studies are publicly and freely available at http://plantgrn.noble.org/MPageRank/.

Reduction theories elucidate the origins of complex biological rhythms generated by interacting delay-induced oscillations.

Directory of Open Access Journals (Sweden)

Ikuhiro Yamaguchi

Full Text Available Time delay is known to induce sustained oscillations in many biological systems such as electroencephalogram (EEG activities and gene regulations. Furthermore, interactions among delay-induced oscillations can generate complex collective rhythms, which play important functional roles. However, due to their intrinsic infinite dimensionality, theoretical analysis of interacting delay-induced oscillations has been limited. Here, we show that the two primary methods for finite-dimensional limit cycles, namely, the center manifold reduction in the vicinity of the Hopf bifurcation and the phase reduction for weak interactions, can successfully be applied to interacting infinite-dimensional delay-induced oscillations. We systematically derive the complex Ginzburg-Landau equation and the phase equation without delay for general interaction networks. Based on the reduced low-dimensional equations, we demonstrate that diffusive (linearly attractive coupling between a pair of delay-induced oscillations can exhibit nontrivial amplitude death and multimodal phase locking. Our analysis provides unique insights into experimentally observed EEG activities such as sudden transitions among different phase-locked states and occurrence of epileptic seizures.

Blended Polyurethane and Tropoelastin as a Novel Class of Biologically Interactive Elastomer

Science.gov (United States)

Wise, Steven G.; Liu, Hongjuan; Yeo, Giselle C.; Michael, Praveesuda L.; Chan, Alex H.P.; Ngo, Alan K.Y.; Bilek, Marcela M.M.; Bao, Shisan

2016-01-01

Polyurethanes are versatile elastomers but suffer from biological limitations such as poor control over cell attachment and the associated disadvantages of increased fibrosis. We address this problem by presenting a novel strategy that retains elasticity while modulating biological performance. We describe a new biomaterial that comprises a blend of synthetic and natural elastomers: the biostable polyurethane Elast-Eon and the recombinant human tropoelastin protein. We demonstrate that the hybrid constructs yield a class of coblended elastomers with unique physical properties. Hybrid constructs displayed higher elasticity and linear stress–strain responses over more than threefold strain. The hybrid materials showed increased overall porosity and swelling in comparison to polyurethane alone, facilitating enhanced cellular interactions. In vitro, human dermal fibroblasts showed enhanced proliferation, while in vivo, following subcutaneous implantation in mice, hybrid scaffolds displayed a reduced fibrotic response and tunable degradation rate. To our knowledge, this is the first example of a blend of synthetic and natural elastomers and is a promising approach for generating tailored bioactive scaffolds for tissue repair. PMID:26857114

Design, Synthesis and Biological Evaluation of Benzohydrazide Derivatives Containing Dihydropyrazoles as Potential EGFR Kinase Inhibitors

Directory of Open Access Journals (Sweden)

Hai-Chao Wang

2016-08-01

Full Text Available A series of novel benzohydrazide derivatives containing dihydropyrazoles have been synthesized as potential epidermal growth factor receptor (EGFR kinase inhibitors and their biological activities as potential antiproliferative agents have been evaluated. Among these compounds, compound H20 exhibited the most potent antiproliferative activity against four cancer cell line variants (A549, MCF-7, HeLa, HepG2 with IC50 values of 0.46, 0.29, 0.15 and 0.21 μM respectively, which showed the most potent EGFR inhibition activities (IC50 = 0.08 μM for EGFR. Molecular modeling simulation studies were performed in order to predict the biological activity and activity relationship (SAR of these benzohydrazide derivatives. These results suggested that compound H20 may be a promising anticancer agent.

Nucleon-nucleon interaction with quark exchange and prediction of the color van der Waals potential

International Nuclear Information System (INIS)

Osman, A.

1988-01-01

The nucleon-nucleon interaction is considered by including the color nucleon clusters. The nucleon-nucleon system is treated as a six-quark system. The obtained local potentials reduce the short-range repulsion. The resulting nucleon-nucleon potential, using a quark-quark potential, agress well with the central-force potentials. The phase shifts calculated by using these local potentials are in good agreement with those obtained from other methods. Introducing the quark-quark potential in the nucleon-nucleon interaction leads to a color van der Waals potential much stronger than that implied by experiments

Nuclear interaction potential in a folded-Yukawa model with diffuse densities

International Nuclear Information System (INIS)

Randrup, J.

1975-09-01

The folded-Yukawa model for the nuclear interaction potential is generalized to diffuse density distributions which are generated by folding a Yukawa function into sharp generating distributions. The effect of a finite density diffuseness or of a finite interaction range is studied. The Proximity Formula corresponding to the generalized model is derived and numerical comparison is made with the exact results. (8 figures)

Mathematical description of drug-target interactions: application to biologics that bind to targets with two binding sites.

Science.gov (United States)

Gibiansky, Leonid; Gibiansky, Ekaterina

2018-02-01

The emerging discipline of mathematical pharmacology occupies the space between advanced pharmacometrics and systems biology. A characteristic feature of the approach is application of advance mathematical methods to study the behavior of biological systems as described by mathematical (most often differential) equations. One of the early application of mathematical pharmacology (that was not called this name at the time) was formulation and investigation of the target-mediated drug disposition (TMDD) model and its approximations. The model was shown to be remarkably successful, not only in describing the observed data for drug-target interactions, but also in advancing the qualitative and quantitative understanding of those interactions and their role in pharmacokinetic and pharmacodynamic properties of biologics. The TMDD model in its original formulation describes the interaction of the drug that has one binding site with the target that also has only one binding site. Following the framework developed earlier for drugs with one-to-one binding, this work aims to describe a rigorous approach for working with similar systems and to apply it to drugs that bind to targets with two binding sites. The quasi-steady-state, quasi-equilibrium, irreversible binding, and Michaelis-Menten approximations of the model are also derived. These equations can be used, in particular, to predict concentrations of the partially bound target (RC). This could be clinically important if RC remains active and has slow internalization rate. In this case, introduction of the drug aimed to suppress target activity may lead to the opposite effect due to RC accumulation.

Prevalence of Potential and Clinically Relevant Statin-Drug Interactions in Frail and Robust Older Inpatients.

Science.gov (United States)

Thai, Michele; Hilmer, Sarah; Pearson, Sallie-Anne; Reeve, Emily; Gnjidic, Danijela

2015-10-01

A significant proportion of older people are prescribed statins and are also exposed to polypharmacy, placing them at increased risk of statin-drug interactions. To describe the prevalence rates of potential and clinically relevant statin-drug interactions in older inpatients according to frailty status. A cross-sectional study of patients aged ≥65 years who were prescribed a statin and were admitted to a teaching hospital between 30 July and 10 October 2014 in Sydney, Australia, was conducted. Data on socio-demographics, comorbidities and medications were collected using a standardized questionnaire. Potential statin-drug interactions were defined if listed in the Australian Medicines Handbook and three international drug information sources: the British National Formulary, Drug Interaction Facts and Drug-Reax(®). Clinically relevant statin-drug interactions were defined as interactions with the highest severity rating in at least two of the three international drug information sources. Frailty was assessed using the Reported Edmonton Frail Scale. A total of 180 participants were recruited (median age 78 years, interquartile range 14), 35.0% frail and 65.0% robust. Potential statin-drug interactions were identified in 10% of participants, 12.7% of frail participants and 8.5% of robust participants. Clinically relevant statin-drug interactions were identified in 7.8% of participants, 9.5% of frail participants and 6.8% of robust participants. Depending on the drug information source used, the prevalence rates of potential and clinically relevant statin-drug interactions ranged between 14.4 and 35.6% and between 14.4 and 20.6%, respectively. In our study of frail and robust older inpatients taking statins, the overall prevalence of potential statin-drug interactions was low and varied significantly according to the drug information source used.

Potential intravenous drug interactions in intensive care.

Science.gov (United States)

Moreira, Maiara Benevides; Mesquita, Maria Gefé da Rosa; Stipp, Marluci Andrade Conceição; Paes, Graciele Oroski

2017-07-20

To analyze potential intravenous drug interactions, and their level of severity associated with the administration of these drugs based on the prescriptions of an intensive care unit. Quantitative study, with aretrospective exploratory design, and descriptive statistical analysis of the ICU prescriptions of a teaching hospital from March to June 2014. The sample consisted of 319 prescriptions and subsamples of 50 prescriptions. The mean number of drugs per patient was 9.3 records, and a higher probability of drug interaction inherent to polypharmacy was evidenced. The study identified severe drug interactions, such as concomitant administration of Tramadol with selective serotonin reuptake inhibitor drugs (e.g., Metoclopramide and Fluconazole), increasing the risk of seizures due to their epileptogenic actions, as well as the simultaneous use of Ranitidine-Fentanyl®, which can lead to respiratory depression. A previous mapping of prescriptions enables the characterization of the drug therapy, contributing to prevent potential drug interactions and their clinical consequences. Analisar as potenciais interações medicamentosas intravenosas e seu grau de severidade associadas à administração desses medicamentos a partir das prescrições do Centro de Terapia Intensiva. Estudo quantitativo, tipologia retrospectiva exploratória, com análise estatística descritiva das prescrições medicamentosas do Centro de Terapia Intensiva de um Hospital Universitário, no período de março-junho/2014. A amostra foi composta de 319 prescrições e subamostras de 50 prescrições. Constatou-se que a média de medicamentos por paciente foi de 9,3 registros, e evidenciou-se maior probabilidade para ocorrência de interação medicamentosa inerente à polifarmácia. O estudo identificou interações medicamentosas graves, como a administração concomitante de Tramadol com medicamentos inibidores seletivos da recaptação da serotonina, (exemplo: Metoclopramida e Fluconazol

Molecular infection biology : interactions between microorganisms and cells

National Research Council Canada - National Science Library

Hacker, Jörg (Jörg Hinrich); Heesemann, Jurgen

2002-01-01

... and epidemiology of infectious diseases. Investigators, specialists, clinicians, and graduate students in biology, pharmacy, and medicine will find Molecular Infection Biology an invaluable addition to their professional libraries...

Shaping Biological Knowledge: Applications in Proteomics

Directory of Open Access Journals (Sweden)

R. Appel

2006-04-01

Full Text Available The central dogma of molecular biology has provided a meaningful principle for data integration in the field of genomics. In this context, integration reflects the known transitions from a chromosome to a protein sequence: transcription, intron splicing, exon assembly and translation. There is no such clear principle for integrating proteomics data, since the laws governing protein folding and interactivity are not quite understood. In our effort to bring together independent pieces of information relative to proteins in a biologically meaningful way, we assess the bias of bioinformatics resources and consequent approximations in the framework of small-scale studies. We analyse proteomics data while following both a data-driven (focus on proteins smaller than 10 kDa and a hypothesis-driven (focus on whole bacterial proteomes approach. These applications are potentially the source of specialized complements to classical biological ontologies.

Shaping biological knowledge: applications in proteomics.

Science.gov (United States)

Lisacek, F; Chichester, C; Gonnet, P; Jaillet, O; Kappus, S; Nikitin, F; Roland, P; Rossier, G; Truong, L; Appel, R

2004-01-01

The central dogma of molecular biology has provided a meaningful principle for data integration in the field of genomics. In this context, integration reflects the known transitions from a chromosome to a protein sequence: transcription, intron splicing, exon assembly and translation. There is no such clear principle for integrating proteomics data, since the laws governing protein folding and interactivity are not quite understood. In our effort to bring together independent pieces of information relative to proteins in a biologically meaningful way, we assess the bias of bioinformatics resources and consequent approximations in the framework of small-scale studies. We analyse proteomics data while following both a data-driven (focus on proteins smaller than 10 kDa) and a hypothesis-driven (focus on whole bacterial proteomes) approach. These applications are potentially the source of specialized complements to classical biological ontologies.

A general transformation to canonical form for potentials in pairwise interatomic interactions.

Science.gov (United States)

Walton, Jay R; Rivera-Rivera, Luis A; Lucchese, Robert R; Bevan, John W

2015-06-14

A generalized formulation of explicit force-based transformations is introduced to investigate the concept of a canonical potential in both fundamental chemical and intermolecular bonding. Different classes of representative ground electronic state pairwise interatomic interactions are referenced to a chosen canonical potential illustrating application of such transformations. Specifically, accurately determined potentials of the diatomic molecules H2, H2(+), HF, LiH, argon dimer, and one-dimensional dissociative coordinates in Ar-HBr, OC-HF, and OC-Cl2 are investigated throughout their bound potentials. Advantages of the current formulation for accurately evaluating equilibrium dissociation energies and a fundamentally different unified perspective on nature of intermolecular interactions will be emphasized. In particular, this canonical approach has significance to previous assertions that there is no very fundamental distinction between van der Waals bonding and covalent bonding or for that matter hydrogen and halogen bonds.

Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology

DEFF Research Database (Denmark)

Rossin, Elizabeth J.; Hansen, Kasper Lage; Raychaudhuri, Soumya

2011-01-01

Genome-wide association studies (GWAS) have defined over 150 genomic regions unequivocally containing variation predisposing to immune-mediated disease. Inferring disease biology from these observations, however, hinges on our ability to discover the molecular processes being perturbed by these r......Genome-wide association studies (GWAS) have defined over 150 genomic regions unequivocally containing variation predisposing to immune-mediated disease. Inferring disease biology from these observations, however, hinges on our ability to discover the molecular processes being perturbed...... in rheumatoid arthritis (RA) and Crohn's disease (CD) GWAS, we build protein-protein interaction (PPI) networks for genes within associated loci and find abundant physical interactions between protein products of associated genes. We apply multiple permutation approaches to show that these networks are more...... that the RA and CD networks have predictive power by demonstrating that proteins in these networks, not encoded in the confirmed list of disease associated loci, are significantly enriched for association to the phenotypes in question in extended GWAS analysis. Finally, we test our method in 3 non...

Three-way interaction between biological control insects, a congener and their shared parasitoid: Evidence of biotic resistance

Science.gov (United States)

Invasive plants are one of the strongest drivers of species extinctions. Weed biological control offers a sustainable and safe means of long-term population reduction of their target. Herbivores introduced for the control of invasive plants interact with the native community in addition to the top-d...

Influence of Pauli principle and polarization on 16O + 16O interaction potential

International Nuclear Information System (INIS)

Nesterov, V.A.

2012-01-01

In the work have studied the dependence of the interaction potential on taking into account the Pauli principle as well as monopole and quadrupole polarization within approaches based on the energy-density formalism and two-center shell model wave functions for 16 O + 16 O system. In the adiabatic approximation it is shown that the contribution of the Pauli principle and polarization in colliding nuclei radically changes the behavior of interaction potential

The acquisition of dangerous biological materials: Technical facts sheets to assist risk assessments of 46 potential BW agents

Energy Technology Data Exchange (ETDEWEB)

Aceto, Donato Gonzalo [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Astuto-Gribble, Lisa M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Gaudioso, Jennifer M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2007-11-01

Numerous terrorist organizations have openly expressed interest in producing and deploying biological weapons. However, a limiting factor for many terrorists has been the acquisition of dangerous biological agents, as evidenced by the very few successful instances of biological weapons use compared to the number of documented hoaxes. Biological agents vary greatly in their ability to cause loss of life and economic damage. Some agents, if released properly, can kill many people and cause an extensive number of secondary infections; other agents will sicken only a small number of people for a short period of time. Consequently, several biological agents can potentially be used to perpetrate a bioterrorism attack but few are likely capable of causing a high consequence event. It is crucial, from a US national security perspective, to more deeply understand the likelihood that terrorist organizations can acquire the range of these agents. Few studies have attempted to comprehensively compile the technical information directly relevant to the acquisition of dangerous bacteria, viruses and toxins. In this report, technical fact sheets were assembled for 46 potentially dangerous biological agents. Much of the information was taken from various research sources which could ultimately and significantly expedite and improve bioterrorism threat assessments. By systematically examining a number of specific agent characteristics included in these fact sheets, it may be possible to detect, target, and implement measures to thwart future terrorist acquisition attempts. In addition, the information in these fact sheets may be used as a tool to help laboratories gain a rudimentary understanding of how attractive a method laboratory theft is relative to other potential acquisition modes.

Effective interactions for valence-hole nuclei with modern meson-exchange potential models

International Nuclear Information System (INIS)

Hjort-Jensen, M.; Osnes, E.; Kuo, E.

1991-10-01

Within the framework of the folded-diagram theory, the authors have studied the effective interaction appropriate for hole-hole nuclei in the mass regions of 16 O and 40 Ca, using the Bonn and Paris potential models. To sum up the folded diagrams the renormalization procedure of Lee and Suzuki has been employed, using a so-called Q-box in which were included all one-body and two-body irreducible valence-linked diagrams through third order in perturbation theory. Discrepancies for the mass dependence of the effective interaction for several JT configurations with respect to empirically deduced mass dependencies is reported. The role of core polarization processes through third order were found to be one of the mechanisms behind these discrepancies. Compared to the results obtained with the Paris potential, more attraction is introduced by the Bonn potential for all matrix elements of concerns, a result which agrees well with previous findings for the particle-particle interaction in the same mass regions. A qualitative agreements with experimental data is obtained. 31 refs., 6 figs., 8 tabs

Ethylene glycol monolayer protected nanoparticles: synthesis, characterization, and interactions with biological molecules.

Science.gov (United States)

Zheng, Ming; Li, Zhigang; Huang, Xueying

2004-05-11

The usefulness of the hybrid materials of nanoparticles and biological molecules on many occasions depends on how well one can achieve a rational design based on specific binding and programmable assembly. Nonspecific binding between nanoparticles and biomolecules is one of the major barriers for achieving their utilities in a biological system. In this paper, we demonstrate a new approach to eliminate nonspecific interactions between nanoparticles and biological molecules by shielding the nanoparticle with a monolayer of ethylene glycol. A direct synthesis of di-, tri-, and tetra(ethylene glycol)-protected gold nanoparticles (Au-S-EGn, n = 2, 3, and 4) was achieved under the condition that the water content was optimized in the range of 9-18% in the reaction mixture. With controlled ratio of [HAuCl4]/[EGn-SH] at 2, the synthesized particles have an average diameter of 3.5 nm and a surface plasma resonance band around 510 nm. Their surface structures were confirmed by 1H NMR spectra. These gold nanoparticles are bonded with a uniform monolayer with defined lengths of 0.8, 1.2, and 1.6 nm for Au-S-EG2, Au-S-EG3, and Au-S-EG4, respectively. They have great stabilities in aqueous solutions with a high concentration of electrolytes as well as in organic solvents. Thermogravimetric analysis revealed that the ethylene glycol monolayer coating is ca. 14% of the total nanoparticle weight. Biological binding tests by using ion-exchange chromatography and gel electrophoresis demonstrated that these Au-S-EGn (n = 2, 3, or 4) nanoparticles are free of any nonspecific bindings with various proteins, DNA, and RNA. These types of nanoparticles provide a fundamental starting material for designing hybrid materials composed of metallic nanoparticles and biomolecules.

The Respon of IKIP BUDI UTOMO Students Toward the Instructional Book of Cell Biology Subject Aided by Interactive Multimedia

OpenAIRE

Hartati, Tri Asih Wahyu; Safitri, Dini

2017-01-01

The development of Science and Technology (Science and Technology) takes place very rapidly. The development of science and technology will impact on graduate competency changes desired by the industry. This change of course will be followed by updating the curriculum, learning resources and teaching materials are used, one of them teaching materials on the subjects of Cell Biology. In the course of Cell Biology, the students only take textbooks without the support of interactive multimedia. ...

Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes.

Science.gov (United States)

Hassani-Pak, Keywan; Rawlings, Christopher

2017-06-13

Genetics and "omics" studies designed to uncover genotype to phenotype relationships often identify large numbers of potential candidate genes, among which the causal genes are hidden. Scientists generally lack the time and technical expertise to review all relevant information available from the literature, from key model species and from a potentially wide range of related biological databases in a variety of data formats with variable quality and coverage. Computational tools are needed for the integration and evaluation of heterogeneous information in order to prioritise candidate genes and components of interaction networks that, if perturbed through potential interventions, have a positive impact on the biological outcome in the whole organism without producing negative side effects. Here we review several bioinformatics tools and databases that play an important role in biological knowledge discovery and candidate gene prioritization. We conclude with several key challenges that need to be addressed in order to facilitate biological knowledge discovery in the future.

Water reuse potential in truck wash using a Rotating Biological Contactor

Directory of Open Access Journals (Sweden)

Eduardo Lucas Subtil

2016-11-01

Full Text Available This study evaluated the water reuse potential for truck washing using the effluent treated by a Rotating Biological Contactor (RBC operated in full scale. In order to evaluate the reuse potential, a mass balance was performed for the reuse system taking into account the concentration of Total Dissolved Solids as the critical contaminant. The treatment system produced an effluent with average concentration of color, turbidity, TDS and BOD5 of 45 ± 14 uC, 15 ± 6.0 NTU, 244 ± 99 mg TDS / L and 14 ± 7.3 mg O2 / L, respectively. Based on the mass balance, and considering the TDS concentration established in NBR 13.696, if the final rinse does not use clean water, the potential for effluent reuse can reach 40%. However, if clean water is used as 30% of the total rinsing volume, it would be possible to reuse 70% of the treated effluent without compromising truck washing performance. This water reuse approach would result in an operational cost reduction of R$ 2,590.75/month.

Potential drug-drug interactions with direct oral anticoagulants in elderly hospitalized patients.

Science.gov (United States)

Forbes, Heather L; Polasek, Thomas M

2017-10-01

To determine the prevalence and nature of potential drug-drug interactions (DDIs) with direct oral anticoagulants (DOACs) in elderly hospitalized patients. This was a retrospective observational study. Inclusion criteria were: aged over 65 years; taking apixaban, rivaroxaban or dabigatran; and admitted to the Repatriation General Hospital between April 2014 and July 2015. A list of clinically relevant 'perpetrator' drugs was compiled from product information, the Australian Medicines Handbook, the Australian National Prescribing Service resources, and local health network guidelines. The prevalence and nature of potential DDIs with DOACs was determined by comparing inpatient drug charts with the list of perpetrator drugs. There were 122 patients in the study with a mean age of 82 years. Most patients had nonvalvular atrial fibrillation and were taking DOACs to prevent thrombotic stroke (83%). Overall, 45 patients (37%) had a total of 54 potential DDIs. Thirty-five patients had potential pharmacodynamic DDIs with antidepressants, nonsteroidal anti-inflammatory drugs and antiplatelets (35/122, 29%). Nineteen patients had potential pharmacokinetic DDIs (19/122, 16%). Of these, 68% (13/19) were taking drugs that increase DOAC plasma concentrations (amiodarone, erythromycin, diltiazem or verapamil) and 32% (6/19) were taking drugs that decrease DOAC plasma concentrations (carbamazepine, primidone or phenytoin). There were no cases of patients taking contraindicated interacting drugs. Potential DDIs with DOACs in elderly hospital inpatients are relatively common, particularly interactions that may increase the risk of bleeding. The risk-benefit ratio of DOACs in elderly patients on polypharmacy should always be carefully considered.

Temperature-dependent optical potential and mean free path based on Skyrme interactions

International Nuclear Information System (INIS)

Ge Lingxiao; Zhuo Yizhong; Noerenberg, W.; Technische Hochschule Darmstadt

1986-03-01

Optical potentials and mean free paths of nucleons at finite temperatures are studied by utilizing effective Skyrme interactions which yield 'good' optical potentials at zero temperature. The results for nuclear matter (symmetric and asymmetric) are applied within the local density approximation of finite nuclei at various temperatures. Because of the limitation due to zero-range forces used and the assumptions of temperature independent nuclear densities and effective Skyrme interactions made, the calculations are expected to be limited to nucleon energies between 10 and 50 MeV above the Fermi energy and to nuclear temperatures of less than 8 MeV. (orig.)

Measuring the evolutionary rewiring of biological networks.

Directory of Open Access Journals (Sweden)

Chong Shou

Full Text Available We have accumulated a large amount of biological network data and expect even more to come. Soon, we anticipate being able to compare many different biological networks as we commonly do for molecular sequences. It has long been believed that many of these networks change, or "rewire", at different rates. It is therefore important to develop a framework to quantify the differences between networks in a unified fashion. We developed such a formalism based on analogy to simple models of sequence evolution, and used it to conduct a systematic study of network rewiring on all the currently available biological networks. We found that, similar to sequences, biological networks show a decreased rate of change at large time divergences, because of saturation in potential substitutions. However, different types of biological networks consistently rewire at different rates. Using comparative genomics and proteomics data, we found a consistent ordering of the rewiring rates: transcription regulatory, phosphorylation regulatory, genetic interaction, miRNA regulatory, protein interaction, and metabolic pathway network, from fast to slow. This ordering was found in all comparisons we did of matched networks between organisms. To gain further intuition on network rewiring, we compared our observed rewirings with those obtained from simulation. We also investigated how readily our formalism could be mapped to other network contexts; in particular, we showed how it could be applied to analyze changes in a range of "commonplace" networks such as family trees, co-authorships and linux-kernel function dependencies.

Potential of the neutron lloyd's mirror interferometer for the search for new interactions

Energy Technology Data Exchange (ETDEWEB)

Pokotilovski, Yu. N., E-mail: pokot@nf.jinr.ru [Joint Institute for Nuclear Research (Russian Federation)

2013-04-15

We discuss the potential of the neutron Lloyd's mirror interferometer in a search for new interactions at small scales. We consider three hypothetical interactions that may be tested using the interferometer. The chameleon scalar field proposed to solve the enigma of accelerating expansion of the Universe produces interaction between particles and matter. The axion-like spin-dependent coupling between a neutron and nuclei or/and electrons may result in a P- and T-noninvariant interaction with matter. Hypothetical non-Newtonian gravitational interactions mediates an additional short-range potential between neutrons and bulk matter. These interactions between the neutron and the mirror of a Lloyd-type neutron interferometer cause a phase shift of neutron waves. We estimate the sensitivity and systematic effects of possible experiments.

An Interactive Tool for Animating Biology, and Its Use in Spatial and Temporal Modeling of a Cancerous Tumor and Its Microenvironment.

Directory of Open Access Journals (Sweden)

Naamah Bloch

Full Text Available The ability to visualize the ongoing events of a computational model of biology is critical, both in order to see the dynamics of the biological system in action and to enable interaction with the model from which one can observe the resulting behavior. To this end, we have built a new interactive animation tool, SimuLife, for visualizing reactive models of cellular biology. SimuLife is web-based, and is freely accessible at http://simulife.weizmann.ac.il/. We have used SimuLife to animate a model that describes the development of a cancerous tumor, based on the individual components of the system and its environment. This has helped in understanding the dynamics of the tumor and its surrounding blood vessels, and in verifying the behavior, fine-tuning the model accordingly, and learning in which way different factors affect the tumor.

Cation-π interactions in structural biology

OpenAIRE

Gallivan, Justin P.; Dougherty, Dennis A.

1999-01-01

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

PRESENTATION POTENTIAL USING IN PEDAGOGICAL INTERACTION PROCESS

Directory of Open Access Journals (Sweden)

Olga V. Ershova

2016-01-01

Full Text Available The given article is aimed at considering multimedia presentation potential and its influence on strengthening classroom teacher-student interaction. In the article the importance of using this kind of activity in the study process is pointed in connection with educational state policy on the one hand. On the other hand, gained students’ skills as a final result of work with presentations met employers’ demand for both parent and world labour-markets and bring competitive benefit to the candidates. Scientific novelty and results. Multimedia presentation is considered as a specific complex of classroom activities. The students are oriented on the self analysis and presentation assessment. It is shown that well-organized process of peer students’ assessment allows to simultaneously helping in solving the didactic and methodical problems. To this purpose the system of assessment criteria should be developed. It has to be clear for students for making assessment feasible and time-saving. The example of a possible variant of criteria system is described; quality of the presentations prepared by students can be defined based on such system criteria. The author also analyzed software products of the three main platforms (Windows, Linux, MacOs which have different tools and allow to follow users’ needs for creating presentations. In the article there is a comparative table of the two most popular software development: the program Microsoft PowerPoint and the web-service Prezi for realizing the relevance of their use in the study process. Practical significance of the present article concludes in author’s suggestions of some recommendations for presentation potential use as a tool of improving pedagogical interaction process with contemporary students. 

Potential of development of the mechanical-biological waste treatment; Entwicklungspotenzial der Mechanisch-Biologischen Abfallbehandlung

Energy Technology Data Exchange (ETDEWEB)

Grundmann, Thomas; Balhar, Michael [ASA e.V., Ennigerloh (Germany); Abfallwirtschaftsgesellschaft des Kreises Warendorf mbH, Ennigerloh (Germany)

2013-03-01

The Consortium Material-Specific Waste Treatment eV (Ennigerloh, Federal Republic of Germany) is an association of plant operators having the opinion that an economic and ecologic waste treatment only can be guaranteed by material-specific processes permanently. Due to the specific treatment processes in plants with mechanical-biological waste treatment (MBA) material flows are resulting being available for the recycling or exploitation. Under this aspect, the authors of the contribution under consideration report on the development potential of the mechanical-biological waste treatment. The state of the art of the technology of mechanical-biological waste treatment in Germany as well as the contribution of this technology to the resource protection and climate protection are described. Further aspects of this contribution are the increase of the energy efficiency and reduction of emissions; further development of the efficient sorting technology; development of integrated total conceptions - MBA-sites as centres for the production of renewable energies.

Biological basis of the sterile insect technique

International Nuclear Information System (INIS)

Lance, D.R.; McInnis, D.O.

2005-01-01

In principle, the sterile insect technique (SIT) is applicable to controlling a wide variety of insect pests, but biological factors, interacting with socio-economic and political forces, restrict its practical use to a narrower set of pest species and situations. This chapter reviews how the biology and ecology of a given pest affect the feasibility and logistics of developing and using the SIT against that pest insect. The subjects of pest abundance, distribution, and population dynamics are discussed in relation to producing and delivering sufficient sterile insects to control target populations. Pest movement and distribution are considered as factors that influence the feasibility and design of SIT projects, including the need for population- or area-wide management approaches. Biological characteristics, that affect the ability of sterile insects to interact with wild populations, are presented, including the nature of mating systems of pests, behavioural and physiological consequences of mass production and sterilization, and mechanisms that males use to block a female's acquisition and/or use of sperm from other males. An adequate knowledge of the biology of the pest species and potential target populations is needed, both for making sound decisions on whether integration of the SIT into an area-wide integrated pest management (AW-IPM) programme is appropriate, and for the efficient and effective application of the technique. (author)

Interaction potential and repulsive force between atoms whose internuclear separations are small

International Nuclear Information System (INIS)

Barbaro, Jacques

1971-01-01

The Thomas-Fermi equation is solved for the homonuclear diatomic molecule. The electronic density and electrostatic potential at each point are used to calculate energies and interaction potentials for very small internuclear separation distances. The repulsive force between atoms is derived by means of the virial theorem. (author) [fr

Cellular Interactions and Biological Responses to Titanium Dioxide Nanoparticles in HepG2 and BEAS-2B Cells: Role of Cell Culture Media

Science.gov (United States)

ABSTRACT We have shown previously that the composition of the biological medium used in vitro can affect the cellular interaction and biological response of titanium dioxide nanoparticles (nano-TiO2) in human lung epithelial cells. However, it is unclear if these effects are co...

TCA Cycle and Mitochondrial Membrane Potential Are Necessary for Diverse Biological Functions.

Science.gov (United States)

Martínez-Reyes, Inmaculada; Diebold, Lauren P; Kong, Hyewon; Schieber, Michael; Huang, He; Hensley, Christopher T; Mehta, Manan M; Wang, Tianyuan; Santos, Janine H; Woychik, Richard; Dufour, Eric; Spelbrink, Johannes N; Weinberg, Samuel E; Zhao, Yingming; DeBerardinis, Ralph J; Chandel, Navdeep S

2016-01-21

Mitochondrial metabolism is necessary for the maintenance of oxidative TCA cycle function and mitochondrial membrane potential. Previous attempts to decipher whether mitochondria are necessary for biological outcomes have been hampered by genetic and pharmacologic methods that simultaneously disrupt multiple functions linked to mitochondrial metabolism. Here, we report that inducible depletion of mitochondrial DNA (ρ(ο) cells) diminished respiration, oxidative TCA cycle function, and the mitochondrial membrane potential, resulting in diminished cell proliferation, hypoxic activation of HIF-1, and specific histone acetylation marks. Genetic reconstitution only of the oxidative TCA cycle function specifically in these inducible ρ(ο) cells restored metabolites, resulting in re-establishment of histone acetylation. In contrast, genetic reconstitution of the mitochondrial membrane potential restored ROS, which were necessary for hypoxic activation of HIF-1 and cell proliferation. These results indicate that distinct mitochondrial functions associated with respiration are necessary for cell proliferation, epigenetics, and HIF-1 activation. Copyright © 2016 Elsevier Inc. All rights reserved.

Probabilistic biological network alignment.

Science.gov (United States)

Todor, Andrei; Dobra, Alin; Kahveci, Tamer

2013-01-01

Interactions between molecules are probabilistic events. An interaction may or may not happen with some probability, depending on a variety of factors such as the size, abundance, or proximity of the interacting molecules. In this paper, we consider the problem of aligning two biological networks. Unlike existing methods, we allow one of the two networks to contain probabilistic interactions. Allowing interaction probabilities makes the alignment more biologically relevant at the expense of explosive growth in the number of alternative topologies that may arise from different subsets of interactions that take place. We develop a novel method that efficiently and precisely characterizes this massive search space. We represent the topological similarity between pairs of aligned molecules (i.e., proteins) with the help of random variables and compute their expected values. We validate our method showing that, without sacrificing the running time performance, it can produce novel alignments. Our results also demonstrate that our method identifies biologically meaningful mappings under a comprehensive set of criteria used in the literature as well as the statistical coherence measure that we developed to analyze the statistical significance of the similarity of the functions of the aligned protein pairs.

Non-potential interactions and the origin of masses of elementary particles

International Nuclear Information System (INIS)

Sun, J.

1982-01-01

We propose a fundamental assumption on internal states of particles. It follows from the fundamental assumption that: (1) the constituents of particles become non-particle objects; and (2) there appear naturally non-potential interactions. This non-potential interaction leads to a series of interesting results, one of which is that it yields the origin of masses of elementary particles. All mass values are given by the theory without pre-assumed mass values of the constituents (except the rest mass of the electron; mass is a physical quantity which appears only in particles but not in their constituents). The theoretically calculated mass values are in excellent agreement with the experimental values. In all calculations, only one constant b = 0.99935867 is introduced (bc being the speed of internal motion)

Interactions between physical, chemical and biological processes in aquatic systems - impacts on receiving waters with different contents of treated wastewater

International Nuclear Information System (INIS)

Kreuzinger, N.

2000-08-01

Two scenarios have be chosen within this PhD Thesis to describe the integrative key-significance of interactions between most relevant physical, chemical and biological processes in aquatic systems. These two case studies are used to illustrate and describe the importance of a detailed synthesis of biological, physical and chemical interactions in aquatic systems in order to provide relevant protection of water resources and to perform a sound water management. Methods are described to allow a detailed assessment of particular aspects within the complexity of the overall integration and therefore serve as a basis to determine the eventual necessity of proposed water management measures. Regarding the anthropogenic influence of treated wastewater on aquatic systems, one case study focuses on the interactions between emitted waters from a wastewater treatment plant and the resulting immission situation of its receiving water (The receiving water is quantitatively influenced by the treated wastewater by 95 %). This thesis proves that the effluent of wastewater treatment plants operated by best available technology meets the quality standards of running waters for the nutrients nitrogen and phosphorus, carbon-parameters, oxygen-regime and ecotoxicology. Within the second case study the focus is put on interactions between immissions and water usage. The general importance of biological phosphorus precipitation on the trophic situation of aquatic systems is described. Nevertheless, this generally known but within the field of applied limnology so far unrespected process of immobilization of phosphorus could be shown to represent a significant and major impact on phytoplannctotic development and eutrification. (author)

Querying Large Biological Network Datasets

Science.gov (United States)

Gulsoy, Gunhan

2013-01-01

New experimental methods has resulted in increasing amount of genetic interaction data to be generated every day. Biological networks are used to store genetic interaction data gathered. Increasing amount of data available requires fast large scale analysis methods. Therefore, we address the problem of querying large biological network datasets.…

Communicative interactions involving plants: information, evolution, and ecology.

Science.gov (United States)

Mescher, Mark C; Pearse, Ian S

2016-08-01

The role of information obtained via sensory cues and signals in mediating the interactions of organisms with their biotic and abiotic environments has been a major focus of work on sensory and behavioral ecology. Information-mediated interactions also have important implications for broader ecological patterns emerging at the community and ecosystem levels that are only now beginning to be explored. Given the extent to which plants dominate the sensory landscapes of terrestrial ecosystems, information-mediated interactions involving plants should be a major focus of efforts to elucidate these broader patterns. Here we explore how such efforts might be enhanced by a clear understanding of information itself-a central and potentially unifying concept in biology that has nevertheless been the subject of considerable confusion-and of its relationship to adaptive evolution and ecology. We suggest that information-mediated interactions should be a key focus of efforts to more fully integrate evolutionary biology and ecology. Copyright © 2016 Elsevier Ltd. All rights reserved.

Multiscale Biological Materials

DEFF Research Database (Denmark)

Frølich, Simon

of multiscale biological systems have been investigated and new research methods for automated Rietveld refinement and diffraction scattering computed tomography developed. The composite nature of biological materials was investigated at the atomic scale by looking at the consequences of interactions between...

Applying the Nernst equation to simulate redox potential variations for biological nitrification and denitrification processes.

Science.gov (United States)

Chang, Cheng-Nan; Cheng, Hong-Bang; Chao, Allen C

2004-03-15

In this paper, various forms of Nernst equations have been developed based on the real stoichiometric relationship of biological nitrification and denitrification reactions. Instead of using the Nernst equation based on a one-to-one stoichiometric relation for the oxidizing and the reducing species, the basic Nernst equation is modified into slightly different forms. Each is suitable for simulating the redox potential (ORP) variation of a specific biological nitrification or denitrification process. Using the data published in the literature, the validity of these developed Nernst equations has been verified by close fits of the measured ORP data with the calculated ORP curve. The simulation results also indicate that if the biological process is simulated using an incorrect form of Nernst equation, the calculated ORP curve will not fit the measured data. Using these Nernst equations, the ORP value that corresponds to a predetermined degree of completion for the biochemical reaction can be calculated. Thus, these Nernst equations will enable a more efficient on-line control of the biological process.

Transferrin adsorption onto PLGA nanoparticles governs their interaction with biological systems from blood circulation to brain cancer cells.

Science.gov (United States)

Chang, Jiang; Paillard, Archibald; Passirani, Catherine; Morille, Marie; Benoit, Jean-Pierre; Betbeder, Didier; Garcion, Emmanuel

2012-06-01

Nanomedicines represent an alternative for the treatment of aggressive glioblastoma tumors. Behaviour of PLGA-nanoparticles (NPs) was here investigated as a function of their protein adsorption characteristics at the different biological interfaces they are expected to face in order to reach brain cancer cells. NPs were studied for size, zeta potential, blood half-life, in vitro endocytic behavior and in vivo accumulation within healthy rat brain and brain tumors. While slightly modifying size (80 to 90 nm) and zeta potential (-44 to -32 mV) protein coating of PLGA-NPs by bovine serum albumin (BSA) or transferrin (Tf) greatly prolonged their blood half-life when intravenously injected in rats and mice. In contrast with THP-1 monocytes, differentiated THP-1 macrophages, F98 glioma cells and astrocytes internalized BSA- and Tf-NPs in vitro. Increase of Tf-NP uptake by F98 cells through caveolae- and clathrin-mediated pathways supports specific interaction between Tf and overexpressed Tf-receptor. Finally, in vivo targeting of healthy brain was found higher with Tf-NPs than with BSA-NPs while both NPs entered massively within brain-developed tumors. Taken together, those data evidence that Tf-NPs represent an interesting nanomedicine to deliver anticancer drugs to glioma cells through systemic or locoregional strategies at early and late tumor stages.

Study of various models of nuclear interaction potentials: nucleon-nucleus and nucleus-nucleus systems

International Nuclear Information System (INIS)

Ngo, H.

1984-01-01

Several models, performed within a mean field theory, are developed for the calculation of nucleon-nucleus interaction potentials. The first part of the thesis deals with the nucleon-nucleus average interaction. It is mainly devoted to the calculation of dynamical corrections to the Hartree-Fock approximation. Two approaches are used: a microscopic model performed in the framework of the nuclear structure approach and a semi-phenomenological one, based on the application of the dispersion relations to the empirical imaginary potential. Both models take into account finite size effects like collectivity or threshold effects which are important at low energy. The Green's function properties are used for both models. The second part of this work is devoted to the interaction potential between two heavy ions. This calculation, which is performed in the framework of the sudden approximation, uses the energy density formalism (Thomas-Fermi approximation). It has been extended to finite temperature. At T=0 the experimental fusion barriers of heavy systems are reproduced within 4%. Their temperature dependence is studied. The proximity scaling is checked and a universal function is obtained at T=0 and at finite temperature. It is found that the proximity theorem is well satisfied on the average. The dispersion around the mean behaviour increases with increasing temperature. At last, P+A* and α+A* interaction potentials are calculated within a double folding model using a schematic effective interaction [fr

Biological ensemble modeling to evaluate potential futures of living marine resources

DEFF Research Database (Denmark)

Gårdmark, Anna; Lindegren, Martin; Neuenfeldt, Stefan

2013-01-01

) as an example. The core of the approach is to expose an ensemble of models with different ecological assumptions to climate forcing, using multiple realizations of each climate scenario. We simulated the long-term response of cod to future fishing and climate change in seven ecological models ranging from...... model assumptions from the statistical uncertainty of future climate, and (3) identified results common for the whole model ensemble. Species interactions greatly influenced the simulated response of cod to fishing and climate, as well as the degree to which the statistical uncertainty of climate...... in all models, intense fishing prevented recovery, and climate change further decreased the cod population. Our study demonstrates how the biological ensemble modeling approach makes it possible to evaluate the relative importance of different sources of uncertainty in future species responses, as well...

Regulation of Spatiotemporal Patterns by Biological Variability: General Principles and Applications to Dictyostelium discoideum.

Directory of Open Access Journals (Sweden)

Miriam Grace

2015-11-01

Full Text Available Spatiotemporal patterns often emerge from local interactions in a self-organizing fashion. In biology, the resulting patterns are also subject to the influence of the systematic differences between the system's constituents (biological variability. This regulation of spatiotemporal patterns by biological variability is the topic of our review. We discuss several examples of correlations between cell properties and the self-organized spatiotemporal patterns, together with their relevance for biology. Our guiding, illustrative example will be spiral waves of cAMP in a colony of Dictyostelium discoideum cells. Analogous processes take place in diverse situations (such as cardiac tissue, where spiral waves occur in potentially fatal ventricular fibrillation so a deeper understanding of this additional layer of self-organized pattern formation would be beneficial to a wide range of applications. One of the most striking differences between pattern-forming systems in physics or chemistry and those in biology is the potential importance of variability. In the former, system components are essentially identical with random fluctuations determining the details of the self-organization process and the resulting patterns. In biology, due to variability, the properties of potentially very few cells can have a driving influence on the resulting asymptotic collective state of the colony. Variability is one means of implementing a few-element control on the collective mode. Regulatory architectures, parameters of signaling cascades, and properties of structure formation processes can be "reverse-engineered" from observed spatiotemporal patterns, as different types of regulation and forms of interactions between the constituents can lead to markedly different correlations. The power of this biology-inspired view of pattern formation lies in building a bridge between two scales: the patterns as a collective state of a very large number of cells on the one hand

Interactions among ecosystem stressors and their importance in conservation

Science.gov (United States)

Darling, Emily S.; Brown, Christopher J.

2016-01-01

Interactions between multiple ecosystem stressors are expected to jeopardize biological processes, functions and biodiversity. The scientific community has declared stressor interactions—notably synergies—a key issue for conservation and management. Here, we review ecological literature over the past four decades to evaluate trends in the reporting of ecological interactions (synergies, antagonisms and additive effects) and highlight the implications and importance to conservation. Despite increasing popularity, and ever-finer terminologies, we find that synergies are (still) not the most prevalent type of interaction, and that conservation practitioners need to appreciate and manage for all interaction outcomes, including antagonistic and additive effects. However, it will not be possible to identify the effect of every interaction on every organism's physiology and every ecosystem function because the number of stressors, and their potential interactions, are growing rapidly. Predicting the type of interactions may be possible in the near-future, using meta-analyses, conservation-oriented experiments and adaptive monitoring. Pending a general framework for predicting interactions, conservation management should enact interventions that are robust to uncertainty in interaction type and that continue to bolster biological resilience in a stressful world. PMID:26865306

Integrating systems biology models and biomedical ontologies.

Science.gov (United States)

Hoehndorf, Robert; Dumontier, Michel; Gennari, John H; Wimalaratne, Sarala; de Bono, Bernard; Cook, Daniel L; Gkoutos, Georgios V

2011-08-11

Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms.

Hulthén and Coulomb-Like Potentials as a Tensor Interaction within the Relativistic Symmetries of the Manning-Rosen Potential

International Nuclear Information System (INIS)

Tokmehdashi, Hadi; Rajabi, Ali Akbar; Hamzavi, Majid

2014-01-01

The bound-state solutions of the Dirac equation for the Manning-Rosen potential are presented approximately for arbitrary spin-orbit quantum number κ with the Hulthén and Coulomb-like potentials as a tensor interaction. The generalized parametric Nikiforov-Uvarov (NU) method is used to obtain energy eigenvalues and corresponding two-component spinors of the two Dirac particles and these are obtained in the closed form by using the framework of the spin symmetry and p-spin symmetry concept. We have also shown that tensor interaction removes degeneracies between spin and p-spin doublets. Some numerical results are also given

Cosmological solutions in string theory with dilaton self interaction potential

International Nuclear Information System (INIS)

Mora, C.; Pimentel, L.O.

2003-01-01

In this work we present homogeneous and isotropic cosmological solutions for the low energy limit of string theory with a self interacting potential for the scalar field. For a potential that is a linear combination of two exponential, a family of exact solutions are found for the different spatial curvatures. Among this family a non singular accelerating solution for positive curvature is singled out and the violation of the energy conditions for that solution is studied, and also its astrophysical consequences. The string coupling for this solution is finite. (Author)

The potential of plants as a system for the development and production of human biologics [version 1; referees: 3 approved

Directory of Open Access Journals (Sweden)

Qiang Chen

2016-05-01

Full Text Available The growing promise of plant-made biologics is highlighted by the success story of ZMapp™ as a potentially life-saving drug during the Ebola outbreak of 2014-2016. Current plant expression platforms offer features beyond the traditional advantages of low cost, high scalability, increased safety, and eukaryotic protein modification. Novel transient expression vectors have been developed that allow the production of vaccines and therapeutics at unprecedented speed to control potential pandemics or bioterrorism attacks. Plant-host engineering provides a method for producing proteins with unique and uniform mammalian post-translational modifications, providing opportunities to develop biologics with increased efficacy relative to their mammalian cell-produced counterparts. Recent demonstrations that plant-made proteins can function as biocontrol agents of foodborne pathogens further exemplify the potential utility of plant-based protein production. However, resolving the technical and regulatory challenges of commercial-scale production, garnering acceptance from large pharmaceutical companies, and obtaining U.S. Food and Drug Administration approval for several major classes of biologics are essential steps to fulfilling the untapped potential of this technology.

Potential drug-drug and drug-disease interactions in well-functioning community-dwelling older adults.

Science.gov (United States)

Hanlon, J T; Perera, S; Newman, A B; Thorpe, J M; Donohue, J M; Simonsick, E M; Shorr, R I; Bauer, D C; Marcum, Z A

2017-04-01

There are few studies examining both drug-drug and drug-disease interactions in older adults. Therefore, the objective of this study was to describe the prevalence of potential drug-drug and drug-disease interactions and associated factors in community-dwelling older adults. This cross-sectional study included 3055 adults aged 70-79 without mobility limitations at their baseline visit in the Health Aging and Body Composition Study conducted in the communities of Pittsburgh PA and Memphis TN, USA. The outcome factors were potential drug-drug and drug-disease interactions as per the application of explicit criteria drawn from a number of sources to self-reported prescription and non-prescription medication use. Over one-third of participants had at least one type of interaction. Approximately one quarter (25·1%) had evidence of had one or more drug-drug interactions. Nearly 10·7% of the participants had a drug-drug interaction that involved a non-prescription medication. % The most common drug-drug interaction was non-steroidal anti-inflammatory drugs (NSAIDs) affecting antihypertensives. Additionally, 16·0% had a potential drug-disease interaction with 3·7% participants having one involving non-prescription medications. The most common drug-disease interaction was aspirin/NSAID use in those with history of peptic ulcer disease without gastroprotection. Over one-third (34·0%) had at least one type of drug interaction. Each prescription medication increased the odds of having at least one type of drug interaction by 35-40% [drug-drug interaction adjusted odds ratio (AOR) = 1·35, 95% confidence interval (CI) = 1·27-1·42; drug-disease interaction AOR = 1·30; CI = 1·21-1·40; and both AOR = 1·45; CI = 1·34-1·57]. A prior hospitalization increased the odds of having at least one type of drug interaction by 49-84% compared with those not hospitalized (drug-drug interaction AOR = 1·49, 95% CI = 1·11-2·01; drug-disease interaction AOR = 1·69, CI = 1·15-2�

Dysfunctional Hematopoietic Stem Cell Biology: Underlying Mechanisms and Potential Therapeutic Strategies

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Anja Geiselhart

2012-01-01

Full Text Available Fanconi anemia (FA is the most common inherited bone marrow failure syndrome. FA patients suffer to varying degrees from a heterogeneous range of developmental defects and, in addition, have an increased likelihood of developing cancer. Almost all FA patients develop a severe, progressive bone marrow failure syndrome, which impacts upon the production of all hematopoietic lineages and, hence, is thought to be driven by a defect at the level of the hematopoietic stem cell (HSC. This hypothesis would also correlate with the very high incidence of MDS and AML that is observed in FA patients. In this paper, we discuss the evidence that supports the role of dysfunctional HSC biology in driving the etiology of the disease. Furthermore, we consider the different model systems currently available to study the biology of cells defective in the FA signaling pathway and how they are informative in terms of identifying the physiologic mediators of HSC depletion and dissecting their putative mechanism of action. Finally, we ask whether the insights gained using such disease models can be translated into potential novel therapeutic strategies for the treatment of the hematologic disorders in FA patients.

Therapeutic Potential of Foldamers: From Chemical Biology Tools To Drug Candidates?

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Gopalakrishnan, Ranganath; Frolov, Andrey I; Knerr, Laurent; Drury, William J; Valeur, Eric

2016-11-10

Over the past decade, foldamers have progressively emerged as useful architectures to mimic secondary structures of proteins. Peptidic foldamers, consisting of various amino acid based backbones, have been the most studied from a therapeutic perspective, while polyaromatic foldamers have barely evolved from their nascency and remain perplexing for medicinal chemists due to their poor drug-like nature. Despite these limitations, this compound class may still offer opportunities to study challenging targets or provide chemical biology tools. The potential of foldamer drug candidates reaching the clinic is still a stretch. Nevertheless, advances in the field have demonstrated their potential for the discovery of next generation therapeutics. In this perspective, the current knowledge of foldamers is reviewed in a drug discovery context. Recent advances in the early phases of drug discovery including hit finding, target validation, and optimization and molecular modeling are discussed. In addition, challenges and focus areas are debated and gaps highlighted.

Scattering at low energies by potentials containing power-law corrections to the Coulomb interaction

International Nuclear Information System (INIS)

Kuitsinskii, A.A.

1986-01-01

The low-energy asymptotic behavior is found for the phase shifts and scattering amplitudes in the case of central potentials which decrease at infinity as n/r+ar /sup -a/,a 1. In problems of atomic and nuclear physics one is generally interested in collisions of clusters consisting of several charged particles. The effective interaction potential of such clusters contains long-range power law corrections to the Coulomb interaction that is presented

Comparative Study on Interaction of Form and Motion Processing Streams by Applying Two Different Classifiers in Mechanism for Recognition of Biological Movement

Science.gov (United States)

2014-01-01

Research on psychophysics, neurophysiology, and functional imaging shows particular representation of biological movements which contains two pathways. The visual perception of biological movements formed through the visual system called dorsal and ventral processing streams. Ventral processing stream is associated with the form information extraction; on the other hand, dorsal processing stream provides motion information. Active basic model (ABM) as hierarchical representation of the human object had revealed novelty in form pathway due to applying Gabor based supervised object recognition method. It creates more biological plausibility along with similarity with original model. Fuzzy inference system is used for motion pattern information in motion pathway creating more robustness in recognition process. Besides, interaction of these paths is intriguing and many studies in various fields considered it. Here, the interaction of the pathways to get more appropriated results has been investigated. Extreme learning machine (ELM) has been implied for classification unit of this model, due to having the main properties of artificial neural networks, but crosses from the difficulty of training time substantially diminished in it. Here, there will be a comparison between two different configurations, interactions using synergetic neural network and ELM, in terms of accuracy and compatibility. PMID:25276860

Comparative Study on Interaction of Form and Motion Processing Streams by Applying Two Different Classifiers in Mechanism for Recognition of Biological Movement

Directory of Open Access Journals (Sweden)

Bardia Yousefi

2014-01-01

Full Text Available Research on psychophysics, neurophysiology, and functional imaging shows particular representation of biological movements which contains two pathways. The visual perception of biological movements formed through the visual system called dorsal and ventral processing streams. Ventral processing stream is associated with the form information extraction; on the other hand, dorsal processing stream provides motion information. Active basic model (ABM as hierarchical representation of the human object had revealed novelty in form pathway due to applying Gabor based supervised object recognition method. It creates more biological plausibility along with similarity with original model. Fuzzy inference system is used for motion pattern information in motion pathway creating more robustness in recognition process. Besides, interaction of these paths is intriguing and many studies in various fields considered it. Here, the interaction of the pathways to get more appropriated results has been investigated. Extreme learning machine (ELM has been implied for classification unit of this model, due to having the main properties of artificial neural networks, but crosses from the difficulty of training time substantially diminished in it. Here, there will be a comparison between two different configurations, interactions using synergetic neural network and ELM, in terms of accuracy and compatibility.

Optical potentials derived from microscopic separable interactions including binding and recoil effects

International Nuclear Information System (INIS)

Siciliano, E.R.; Walker, G.E.

1976-01-01

We first consider a projectile scattering from a nucleon bound in a fixed potential. A separable Galilean invariant projectile-nucleon interaction is adopted. Without using the fixed scatterer approximation or using closure on the intermediate target nucleon states we obtain various forms for the projectile-bound nucleon t matrix. Effects due to intermediate target excitation and nucleon recoil are discussed. By making the further approximations of closure and fixed scatterers we make connection with the work of previous authors. By generalizing to projectile interaction with several bound nucleons and examining the appropriate multiple scattering series we identify the optical potential for projectile elastic scattering from the many-body system. Different optical potentials are obtained for different projectile-bound nucleon t matrices, and we study the differences predicted by these dissimilar optical potentials for elastic scattering. In a model problem, we study pion-nucleus elastic scattering and compare the predictions obtained by adopting procedures used by (1) Landau, Phatak, and Tabakin and (2) Piepho-Walker to the predictions obtained in a less restrictive, but computationally difficult treatment

Occupational exposure to potentially infectious biological material in a dental teaching environment.

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Machado-Carvalhais, Helenaura P; Ramos-Jorge, Maria L; Auad, Sheyla M; Martins, Laura H P M; Paiva, Saul M; Pordeus, Isabela A

2008-10-01

The aims of this cross-sectional study were to determine the prevalence of occupational accidents with exposure to biological material among undergraduate students of dentistry and to estimate potential risk factors associated with exposure to blood. Data were collected through a self-administered questionnaire (86.4 percent return rate), which was completed by a sample of 286 undergraduate dental students (mean age 22.4 +/-2.4 years). The students were enrolled in the clinical component of the curriculum, which corresponds to the final six semesters of study. Descriptive, bivariate, simple logistic regression and multiple logistic regression (Forward Stepwise Procedure) analyses were performed. The level of statistical significance was set at 5 percent. Percutaneous and mucous exposures to potentially infectious biological material were reported by 102 individuals (35.6 percent); 26.8 percent reported the occurrence of multiple episodes of exposure. The logistic regression analyses revealed that the incomplete use of individual protection equipment (OR=3.7; 95 percent CI 1.5-9.3), disciplines where surgical procedures are carried out (OR=16.3; 95 percent CI 7.1-37.2), and handling sharp instruments (OR=4.4; 95 percent CI 2.1-9.1), more specifically, hollow-bore needles (OR=6.8; 95 percent CI 2.1-19.0), were independently associated with exposure to blood. Policies of reviewing the procedures during clinical practice are recommended in order to reduce occupational exposure.

Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology

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Rossin, Elizabeth J.; Lage, Kasper; Raychaudhuri, Soumya; Xavier, Ramnik J.; Tatar, Diana; Benita, Yair

2011-01-01

Genome-wide association studies (GWAS) have defined over 150 genomic regions unequivocally containing variation predisposing to immune-mediated disease. Inferring disease biology from these observations, however, hinges on our ability to discover the molecular processes being perturbed by these risk variants. It has previously been observed that different genes harboring causal mutations for the same Mendelian disease often physically interact. We sought to evaluate the degree to which this is true of genes within strongly associated loci in complex disease. Using sets of loci defined in rheumatoid arthritis (RA) and Crohn's disease (CD) GWAS, we build protein–protein interaction (PPI) networks for genes within associated loci and find abundant physical interactions between protein products of associated genes. We apply multiple permutation approaches to show that these networks are more densely connected than chance expectation. To confirm biological relevance, we show that the components of the networks tend to be expressed in similar tissues relevant to the phenotypes in question, suggesting the network indicates common underlying processes perturbed by risk loci. Furthermore, we show that the RA and CD networks have predictive power by demonstrating that proteins in these networks, not encoded in the confirmed list of disease associated loci, are significantly enriched for association to the phenotypes in question in extended GWAS analysis. Finally, we test our method in 3 non-immune traits to assess its applicability to complex traits in general. We find that genes in loci associated to height and lipid levels assemble into significantly connected networks but did not detect excess connectivity among Type 2 Diabetes (T2D) loci beyond chance. Taken together, our results constitute evidence that, for many of the complex diseases studied here, common genetic associations implicate regions encoding proteins that physically interact in a preferential manner, in

Ozone dosing alters the biological potential and therapeutic outcomes of plasma rich in growth factors.

Science.gov (United States)

Anitua, E; Zalduendo, M M; Troya, M; Orive, G

2015-04-01

Until now, ozone has been used in a rather empirical way. This in-vitro study investigates, for the first time, whether different ozone treatments of plasma rich in growth factors (PRGF) alter the biological properties and outcomes of this autologous platelet-rich plasma. Human plasma rich in growth factors was treated with ozone using one of the following protocols: a continuous-flow method; or a syringe method in which constant volumes of ozone and PRGF were mixed. In both cases, ozone was added before, during and after the addition of calcium chloride. Three ozone concentrations, of the therapeutic range 20, 40 and 80 μg/mL, were tested. Fibrin clot properties, growth factor content and the proliferative effect on primary osteoblasts and gingival fibroblasts were evaluated. Ozone treatment of PRGF using the continuous flow protocol impaired formation of the fibrin scaffold, drastically reduced the levels of growth factors and significantly decreased the proliferative potential of PRGF on primary osteoblasts and gingival fibroblasts. In contrast, treatment of PRGF with ozone using the syringe method, before, during and after the coagulation process, did not alter the biological outcomes of the autologous therapy. These findings suggest that ozone dose and the way that ozone combines with PRGF may alter the biological potential and therapeutic outcomes of PRGF. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Characterization of the In Vitro Kinetic Interaction of Chlorpyrifos-Oxon with Rat Salivary Cholinesterase: A Potential Biomonitoring Matrix

Energy Technology Data Exchange (ETDEWEB)

Kousba, Ahmed A.(BATTELLE (PACIFIC NW LAB)); Poet, Torka S.(BATTELLE (PACIFIC NW LAB)); Timchalk, Charles (Pacific Northwest National Laboratory)

2003-02-12

Chlorpyrifos (CPF) is a commonly used organophosphate insecticide (OP). The primary mechanism of action for CPF involves the inhibition of acetylcholinesterase (AChE) by the active metabolite, CPF-oxon, with subsequent accumulation of acetylcholine (ACh) resulting in a wide range of neutotoxicity. CPF-oxon, can likewise inhibit other non-target cholinesterases (ChE) such as butyrylcholinesterase (BuChE), which represents a detoxification mechanism and a potential biomarker of exposure/response. Biological monitoring for OPs has focused on measuring parent chemical or metabolite in blood and urine or blood ChE inhibition. Salivary biomonitoring has recently been explored as a practical method for examination of chemical exposure; however, there are a limited number of studies exploring its use for OPs. To evaluate the use of salivary ChE as a biological monitor for OP exposure, the current study characterized salivary ChE activity in Sprague-Dawley rats through its comparison with brain and plasma ChE using BW284C51 and iso-OMPA as selective inhibitors of AChE and BuChE, respectively. The study also estimated the kinetic constants describing BuChE interaction with CPF-oxon. A modified Ellman assay in conjunction with pharmacodynamic (PD) modeling was used to characterize the in vitro titration of diluted rat salivary ChE enzyme with CPF-oxon. The results indicated that, more than 95% of rat salivary ChE activity was associated with BuChE activity, total BuChE active site concentration was 0.0012 0.00013 nmol/ml saliva, reactivation rate constant (Kr) was 0.068 0.008 h-1 and inhibitory (Ki) rate constant of 8.825 and 9.80 nM-1h-1 determined experimentally and using model optimization respectively. These study results would be helpful for further evaluating the potential utility of salivary ChE as a practical tool for biological monitor of OP exposures.

Fundamental host range of Leptoypha hospita (Hemiptera: Tingidae), a potential biological control agent of Chinese privet

Science.gov (United States)

Yanzhuo Zhang; James L. Hanula; Scott Horn; Cera Jones; S. Kristine Braman; Jianghua Sun

2016-01-01

Chinese privet, Ligustrum sinense Lour., is an invasive shrub within riparian areas of the southeastern United States. Biological control is considered the most suitable management option for Chinese privet. The potential host range of the lace bug, Leptoypha hospita Drake et...

[Clinical treatment adherence of health care workers and students exposed to potentially infectious biological material].

Science.gov (United States)

Almeida, Maria Cristina Mendes de; Canini, Silvia Rita Marin da Silva; Reis, Renata Karina; Toffano, Silmara Elaine Malaguti; Pereira, Fernanda Maria Vieira; Gir, Elucir

2015-04-01

To assess adherence to clinical appointments by health care workers (HCW) and students who suffered accidents with potentially infectious biological material. A retrospective cross-sectional study that assessed clinical records of accidents involving biological material between 2005 and 2010 in a specialized unit. A total of 461 individuals exposed to biological material were treated, of which 389 (84.4%) were HCWs and 72 (15.6%) students. Of the 461 exposed individuals, 307 (66.6%) attended a follow-up appointment. Individuals who had suffered an accident with a known source patient were 29 times more likely to show up to their scheduled follow-up appointments (OR: 29.98; CI95%: 16.09-55.83). The predictor in both univariate and multivariate analyses for adherence to clinical follow-up appointment was having a known source patient with nonreactive serology for the human immunodeficiency virus and/or hepatitis B and C.

Development of interactive hypermedia software for high school biology: A research and development study

Science.gov (United States)

Alturki, Uthman T.

The goal of this research was to research, design, and develop a hypertext program for students who study biology. The Ecology Hypertext Program was developed using Research and Development (R&D) methodology. The purpose of this study was to place the final "product", a CD-ROM for learning biology concepts, in the hands of teachers and students to help them in learning and teaching process. The product was created through a cycle of literature review, needs assessment, development, and a cycle of field tests and revisions. I applied the ten steps of R&D process suggested by Borg and Gall (1989) which, consisted of: (1) Literature review, (2) Needs assessment, (3) Planning, (4) Develop preliminary product, (5) Preliminary field-testing, (6) Preliminary revision, (7) Main field-testing, (8) Main revision, (9) Final field-testing, and (10) Final product revision. The literature review and needs assessment provided a support and foundation for designing the preliminary product---the Ecology Hypertext Program. Participants in the needs assessment joined a focus group discussion. They were a group of graduate students in education who suggested the importance for designing this product. For the preliminary field test, the participants were a group of high school students studying biology. They were the potential user of the product. They reviewed the preliminary product and then filled out a questionnaire. Their feedback and suggestions were used to develop and improve the product in a step called preliminary revision. The second round of field tasting was the main field test in which the participants joined a focus group discussion. They were the same group who participated in needs assessment task. They reviewed the revised product and then provided ideas and suggestions to improve the product. Their feedback were categorized and implemented to develop the product as in the main revision task. Finally, a group of science teachers participated in this study by reviewing

Topology and weights in a protein domain interaction network--a novel way to predict protein interactions.

Science.gov (United States)

Wuchty, Stefan

2006-05-23

While the analysis of unweighted biological webs as diverse as genetic, protein and metabolic networks allowed spectacular insights in the inner workings of a cell, biological networks are not only determined by their static grid of links. In fact, we expect that the heterogeneity in the utilization of connections has a major impact on the organization of cellular activities as well. We consider a web of interactions between protein domains of the Protein Family database (PFAM), which are weighted by a probability score. We apply metrics that combine the static layout and the weights of the underlying interactions. We observe that unweighted measures as well as their weighted counterparts largely share the same trends in the underlying domain interaction network. However, we only find weak signals that weights and the static grid of interactions are connected entities. Therefore assuming that a protein interaction is governed by a single domain interaction, we observe strong and significant correlations of the highest scoring domain interaction and the confidence of protein interactions in the underlying interactions of yeast and fly. Modeling an interaction between proteins if we find a high scoring protein domain interaction we obtain 1, 428 protein interactions among 361 proteins in the human malaria parasite Plasmodium falciparum. Assessing their quality by a logistic regression method we observe that increasing confidence of predicted interactions is accompanied by high scoring domain interactions and elevated levels of functional similarity and evolutionary conservation. Our results indicate that probability scores are randomly distributed, allowing to treat static grid and weights of domain interactions as separate entities. In particular, these finding confirms earlier observations that a protein interaction is a matter of a single interaction event on domain level. As an immediate application, we show a simple way to predict potential protein interactions

From biology to mathematical models and back: teaching modeling to biology students, and biology to math and engineering students.

Science.gov (United States)

Chiel, Hillel J; McManus, Jeffrey M; Shaw, Kendrick M

2010-01-01

We describe the development of a course to teach modeling and mathematical analysis skills to students of biology and to teach biology to students with strong backgrounds in mathematics, physics, or engineering. The two groups of students have different ways of learning material and often have strong negative feelings toward the area of knowledge that they find difficult. To give students a sense of mastery in each area, several complementary approaches are used in the course: 1) a "live" textbook that allows students to explore models and mathematical processes interactively; 2) benchmark problems providing key skills on which students make continuous progress; 3) assignment of students to teams of two throughout the semester; 4) regular one-on-one interactions with instructors throughout the semester; and 5) a term project in which students reconstruct, analyze, extend, and then write in detail about a recently published biological model. Based on student evaluations and comments, an attitude survey, and the quality of the students' term papers, the course has significantly increased the ability and willingness of biology students to use mathematical concepts and modeling tools to understand biological systems, and it has significantly enhanced engineering students' appreciation of biology.

From Biology to Mathematical Models and Back: Teaching Modeling to Biology Students, and Biology to Math and Engineering Students

Science.gov (United States)

McManus, Jeffrey M.; Shaw, Kendrick M.

2010-01-01

We describe the development of a course to teach modeling and mathematical analysis skills to students of biology and to teach biology to students with strong backgrounds in mathematics, physics, or engineering. The two groups of students have different ways of learning material and often have strong negative feelings toward the area of knowledge that they find difficult. To give students a sense of mastery in each area, several complementary approaches are used in the course: 1) a “live” textbook that allows students to explore models and mathematical processes interactively; 2) benchmark problems providing key skills on which students make continuous progress; 3) assignment of students to teams of two throughout the semester; 4) regular one-on-one interactions with instructors throughout the semester; and 5) a term project in which students reconstruct, analyze, extend, and then write in detail about a recently published biological model. Based on student evaluations and comments, an attitude survey, and the quality of the students' term papers, the course has significantly increased the ability and willingness of biology students to use mathematical concepts and modeling tools to understand biological systems, and it has significantly enhanced engineering students' appreciation of biology. PMID:20810957

Human Possibilities: The Interaction of Biology and Culture

Directory of Open Access Journals (Sweden)

Riane Eisler

2015-06-01

Full Text Available This article briefly describes the two main strands of a new unified theory about human nature and human possibilities: cultural transformation theory and bio-culturalism. Bio-culturalism combines findings from neuroscience about how our brains develop in interaction with our environments with findings from the study of relational dynamics, a new method of social analysis focusing on what kinds of relations—from intimate to international—a particular culture or subculture supports. Bio-culturalism recognizes that our species has a vast spectrum of genetic capacities, ranging from consciousness, caring, empathy, cooperation, and creativity to insensitivity, cruelty, exploitation, and destructiveness, and proposes that which of these capacities are expressed or inhibited largely hinges on the nature of our cultural environments. Cultural transformation theory looks at the whole span of human cultural evolution from the perspective of the tension between the contrasting configurations of the partnership system and the domination system as two underlying possibilities for structuring beliefs, institutions, and relationships. The article describes the core components of partnership- and domination-oriented societies, provides examples of each, and proposes that our future hinges on accelerating the cultural transformation from domination to partnership in our time of nuclear and biological weapons and the ever more efficient despoliation of nature, when high technology guided by an ethos of domination and conquest could take us to an evolutionary dead end.

Solid phase stability of a double-minimum interaction potential system

International Nuclear Information System (INIS)

Suematsu, Ayumi; Yoshimori, Akira; Saiki, Masafumi; Matsui, Jun; Odagaki, Takashi

2014-01-01

We study phase stability of a system with double-minimum interaction potential in a wide range of parameters by a thermodynamic perturbation theory. The present double-minimum potential is the Lennard-Jones-Gauss potential, which has a Gaussian pocket as well as a standard Lennard-Jones minimum. As a function of the depth and position of the Gaussian pocket in the potential, we determine the coexistence pressure of crystals (fcc and bcc). We show that the fcc crystallizes even at zero pressure when the position of the Gaussian pocket is coincident with the first or third nearest neighbor site of the fcc crystal. The bcc crystal is more stable than the fcc crystal when the position of the Gaussian pocket is coincident with the second nearest neighbor sites of the bcc crystal. The stable crystal structure is determined by the position of the Gaussian pocket. These results show that we can control the stability of the solid phase by tuning the potential function

Assessment of students’ health condition by indicators of adaptation potential, biological age and bio-energetic reserves of organism

Directory of Open Access Journals (Sweden)

O.V. Martyniuk

2015-06-01

Full Text Available Purpose: to assess students’ health condition by indicators of adaptation potential, biological age and express-assessment. Material: in the research 47 first and second year girl students participated, who belonged to main health group. Results: we distributed the girl students into three groups: 14.89% of them were included in group with “safe” health condition; 34.04% - in group of “third state”; 51.06% were related to group with “ dangerous” health condition. We established that dangerous level was characterized by energy potential of below middle and low level. It is accompanied by accelerated processes of organism’s age destructions and tension of regulation mechanisms. Conclusions: the received results permit to further develop and generalize the data of students’ health’s assessment by indicators of adaptation potentials, biological age and physical health’s condition.

Prevalence and typology of potential drug interactions occurring in primary care patients.

Science.gov (United States)

Lopez-Picazo, Julio J; Ruiz, Juan C; Sanchez, Jose F; Ariza, Angeles; Aguilera, Belen; Lazaro, Dolores; Sanz, Gonzalo R

2010-06-01

To investigate the prevalence and types of potential drug interactions in primary care patients to detect risky prescriptions as an essential condition to design intervention policies leading to an improvement in patient safety. Cross-sectional descriptive study. Two areas in Spain comprising 715,661 inhabitants. 430,525 subjects with electronic medical records and assigned to a family doctor regularly updating them. On a random day, 29.4% of the population was taking medication. Of these, 73.9% were at risk of suffering interactions, and these were found in 20.6% of them. The amount of interactions was higher among people with chronic conditions, the elderly, females and polymedicated patients. From the total of interactions, 55.1% belonged to the highest clinical relevance 'A' level, and 28.3% should have been avoided. The active ingredients primarily involved were hydrochlorothiazide and ibuprofen and, when focusing on those that should be avoided, omeprazole and acenocoumarol. The most frequent 'A' interaction that should be avoided was between non-conjugated excreted benzodiazepines and proton-pump inhibitors, followed by some NSAIDs and diuretics. 1 in 20 Spanish citizens is currently undergoing a potential drug interaction, including a high rate of clinically relevant ones that should be avoided. These results confirm the existence of a serious safety issue that should be approached and where all parties involved (physicians, health services, medical societies and patients) must do our bit to improve. Health services should foster the implementation of prescription alert systems linked with electronic medical records including clinical data.

Flexible Organic Electronics in Biology: Materials and Devices.

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Liao, Caizhi; Zhang, Meng; Yao, Mei Yu; Hua, Tao; Li, Li; Yan, Feng

2015-12-09

At the convergence of organic electronics and biology, organic bioelectronics attracts great scientific interest. The potential applications of organic semiconductors to reversibly transmit biological signals or stimulate biological tissues inspires many research groups to explore the use of organic electronics in biological systems. Considering the surfaces of movable living tissues being arbitrarily curved at physiological environments, the flexibility of organic bioelectronic devices is of paramount importance in enabling stable and reliable performances by improving the contact and interaction of the devices with biological systems. Significant advances in flexible organic bio-electronics have been achieved in the areas of flexible organic thin film transistors (OTFTs), polymer electrodes, smart textiles, organic electrochemical ion pumps (OEIPs), ion bipolar junction transistors (IBJTs) and chemiresistors. This review will firstly discuss the materials used in flexible organic bioelectronics, which is followed by an overview on various types of flexible organic bioelectronic devices. The versatility of flexible organic bioelectronics promises a bright future for this emerging area. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biological origins of color categorization.

Science.gov (United States)

Skelton, Alice E; Catchpole, Gemma; Abbott, Joshua T; Bosten, Jenny M; Franklin, Anna

2017-05-23

The biological basis of the commonality in color lexicons across languages has been hotly debated for decades. Prior evidence that infants categorize color could provide support for the hypothesis that color categorization systems are not purely constructed by communication and culture. Here, we investigate the relationship between infants' categorization of color and the commonality across color lexicons, and the potential biological origin of infant color categories. We systematically mapped infants' categorical recognition memory for hue onto a stimulus array used previously to document the color lexicons of 110 nonindustrialized languages. Following familiarization to a given hue, infants' response to a novel hue indicated that their recognition memory parses the hue continuum into red, yellow, green, blue, and purple categories. Infants' categorical distinctions aligned with common distinctions in color lexicons and are organized around hues that are commonly central to lexical categories across languages. The boundaries between infants' categorical distinctions also aligned, relative to the adaptation point, with the cardinal axes that describe the early stages of color representation in retinogeniculate pathways, indicating that infant color categorization may be partly organized by biological mechanisms of color vision. The findings suggest that color categorization in language and thought is partially biologically constrained and have implications for broader debate on how biology, culture, and communication interact in human cognition.

Dermal Squamomelanocytic Tumor: Neoplasm of Uncertain Biological Potential

Directory of Open Access Journals (Sweden)

Mirsad Dorić

2008-05-01

Full Text Available We report a case of exceedingly rare cutaneous neoplasm with histological features of malignancy and uncertain biological potential. The nodular, darkly pigmented facial tumor with central exulceration, size 12x10x7 mm, of the skin 61-year-old man preauricular left was completely exised.Histologically tumor consists of atypical squamous cells, which express signs of moderate to significant pleomorphism, mitotically active, with foci forming of parakeratotic horn cysts (“pearls”. Characteristically tumor also consists of large number of atypical melanocytes with multifocal pattern, inserted between atypical squamous cells, and which contain large amount of dark brown pigment melanin. Immunohistochemically, squamous cells stain positively with keratin (CK116, melanocytes were stained with S -100 protein, HMB 45, and vimentin, but failed to stain with CK 116.To our knowledge this is the sixth reported case in world literature. The follow-up time of four years no evidence of recurrence or metastasis, similar all reported cases, but it is too short period in estimation to guarantee a benign course. However, it appears that this group of neoplasm may have different prognosis from pure squamous carcinoma or malignant melanoma.

Urgent Biophilia: Human-Nature Interactions and Biological Attractions in Disaster Resilience

Directory of Open Access Journals (Sweden)

Keith G. Tidball

2012-06-01

Full Text Available This contribution builds upon contemporary work on principles of biological attraction as well as earlier work on biophilia while synthesizing literatures on restorative environments, community-based ecological restoration, and both community and social-ecological disaster resilience. It suggests that when humans, faced with a disaster, as individuals and as communities and populations, seek engagement with nature to further their efforts to summon and demonstrate resilience in the face of a crisis, they exemplify an urgent biophilia. This urgent biophilia represents an important set of human-nature interactions in SES characterized by hazard, disaster, or vulnerability, often appearing in the 'backloop' of the adaptive cycle. The relationships that human-nature interactions have to other components within interdependent systems at many different scales may be one critical source of resilience in disaster and related contexts. In other words, the affinity we humans have for the rest of nature, the process of remembering that attraction, and the urge to express it through creation of restorative environments, which may also restore or increase ecological function, may confer resilience across multiple scales. In making this argument, the paper also represents a novel contribution to further theorizing alternatives to anthropocentric understandings of human-nature relations, and strongly makes the case for humans as part of, not separate from, ecosystems.

Stability of stationary states of non-local equations with singular interaction potentials

KAUST Repository

Fellner, Klemens; Raoul, Gaë l

2011-01-01

repulsive interaction potentials we show the stability of stationary states of uniformly bounded solutions under a convexity condition.Finally, we present numerical simulations to illustrate our results. © 2010 Elsevier Ltd.

Proper construction of ab initio global potential surfaces with accurate long-range interactions

International Nuclear Information System (INIS)

Ho, Tak-San; Rabitz, Herschel

2000-01-01

An efficient procedure based on the reproducing kernel Hilbert space interpolation method is presented for constructing intermolecular potential energy surfaces (PES) using not only calculated ab initio data but also a priori information on long-range interactions. Explicitly, use of the reciprocal power reproducing kernel on the semiinfinite interval [0,∞) yields a set of exact linear relations between dispersion (multipolar) coefficients and PES data points at finite internuclear separations. Consequently, given a combined set of ab initio data and the values of dispersion (multipolar) coefficients, the potential interpolation problem subject to long-range interaction constraints can be solved to render globally smooth, asymptotically accurate ab initio potential energy surfaces. Very good results have been obtained for the one-dimensional He-He potential curve and the two-dimensional Ne-CO PES. The construction of the Ne-CO PES was facilitated by invoking a new reproducing kernel for the angular coordinate based on the optimally stable and shape-preserving Bernstein basis functions. (c) 2000 American Institute of Physics

Use of total cross sections for obtaining the anisotropic interaction potential in atom--diatom system

International Nuclear Information System (INIS)

Eccles, J.; Secrest, D.

1977-01-01

A study is made of the ''conservation of the total cross section'' and the ''equivalence of the total cross section'' rules for scattering from H 2 . It is shown that these rules are a better approximation than the random phase approximation would indicate. Cross section formulas are given for scattering atoms from m/sub j/ state selected molecules and it is shown that total cross sections for state selected molecules depend on the anisotropic part of the interaction potential, while the spin-averaged total cross section often depends only on the spherically symmetric part of the interaction potential. The total spin-averaged cross section is thus independent of the initial rotation state of the molecule and depends only on the relative collision energy. It is further demonstrated that isotopic substitution, which shifts the center of mass changing the symmetric part of the interaction potential, has too small an effect on the total cross section to be useful as a means of determining the anisotropy of the potential

[Biological effects of non-ionizing electromagnetic radiation].

Science.gov (United States)

Fedorowski, A; Steciwko, A

1998-01-01

Since the mid 1970's, when Adey discovered that extremely-low-frequency electromagnetic field (ELF EMF) may affect the calcium ions efflux from various cells, bioeffects of non-ionizing radiation (NIR) have become the subject of growing interest and numerous research projects. At present, the fact that NIR exerts both stimulatory and inhibitory effects on different physiological cellular parameters is rather unquestionable. At the same time, some epidemiological studies suggest that exposure to EMF is potentially harmful even if its intensity is very low. It has been proved that thermal factors are not responsible for these effects, therefore nowadays, they are called 'non-thermal effects'. Our paper deals with three different aspects of biological effects of non-ionizing radiation, bioelectromagnetism, electromagnetobiology and electromagnetic bioinformation. Firstly, we describe how EMF and photons can be produced within a living cell, how biological cycles are controlled, and what are the features of endogenous electromagnetic radiation. Secondly, we discuss various facets of external EMF interactions with living matter, focusing on extremely-low-frequencies, radio- and microwaves. Possible mechanisms of these interactions are also mentioned. Finally, we present a short overview of current theories which explain how electromagnetic couplings may control an open and dissipative structure, namely the living organism. The theory of electromagnetic bioinformation seems to explain how different physiological processes are triggered and controlled, as well as how long-range interactions may possibly occur within the complex biological system. The review points out that the presented research data must be assessed very carefully since its evaluation is crucial to set the proper limits of EMF exposure, both occupational and environmental. The study of biological effects of non-ioinizing radiation may also contribute to the development of new diagnostic and therapeutic

Clinical treatment adherence of health care workers and students exposed to potentially infectious biological material

Directory of Open Access Journals (Sweden)

Maria Cristina Mendes de Almeida

2015-04-01

Full Text Available OBJECTIVE To assess adherence to clinical appointments by health care workers (HCW and students who suffered accidents with potentially infectious biological material. METHOD A retrospective cross-sectional study that assessed clinical records of accidents involving biological material between 2005 and 2010 in a specialized unit. RESULTS A total of 461 individuals exposed to biological material were treated, of which 389 (84.4% were HCWs and 72 (15.6% students. Of the 461 exposed individuals, 307 (66.6% attended a follow-up appointment. Individuals who had suffered an accident with a known source patient were 29 times more likely to show up to their scheduled follow-up appointments (OR: 29.98; CI95%: 16.09-55.83. CONCLUSION The predictor in both univariate and multivariate analyses for adherence to clinical follow-up appointment was having a known source patient with nonreactive serology for the human immunodeficiency virus and/or hepatitis B and C.

Replacement of the double bond of antitubulin chalcones with triazoles and tetrazoles: Synthesis and biological evaluation.

Science.gov (United States)

Mesenzani, Ornella; Massarotti, Alberto; Giustiniano, Mariateresa; Pirali, Tracey; Bevilacqua, Valentina; Caldarelli, Antonio; Canonico, Pierluigi; Sorba, Giovanni; Novellino, Ettore; Genazzani, Armando A; Tron, Gian Cesare

2011-01-15

In the chalcone scaffold, it is thought that the double bond is an important structural linker but it is likely not essential for the interaction with tubulin. Yet, it may be a potential site of metabolic degradation and interaction with biological nucleophiles. In this letter, we have replaced this olefinic portion of chalcones with two metabolically stable and chemically inert heterocyclic rings, namely triazole or tetrazole. Yet, our biologic data suggest that, unlike in other antitubulinic structures, the olephinic ring might not be merely a structural linker. Copyright © 2010 Elsevier Ltd. All rights reserved.

Topology and weights in a protein domain interaction network – a novel way to predict protein interactions

Directory of Open Access Journals (Sweden)

Wuchty Stefan

2006-05-01

Full Text Available Abstract Background While the analysis of unweighted biological webs as diverse as genetic, protein and metabolic networks allowed spectacular insights in the inner workings of a cell, biological networks are not only determined by their static grid of links. In fact, we expect that the heterogeneity in the utilization of connections has a major impact on the organization of cellular activities as well. Results We consider a web of interactions between protein domains of the Protein Family database (PFAM, which are weighted by a probability score. We apply metrics that combine the static layout and the weights of the underlying interactions. We observe that unweighted measures as well as their weighted counterparts largely share the same trends in the underlying domain interaction network. However, we only find weak signals that weights and the static grid of interactions are connected entities. Therefore assuming that a protein interaction is governed by a single domain interaction, we observe strong and significant correlations of the highest scoring domain interaction and the confidence of protein interactions in the underlying interactions of yeast and fly. Modeling an interaction between proteins if we find a high scoring protein domain interaction we obtain 1, 428 protein interactions among 361 proteins in the human malaria parasite Plasmodium falciparum. Assessing their quality by a logistic regression method we observe that increasing confidence of predicted interactions is accompanied by high scoring domain interactions and elevated levels of functional similarity and evolutionary conservation. Conclusion Our results indicate that probability scores are randomly distributed, allowing to treat static grid and weights of domain interactions as separate entities. In particular, these finding confirms earlier observations that a protein interaction is a matter of a single interaction event on domain level. As an immediate application, we

Forward detectors around the CMS interaction point at LHC and their physics potential

CERN Document Server

Grothe, Monika

2008-01-01

Forward physics with CMS at the LHC covers a wide range of physics subjects, including very low-x QCD, underlying event and multiple interactions characteristics, gamma-mediated processes, shower development at the energy scale of primary cosmic ray interactions with the atmosphere, diffraction in the presence of a hard scale and even MSSM Higgs discovery in central exclusive production. We describe the forward detector instrumentation around the CMS interaction point and present selected feasibility studies to illustrate their physics potential.

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

Redox-capacitor to connect electrochemistry to redox-biology.

Science.gov (United States)

Kim, Eunkyoung; Leverage, W Taylor; Liu, Yi; White, Ian M; Bentley, William E; Payne, Gregory F

2014-01-07

It is well-established that redox-reactions are integral to biology for energy harvesting (oxidative phosphorylation), immune defense (oxidative burst) and drug metabolism (phase I reactions), yet there is emerging evidence that redox may play broader roles in biology (e.g., redox signaling). A critical challenge is the need for tools that can probe biologically-relevant redox interactions simply, rapidly and without the need for a comprehensive suite of analytical methods. We propose that electrochemistry may provide such a tool. In this tutorial review, we describe recent studies with a redox-capacitor film that can serve as a bio-electrode interface that can accept, store and donate electrons from mediators commonly used in electrochemistry and also in biology. Specifically, we (i) describe the fabrication of this redox-capacitor from catechols and the polysaccharide chitosan, (ii) discuss the mechanistic basis for electron exchange, (iii) illustrate the properties of this redox-capacitor and its capabilities for promoting redox-communication between biology and electrodes, and (iv) suggest the potential for enlisting signal processing strategies to "extract" redox information. We believe these initial studies indicate broad possibilities for enlisting electrochemistry and signal processing to acquire "systems level" redox information from biology.

Graphics processing units in bioinformatics, computational biology and systems biology.

Science.gov (United States)

Nobile, Marco S; Cazzaniga, Paolo; Tangherloni, Andrea; Besozzi, Daniela

2017-09-01

Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity, ranging from the interaction of atoms in single molecules up to genome-wide interaction networks. Traditional computational methods and software tools developed in these research fields share a common trait: they can be computationally demanding on Central Processing Units (CPUs), therefore limiting their applicability in many circumstances. To overcome this issue, general-purpose Graphics Processing Units (GPUs) are gaining an increasing attention by the scientific community, as they can considerably reduce the running time required by standard CPU-based software, and allow more intensive investigations of biological systems. In this review, we present a collection of GPU tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures. The complete list of GPU-powered tools here reviewed is available at http://bit.ly/gputools. © The Author 2016. Published by Oxford University Press.

Examining ecological validity in social interaction: problems of visual fidelity, gaze, and social potential.

Science.gov (United States)

Reader, Arran T; Holmes, Nicholas P

2016-01-01

Social interaction is an essential part of the human experience, and much work has been done to study it. However, several common approaches to examining social interactions in psychological research may inadvertently either unnaturally constrain the observed behaviour by causing it to deviate from naturalistic performance, or introduce unwanted sources of variance. In particular, these sources are the differences between naturalistic and experimental behaviour that occur from changes in visual fidelity (quality of the observed stimuli), gaze (whether it is controlled for in the stimuli), and social potential (potential for the stimuli to provide actual interaction). We expand on these possible sources of extraneous variance and why they may be important. We review the ways in which experimenters have developed novel designs to remove these sources of extraneous variance. New experimental designs using a 'two-person' approach are argued to be one of the most effective ways to develop more ecologically valid measures of social interaction, and we suggest that future work on social interaction should use these designs wherever possible.

Drug-drug interactions involving lysosomes: mechanisms and potential clinical implications.

Science.gov (United States)

Logan, Randall; Funk, Ryan S; Axcell, Erick; Krise, Jeffrey P

2012-08-01

Many commercially available, weakly basic drugs have been shown to be lysosomotropic, meaning they are subject to extensive sequestration in lysosomes through an ion trapping-type mechanism. The extent of lysosomal trapping of a drug is an important therapeutic consideration because it can influence both activity and pharmacokinetic disposition. The administration of certain drugs can alter lysosomes such that their accumulation capacity for co-administered and/or secondarily administered drugs is altered. In this review the authors explore what is known regarding the mechanistic basis for drug-drug interactions involving lysosomes. Specifically, the authors address the influence of drugs on lysosomal pH, volume and lipid processing. Many drugs are known to extensively accumulate in lysosomes and significantly alter their structure and function; however, the therapeutic and toxicological implications of this remain controversial. The authors propose that drug-drug interactions involving lysosomes represent an important potential source of variability in drug activity and pharmacokinetics. Most evaluations of drug-drug interactions involving lysosomes have been performed in cultured cells and isolated tissues. More comprehensive in vivo evaluations are needed to fully explore the impact of this drug-drug interaction pathway on therapeutic outcomes.

The triel bond: a potential force for tuning anion-π interactions

Science.gov (United States)

Esrafili, Mehdi D.; Mousavian, Parisasadat

2018-02-01

Using ab-initio calculations, the mutual influence between anion-π and B···N or B···C triel bond interactions is investigated in some model complexes. The properties of these complexes are studied by molecular electrostatic potential, noncovalent interaction index, quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses. According to the results, the formation of B···N or B···C triel bond interactions in the multi-component systems makes a significant shortening of anion-π distance. Such remarkable variation in the anion-π distances has not been reported previously. The strengthening of the anion-π bonding in the multi-component systems depend significantly on the nature of the anion, and it becomes larger in the order Br- > Cl- > F-. The parameters derived from the QTAIM and NBO methodologies are used to study the mechanism of the cooperativity between the anion-π and triel bond interactions in the multi-component complexes.

Microbiology and atmospheric processes: chemical interactions of primary biological aerosols

Directory of Open Access Journals (Sweden)

L. Deguillaume

2008-07-01

Full Text Available This paper discusses the influence of primary biological aerosols (PBA on atmospheric chemistry and vice versa through microbiological and chemical properties and processes. Several studies have shown that PBA represent a significant fraction of air particulate matter and hence affect the microstructure and water uptake of aerosol particles. Moreover, airborne micro-organisms, namely fungal spores and bacteria, can transform chemical constituents of the atmosphere by metabolic activity. Recent studies have emphasized the viability of bacteria and metabolic degradation of organic substances in cloud water. On the other hand, the viability and metabolic activity of airborne micro-organisms depend strongly on physical and chemical atmospheric parameters such as temperature, pressure, radiation, pH value and nutrient concentrations. In spite of recent advances, however, our knowledge of the microbiological and chemical interactions of PBA in the atmosphere is rather limited. Further targeted investigations combining laboratory experiments, field measurements, and modelling studies will be required to characterize the chemical feedbacks, microbiological activities at the air/snow/water interface supplied to the atmosphere.

Systems Biology Model of Interactions Between Tissue Growth Factors and DNA Damage Pathways: Low Dose Response and Cross-Talk in TGFbeta and ATM Signaling

Energy Technology Data Exchange (ETDEWEB)

O' Neill, Peter [University of Oxford; Anderson, Jennifer [University of Oxford

2014-10-02

The etiology of radiation carcinogenesis has been described in terms of aberrant changes that span several levels of biological organization. Growth factors regulate many important cellular and tissue functions including apoptosis, differentiation and proliferation. A variety of genetic and epigenetic changes of growth factors have been shown to contribute to cancer initiation and progression. It is known that cellular and tissue damage to ionizing radiation is in part initiated by the production of reactive oxygen species, which can activate cytokine signaling, and the DNA damage response pathways, most notably the ATM signaling pathway. Recently the transforming growth factor β (TGFβ) pathway has been shown to regulate or directly interact with the ATM pathway in the response to radiation. The relevance of this interaction with the ATM pathway is not known although p53 becomes phosphorylated and DNA damage responses are involved. However, growth factor interactions with DNA damage responses have not been elucidated particularly at low doses and further characterization of their relationship to cancer processes is warranted. Our goal will be to use a systems biology approach to mathematically and experimentally describe the low dose responses and cross-talk between the ATM and TGFβ pathways initiated by low and high LET radiation. We will characterize ATM and TGFβ signaling in epithelial and fibroblast cells using 2D models and ultimately extending to 3D organotypic cell culture models to begin to elucidate possible differences that may occur for different cell types and/or inter-cellular communication. We will investigate the roles of the Smad and Activating transcription factor 2 (ATF2) proteins as the potential major contributors to cross- talk between the TGFβ and ATM pathways, and links to cell cycle control and/or the DNA damage response, and potential differences in their responses at low and high doses. We have developed various experimental

Systems Biology Model of Interactions between Tissue Growth Factors and DNA Damage Pathways: Low Dose Response and Cross-Talk in TGFβ and ATM Signaling

International Nuclear Information System (INIS)

Cucinotta, Francis A

2016-01-01

The etiology of radiation carcinogenesis has been described in terms of aberrant changes that span several levels of biological organization. Growth factors regulate many important cellular and tissue functions including apoptosis, differentiation and proliferation. A variety of genetic and epigenetic changes of growth factors have been shown to contribute to cancer initiation and progression. It is known that cellular and tissue damage to ionizing radiation is in part initiated by the production of reactive oxygen species, which can activate cytokine signaling, and the DNA damage response pathways, most notably the ATM signaling pathway. Recently, the transforming growth factor β (TGFβ) pathway has been shown to regulate or directly interact with the ATM pathway in the response to radiation. The relevance of this interaction with the ATM pathway is not known although p53 becomes phosphorylated and DNA damage responses are involved. However, growth factor interactions with DNA damage responses have not been elucidated particularly at low doses, and further characterization of their relationship to cancer processes is warranted. Our goal will be to use a systems biology approach to mathematically and experimentally describe the low-dose responses and cross-talk between the ATM and TGFβ pathways initiated by low- and high-LET radiation. We will characterize ATM and TGFβ signaling in epithelial and fibroblast cells using 2D models and ultimately extending to 3D organotypic cell culture models to begin to elucidate possible differences that may occur for different cell types and/or inter-cellular communication. We will investigate the roles of the Smad and Activating transcription factor 2 (ATF2) proteins as the potential major contributors to crosstalk between the TGFβ and ATM pathways, and links to cell cycle control and/or the DNA damage response, and potential differences in their responses at low and high doses. We have developed various experimental

Systems Biology Model of Interactions between Tissue Growth Factors and DNA Damage Pathways: Low Dose Response and Cross-Talk in TGFβ and ATM Signaling

Energy Technology Data Exchange (ETDEWEB)

Cucinotta, Francis A [Univ. of Nevada, Las Vegas, NV (United States)

2016-09-01

The etiology of radiation carcinogenesis has been described in terms of aberrant changes that span several levels of biological organization. Growth factors regulate many important cellular and tissue functions including apoptosis, differentiation and proliferation. A variety of genetic and epigenetic changes of growth factors have been shown to contribute to cancer initiation and progression. It is known that cellular and tissue damage to ionizing radiation is in part initiated by the production of reactive oxygen species, which can activate cytokine signaling, and the DNA damage response pathways, most notably the ATM signaling pathway. Recently, the transforming growth factor β (TGFβ) pathway has been shown to regulate or directly interact with the ATM pathway in the response to radiation. The relevance of this interaction with the ATM pathway is not known although p53 becomes phosphorylated and DNA damage responses are involved. However, growth factor interactions with DNA damage responses have not been elucidated particularly at low doses, and further characterization of their relationship to cancer processes is warranted. Our goal will be to use a systems biology approach to mathematically and experimentally describe the low-dose responses and cross-talk between the ATM and TGFβ pathways initiated by low- and high-LET radiation. We will characterize ATM and TGFβ signaling in epithelial and fibroblast cells using 2D models and ultimately extending to 3D organotypic cell culture models to begin to elucidate possible differences that may occur for different cell types and/or inter-cellular communication. We will investigate the roles of the Smad and Activating transcription factor 2 (ATF2) proteins as the potential major contributors to crosstalk between the TGFβ and ATM pathways, and links to cell cycle control and/or the DNA damage response, and potential differences in their responses at low and high doses. We have developed various experimental

Synthetic Biology: Advancing Biological Frontiers by Building Synthetic Systems

OpenAIRE

Chen, Yvonne Yu-Hsuan; Galloway, Kate E; Smolke, Christina D

2012-01-01

Advances in synthetic biology are contributing to diverse research areas, from basic biology to biomanufacturing and disease therapy. We discuss the theoretical foundation, applications, and potential of this emerging field.

Coupled dynamics of interacting spin-1 bosons in a double-well potential

Science.gov (United States)

Carvalho, D. W. S.; Foerster, A.; Gusmão, M. A.

2018-03-01

We present a detailed analysis of dynamical processes involving two or three particles in a double-well potential. Motivated by experimental realizations of such a system with optically trapped cold atoms, we focus on spin-1 bosons with special attention on the effects of a spin-dependent interaction in addition to the usual Hubbard-like repulsive one. For a sufficiently weak tunneling amplitude in comparison to the dominant Hubbard coupling, particle motion is strongly correlated, occurring only under fine-tuned relationships between well-depth asymmetry and interactions. We highlight processes involving tunneling of coupled particle pairs and triads, emphasizing the role of the spin-dependent interaction in resonance conditions.

Evaluation of Potential Biological Threats in Ukraine

International Nuclear Information System (INIS)

Pozdnyakova, L.; Slavina, N.; Pozdnyakov, S.

2007-01-01

Dilating of biological threats spectrum, EDI diffusion opportunities and routes, unpredictability of outbreaks connected with connatural, technogenic, terrorist factors determines constant monitoring and readiness for operative BPA indication and identification. Scientific analytical approach of existing and probable regional bio-threats evaluation is necessary for adequate readiness system creation and maintenance of medical counteraction tactics to probable biological threats. Basing on the international experience, we carry out analysis of a situation present in Ukraine and routes for the decisions. The basic directions are: - Evaluation of a reality for EDI penetration from abroad and presence of conditions for their further diffusion inside the country. - Revealing of presence and definition of connatural EDI foci biocenoses features and BPAs. - Appropriate level of biological safety and physical protection of bio-laboratories and pathogens collections maintenance. - Gene/molecular and phenotypical definition of EDI circulating strains. - Creation of the circulating EDI gene/ phenotypic characteristics regional data bank. - Ranging of EDI actual for area. - Introduction of GPT, mathematical modeling and forecasting for tactics development in case of technogenic accidents and connatural outbreaks. - Methodical basis and equipment improvement for BPA system indication for well-timed identification of natural, or modified agent. - Education and training The international cooperation in maintenance of biosafety and bioprotection within the framework of scientific programs, grants, exchange of experience, introduction of international standards and rules are among basic factors in the decision for creating system national biosafety for countries not included in EU and the NATO. (author)

Host range of Secusio extensa (Lepidoptera: Arctiidae), and potential for biological control of Senecio madagascariensis (Asteraceae)

Science.gov (United States)

M. M. Ramadan; K. T. Murai; T. Johnson

2010-01-01

Secusio extensa (Lepidoptera: Arctiidae) was evaluated as a potential biological control agent for Madagascar fireweed, Senecio madagascariensis (Asteraceae), which has invaded over 400 000 acres of rangeland in the Hawaiian Islands and is toxic to cattle and horses. The moth was introduced from southeastern Madagascar...

Potential effect of cationic liposomes on interactions with oral bacterial cells and biofilms.

Science.gov (United States)

Sugano, Marika; Morisaki, Hirobumi; Negishi, Yoichi; Endo-Takahashi, Yoko; Kuwata, Hirotaka; Miyazaki, Takashi; Yamamoto, Matsuo

2016-01-01

Although oral infectious diseases have been attributed to bacteria, drug treatments remain ineffective because bacteria and their products exist as biofilms. Cationic liposomes have been suggested to electrostatically interact with the negative charge on the bacterial surface, thereby improving the effects of conventional drug therapies. However, the electrostatic interaction between oral bacteria and cationic liposomes has not yet been examined in detail. The aim of the present study was to examine the behavior of cationic liposomes and Streptococcus mutans in planktonic cells and biofilms. Liposomes with or without cationic lipid were prepared using a reverse-phase evaporation method. The zeta potentials of conventional liposomes (without cationic lipid) and cationic liposomes were -13 and 8 mV, respectively, and both had a mean particle size of approximately 180 nm. We first assessed the interaction between liposomes and planktonic bacterial cells with a flow cytometer. We then used a surface plasmon resonance method to examine the binding of liposomes to biofilms. We confirmed the binding behavior of liposomes with biofilms using confocal laser scanning microscopy. The interactions between cationic liposomes and S. mutans cells and biofilms were stronger than those of conventional liposomes. Microscopic observations revealed that many cationic liposomes interacted with the bacterial mass and penetrated the deep layers of biofilms. In this study, we demonstrated that cationic liposomes had higher affinity not only to oral bacterial cells, but also biofilms than conventional liposomes. This electrostatic interaction may be useful as a potential drug delivery system to biofilms.

Biological characteristics of human-urine-derived stem cells: potential for cell-based therapy in neurology.

Science.gov (United States)

Guan, Jun-Jie; Niu, Xin; Gong, Fei-Xiang; Hu, Bin; Guo, Shang-Chun; Lou, Yuan-Lei; Zhang, Chang-Qing; Deng, Zhi-Feng; Wang, Yang

2014-07-01

Stem cells in human urine have gained attention in recent years; however, urine-derived stem cells (USCs) are far from being well elucidated. In this study, we compared the biological characteristics of USCs with adipose-derived stem cells (ASCs) and investigated whether USCs could serve as a potential cell source for neural tissue engineering. USCs were isolated from voided urine with a modified culture medium. Through a series of experiments, we examined the growth rate, surface antigens, and differentiation potential of USCs, and compared them with ASCs. USCs showed robust proliferation ability. After serial propagation, USCs retained normal karyotypes. Cell surface antigen expression of USCs was similar to ASCs. With lineage-specific induction factors, USCs could differentiate toward the osteogenic, chondrogenic, adipogenic, and neurogenic lineages. To assess the ability of USCs to survive, differentiate, and migrate, they were seeded onto hydrogel scaffold and transplanted into rat brain. The results showed that USCs were able to survive in the lesion site, migrate to other areas, and express proteins that were associated with neural phenotypes. The results of our study demonstrate that USCs possess similar biological characteristics with ASCs and have multilineage differentiation potential. Moreover USCs can differentiate to neuron-like cells in rat brain. The present study shows that USCs are a promising cell source for tissue engineering and regenerative medicine.

Synthesis, spectroscopic characterization and in vitro cytotoxicities of new organometallic palladium complexes with biologically active β-diketones; Biological evaluation probing of the interaction mechanism with DNA/Protein and molecular docking

Science.gov (United States)

Karami, Kazem; Rafiee, Mina; Lighvan, Zohreh Mehri; Zakariazadeh, Mostafa; Faal, Ali Yeganeh; Esmaeili, Seyed-Alireza; Momtazi-Borojeni, Amir Abbas

2018-02-01

[Pd{(C,N)sbnd C6H4CH (CH3)NH}(CUR)] (3) and [Pd2{(C,N)sbnd C6H4CH(CH3)NH2}2(μ-N3CS2)] (4) [cur = 1,7-bis(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5-dion] novel organometallic complexes with biologically active ligands have been prepared and characterized via elemental analysis, multinuclear spectroscopic techniques (1H, and 13C NMR and IR) and their biological activities, including antitumoral activity and DNA-protein interactions have been investigated. Fluorescence spectroscopy used to study the interaction of the complexes with BSA have shown the affinity of the complexes for these proteins with relatively high binding constant values and the changed secondary structure of BSA in the presence of the complexes. In the meantime, spectroscopy and competitive titration have been applied to investigate the interaction of complexes with Warfarin and Ibuprofen site markers for sites I and II, respectively, with BSA. The results have suggested that the locations of complexes 3 and 4 are sites II and I, respectively. UV-Vis spectroscopy, emission titration and helix melting methods have been used to study the interaction of these complexes with CT-DNA, indicating that complexes are bound to CT-DNA by intercalation binding mode. In addition, good cytotoxic activity against MCF-7 (human breast cancer) and JURKAT (human leukemia) cell line has been shown by both complexes whereas low cytotoxicity was exerted on normal peripheral blood mononuclear cells.

Prevalence of potential drug-drug interactions in cancer patients treated with oral anticancer drugs

NARCIS (Netherlands)

van Leeuwen, R. W. F.; Brundel, D. H. S.; Neef, C.; van Gelder, T.; Mathijssen, R. H. J.; Burger, D. M.; Jansman, F. G. A.

2013-01-01

Background: Potential drug-drug interactions (PDDIs) in patients with cancer are common, but have not previously been quantified for oral anticancer treatment. We assessed the prevalence and seriousness of potential PDDIs among ambulatory cancer patients on oral anticancer treatment. Methods: A

Prevalence of potential drug-drug interactions in cancer patients treated with oral anticancer drugs

NARCIS (Netherlands)

R.W.F. van Leeuwen (Roelof); D.H.S. Brundel (D. H S); C. Neef (Cees); T. van Gelder (Teun); A.H.J. Mathijssen (Ron); D.M. Burger (David); F.G.A. Jansman (Frank)

2013-01-01

textabstractBackground: Potential drug-drug interactions (PDDIs) in patients with cancer are common, but have not previously been quantified for oral anticancer treatment. We assessed the prevalence and seriousness of potential PDDIs among ambulatory cancer patients on oral anticancer treatment.

The influence of interactive technology on student performance in an Oklahoma secondary Biology I program

Science.gov (United States)

Feltman, Vallery

Over the last decade growth in technologies available to teach students and enhance curriculum has become an important consideration in the educational system. The profile of today's secondary students have also been found to be quite different than those of the past. Their learning styles and preferences are issues that should be addressed by educators. With the growth and availability of new technologies students are increasingly expecting to use these as learning tools in their classrooms. This study investigates how interactive technology may impact student performance. This study specifically focuses on the use of the Apple Ipad in 4 Biology I classrooms. This study used an experimental mixed method design to examine how using Ipads for learning impacted student achievement, motivation to learn, and learning strategies. Qualitatively the study examined observed student behaviors and student perceptions regarding the use of interactive technologies. Data was analyzed using descriptive statistics, t-tests, 2-way ANOVAs, and qualitative analysis. Quantitatively the results revealed no significant difference between students who used the interactive technology to learn and those who did not. Qualitative data revealed behaviors indicative of being highly engaged with the subject matter and the development of critical thinking skills which may improve student performance. Student perceptions also revealed overall positive experiences with using interactive technology in the classroom. It is recommended that further studies be done to look at using interactive technologies for a longer period of time using multiple subjects areas. This would provide a more in-depth exploration of interactive technologies on student achievement.

Marine molecular biology: An emerging field of biological sciences

Digital Repository Service at National Institute of Oceanography (India)

Thakur, N.L.; Jain, R.; Natalio, F.; Hamer, B.; Thakur, A.N.; Muller, W.E.G.

An appreciation of the potential applications of molecular biology is of growing importance in many areas of life sciences, including marine biology. During the past two decades, the development of sophisticated molecular technologies...

Virus–Bacteria Interactions: Implications and Potential for the Applied and Agricultural Sciences

Directory of Open Access Journals (Sweden)

Matthew D. Moore

2018-02-01

Full Text Available Eukaryotic virus–bacteria interactions have recently become an emerging topic of study due to multiple significant examples related to human pathogens of clinical interest. However, such omnipresent and likely important interactions for viruses and bacteria relevant to the applied and agricultural sciences have not been reviewed or compiled. The fundamental basis of this review is that these interactions have importance and deserve more investigation, as numerous potential consequences and applications arising from their discovery are relevant to the applied sciences. The purpose of this review is to highlight and summarize eukaryotic virus–bacteria findings in the food/water, horticultural, and animal sciences. In many cases in the agricultural sciences, mechanistic understandings of the effects of virus–bacteria interactions remain unstudied, and many studies solely focus on co-infections of bacterial and viral pathogens. Given recent findings relative to human viral pathogens, further research related to virus–bacteria interactions would likely result in numerous discoveries and beneficial applications.

Virus-Bacteria Interactions: Implications and Potential for the Applied and Agricultural Sciences.

Science.gov (United States)

Moore, Matthew D; Jaykus, Lee-Ann

2018-02-02

Eukaryotic virus-bacteria interactions have recently become an emerging topic of study due to multiple significant examples related to human pathogens of clinical interest. However, such omnipresent and likely important interactions for viruses and bacteria relevant to the applied and agricultural sciences have not been reviewed or compiled. The fundamental basis of this review is that these interactions have importance and deserve more investigation, as numerous potential consequences and applications arising from their discovery are relevant to the applied sciences. The purpose of this review is to highlight and summarize eukaryotic virus-bacteria findings in the food/water, horticultural, and animal sciences. In many cases in the agricultural sciences, mechanistic understandings of the effects of virus-bacteria interactions remain unstudied, and many studies solely focus on co-infections of bacterial and viral pathogens. Given recent findings relative to human viral pathogens, further research related to virus-bacteria interactions would likely result in numerous discoveries and beneficial applications.

Temperature-dependent interaction potential between NF3 molecules and thermophysical properties of gaseous NF3

International Nuclear Information System (INIS)

Damyanova, M; Balabanova, E; Hohm, U

2014-01-01

A temperature-dependent effective intermolecular interaction potential is applied to describe the interaction between two nitrogen fluoride (NF 3 ) molecules in gas phase. To this end, a spherically-symmetric (n-6) Lennard-Jones temperature-dependent potential (LJTDP) is used. The (n-6) LJTDP takes into account the influence of vibrational excitation of the molecules on the potential parameters, namely, the equilibrium distance r m and the potential well depth ε. The potential parameters at T = 0 K were obtained from the very small amount of existing thermophysical equilibrium and transport properties of low-density NF 3 gas. Fitting formulae are tabulated for a fast and reliable prediction of the thermophysical properties and potential parameters in the temperature range between 200 K and 1200 K. A comparison is also presented between our estimates for some thermophysical properties of the NF 3 gas with the available experimental and calculated data.

Calculation of parameters of the interaction potential between excited alkali atoms and mercury atoms: The Cs*, Pr*-Hg interaction

International Nuclear Information System (INIS)

Glushkov, A.V.

1994-01-01

Based on the method of effective potential involving the new polarization interaction potential calculated from polarization diagrams of the perturbation theory in the Thomas-Fermi approximation, the main parameters of the interatomic potentials (equilibrium distances, potential well depth) are evaluated for a system consisting of an alkali atom in the ground and excited states and of a mercury atom. The results of calculations of quasi-molecular terms for the A-Hg system, where A = Na, Cs, Fr, are reported, some of which are obtained for the first time. A comparison is made with available experimental and theoretical data. 29 refs., 2 figs., 1 tab

Drivers potentially influencing host-bat fly interactions in anthropogenic neotropical landscapes at different spatial scales.

Science.gov (United States)

Hernández-Martínez, Jacqueline; Morales-Malacara, Juan B; Alvarez-Añorve, Mariana Yolotl; Amador-Hernández, Sergio; Oyama, Ken; Avila-Cabadilla, Luis Daniel

2018-05-21

The anthropogenic modification of natural landscapes, and the consequent changes in the environmental conditions and resources availability at multiple spatial scales can affect complex species interactions involving key-stone species such as bat-parasite interactions. In this study, we aimed to identify the drivers potentially influencing host-bat fly interactions at different spatial scales (at the host, vegetation stand and landscape level), in a tropical anthropogenic landscape. For this purpose, we mist-netted phyllostomid and moormopid bats and collected the bat flies (streblids) parasitizing them in 10 sites representing secondary and old growth forest. In general, the variation in fly communities largely mirrored the variation in bat communities as a result of the high level of specialization characterizing host-bat fly interaction networks. Nevertheless, we observed that: (1) bats roosting dynamics can shape bat-streblid interactions, modulating parasite prevalence and the intensity of infestation; (2) a degraded matrix could favor crowding and consequently the exchange of ectoparasites among bat species, lessening the level of specialization of the interaction networks and promoting novel interactions; and (3) bat-fly interaction can also be shaped by the dilution effect, as a decrease in bat diversity could be associated with a potential increase in the dissemination and prevalence of streblids.

The role of the ion-molecule and molecule-molecule interactions in the formation of the two-ion average force interaction potential

CERN Document Server

Ajrian, E A; Sidorenko, S N

2002-01-01

The effect of the ion-molecule and intermolecular interactions on the formation of inter-ion average force potentials is investigated within the framework of a classical ion-dipole model of electrolyte solutions. These potentials are shown to possess the Coulomb asymptotics at large distances while in the region of mean distances they reveal creation and disintegration of solvent-shared ion pairs. The calculation results provide a qualitatively authentic physical picture which is experimentally observed in strong electrolytes solutions. In particular, an increased interaction between an ion and a molecule enhances formation of ion pairs in which the ions are separated by one solvent molecule

Potential of Biological Agents in Decontamination of Agricultural Soil

Directory of Open Access Journals (Sweden)

Muhammad Kashif Javaid

2016-01-01

Full Text Available Pesticides are widely used for the control of weeds, diseases, and pests of cultivated plants all over the world, mainly since the period after the Second World War. The use of pesticides is very extensive to control harm of pests all over the globe. Persistent nature of most of the synthetic pesticides causes serious environmental concerns. Decontamination of these hazardous chemicals is very essential. This review paper elaborates the potential of various biological agents in decontamination of agricultural soils. The agricultural crop fields are contaminated by the periodic applications of pesticides. Biodegradation is an ecofriendly, cost-effective, highly efficient approach compared to the physical and chemical methods which are expensive as well as unfriendly towards environment. Biodegradation is sensitive to the concentration levels of hydrogen peroxide and nitrogen along with microbial community, temperature, and pH changes. Experimental work for optimum conditions at lab scale can provide very fruitful results about specific bacterial, fungal strains. This study revealed an upper hand of bioremediation over physicochemical approaches. Further studies should be carried out to understand mechanisms of biotransformation.

Potential of Biological Agents in Decontamination of Agricultural Soil.

Science.gov (United States)

Javaid, Muhammad Kashif; Ashiq, Mehrban; Tahir, Muhammad

2016-01-01

Pesticides are widely used for the control of weeds, diseases, and pests of cultivated plants all over the world, mainly since the period after the Second World War. The use of pesticides is very extensive to control harm of pests all over the globe. Persistent nature of most of the synthetic pesticides causes serious environmental concerns. Decontamination of these hazardous chemicals is very essential. This review paper elaborates the potential of various biological agents in decontamination of agricultural soils. The agricultural crop fields are contaminated by the periodic applications of pesticides. Biodegradation is an ecofriendly, cost-effective, highly efficient approach compared to the physical and chemical methods which are expensive as well as unfriendly towards environment. Biodegradation is sensitive to the concentration levels of hydrogen peroxide and nitrogen along with microbial community, temperature, and pH changes. Experimental work for optimum conditions at lab scale can provide very fruitful results about specific bacterial, fungal strains. This study revealed an upper hand of bioremediation over physicochemical approaches. Further studies should be carried out to understand mechanisms of biotransformation.

The potential biological mechanisms of arsenic-induced diabetes mellitus

International Nuclear Information System (INIS)

Tseng, C.-H.

2004-01-01

Although epidemiologic studies carried out in Taiwan, Bangladesh, and Sweden have demonstrated a diabetogenic effect of arsenic, the mechanisms remain unclear and require further investigation. This paper reviewed the potential biological mechanisms of arsenic-induced diabetes mellitus based on the current knowledge of the biochemical properties of arsenic. Arsenate can substitute phosphate in the formation of adenosine triphosphate (ATP) and other phosphate intermediates involved in glucose metabolism, which could theoretically slow down the normal metabolism of glucose, interrupt the production of energy, and interfere with the ATP-dependent insulin secretion. However, the concentration of arsenate required for such reaction is high and not physiologically relevant, and these effects may only happen in acute intoxication and may not be effective in subjects chronically exposed to low-dose arsenic. On the other hand, arsenite has high affinity for sulfhydryl groups and thus can form covalent bonds with the disulfide bridges in the molecules of insulin, insulin receptors, glucose transporters (GLUTs), and enzymes involved in glucose metabolism (e.g., pyruvate dehydrogenase and α-ketoglutarate dehydrogenase). As a result, the normal functions of these molecules can be hampered. However, a direct effect on these molecules caused by arsenite at physiologically relevant concentrations seems unlikely. Recent evidence has shown that treatment of arsenite at lower and physiologically relevant concentrations can stimulate glucose transport, in contrary to an inhibitory effect exerted by phenylarsine oxide (PAO) or by higher doses of arsenite. Induction of oxidative stress and interferences in signal transduction or gene expression by arsenic or by its methylated metabolites are the most possible causes to arsenic-induced diabetes mellitus through mechanisms of induction of insulin resistance and β cell dysfunction. Recent studies have shown that, in subjects with chronic

BiologicalNetworks 2.0 - an integrative view of genome biology data

Directory of Open Access Journals (Sweden)

Ponomarenko Julia

2010-12-01

Full Text Available Abstract Background A significant problem in the study of mechanisms of an organism's development is the elucidation of interrelated factors which are making an impact on the different levels of the organism, such as genes, biological molecules, cells, and cell systems. Numerous sources of heterogeneous data which exist for these subsystems are still not integrated sufficiently enough to give researchers a straightforward opportunity to analyze them together in the same frame of study. Systematic application of data integration methods is also hampered by a multitude of such factors as the orthogonal nature of the integrated data and naming problems. Results Here we report on a new version of BiologicalNetworks, a research environment for the integral visualization and analysis of heterogeneous biological data. BiologicalNetworks can be queried for properties of thousands of different types of biological entities (genes/proteins, promoters, COGs, pathways, binding sites, and other and their relations (interactions, co-expression, co-citations, and other. The system includes the build-pathways infrastructure for molecular interactions/relations and module discovery in high-throughput experiments. Also implemented in BiologicalNetworks are the Integrated Genome Viewer and Comparative Genomics Browser applications, which allow for the search and analysis of gene regulatory regions and their conservation in multiple species in conjunction with molecular pathways/networks, experimental data and functional annotations. Conclusions The new release of BiologicalNetworks together with its back-end database introduces extensive functionality for a more efficient integrated multi-level analysis of microarray, sequence, regulatory, and other data. BiologicalNetworks is freely available at http://www.biologicalnetworks.org.

Fostering synergy between cell biology and systems biology.

Science.gov (United States)

Eddy, James A; Funk, Cory C; Price, Nathan D

2015-08-01

In the shared pursuit of elucidating detailed mechanisms of cell function, systems biology presents a natural complement to ongoing efforts in cell biology. Systems biology aims to characterize biological systems through integrated and quantitative modeling of cellular information. The process of model building and analysis provides value through synthesizing and cataloging information about cells and molecules, predicting mechanisms and identifying generalizable themes, generating hypotheses and guiding experimental design, and highlighting knowledge gaps and refining understanding. In turn, incorporating domain expertise and experimental data is crucial for building towards whole cell models. An iterative cycle of interaction between cell and systems biologists advances the goals of both fields and establishes a framework for mechanistic understanding of the genome-to-phenome relationship. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Discrimination between biological interfaces and crystal-packing contacts

Directory of Open Access Journals (Sweden)

Yuko Tsuchiya

2008-11-01

Full Text Available Yuko Tsuchiya1, Haruki Nakamura2, Kengo Kinoshita1,31Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo, 108-8639, Japan; 2Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan; 3Bioinformatics Research and Development, JST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, JapanAbstract: A discrimination method between biologically relevant interfaces and artificial crystal-packing contacts in crystal structures was constructed. The method evaluates protein-protein interfaces in terms of complementarities for hydrophobicity, electrostatic potential and shape on the protein surfaces, and chooses the most probable biological interfaces among all possible contacts in the crystal. The method uses a discriminator named as “COMP”, which is a linear combination of the complementarities for the above three surface features and does not correlate with the contact area. The discrimination of homo-dimer interfaces from symmetry-related crystal-packing contacts based on the COMP value achieved the modest success rate. Subsequent detailed review of the discrimination results raised the success rate to about 88.8%. In addition, our discrimination method yielded some clues for understanding the interaction patterns in several examples in the PDB. Thus, the COMP discriminator can also be used as an indicator of the “biological-ness” of protein-protein interfaces.Keywords: protein-protein interaction, complementarity analysis, homo-dimer interface, crystal-packing contact, biological interfaces

Biology-inspired AMO physics

Science.gov (United States)

Mathur, Deepak

2015-01-01

This Topical Review presents an overview of increasingly robust interconnects that are being established between atomic, molecular and optical (AMO) physics and the life sciences. AMO physics, outgrowing its historical role as a facilitator—a provider of optical methodologies, for instance—now seeks to partner biology in its quest to link systems-level descriptions of biological entities to insights based on molecular processes. Of course, perspectives differ when AMO physicists and biologists consider various processes. For instance, while AMO physicists link molecular properties and dynamics to potential energy surfaces, these have to give way to energy landscapes in considerations of protein dynamics. But there are similarities also: tunnelling and non-adiabatic transitions occur both in protein dynamics and in molecular dynamics. We bring to the fore some such differences and similarities; we consider imaging techniques based on AMO concepts, like 4D fluorescence microscopy which allows access to the dynamics of cellular processes, multiphoton microscopy which offers a built-in confocality, and microscopy with femtosecond laser beams to saturate the suppression of fluorescence in spatially controlled fashion so as to circumvent the diffraction limit. Beyond imaging, AMO physics contributes with optical traps that probe the mechanical and dynamical properties of single ‘live’ cells, highlighting differences between healthy and diseased cells. Trap methodologies have also begun to probe the dynamics governing of neural stem cells adhering to each other to form neurospheres and, with squeezed light to probe sub-diffusive motion of yeast cells. Strong field science contributes not only by providing a source of energetic electrons and γ-rays via laser-plasma accelerations schemes, but also via filamentation and supercontinuum generation, enabling mainstream collision physics into play in diverse processes like DNA damage induced by low-energy collisions to

Comparison of the effect of soft-core potentials and Coulombic potentials on bremsstrahlung during laser matter interaction

Science.gov (United States)

Pandit, Rishi R.; Becker, Valerie R.; Barrington, Kasey; Thurston, Jeremy; Ramunno, Lora; Ackad, Edward

2018-04-01

An intense, short laser pulse incident on rare-gas clusters can produce nano-plasmas containing energetic electrons. As these electrons undergo scattering, from both phonons and ions, they emit bremsstrahlung radiation. Here, we compare a theory of bremsstrahlung emission appropriate for the interaction of intense lasers with matter using soft-core potentials and Coulombic potentials. A new scaling for the radiation cross-section and the radiated power via bremsstrahlung is derived for a soft-core potential (which depends on the potential depth) and compared with the Coulomb potential. Calculations using the new scaling are performed for electrons in vacuum ultraviolet, infrared and mid-infrared laser pulses. The radiation cross-section and the radiation power via bremsstrahlung are found to increase rapidly with increases in the potential depth of up to around 200 eV and then become mostly saturated for larger depths while remaining constant for the Coulomb potential. In both cases, the radiation cross-section and the radiation power of bremsstrahlung decrease with increases in the laser wavelength. The ratio of the scattering amplitude for the soft-core potential and that for the Coulombic potential decreases exponentially with an increase in momentum transfer. The bremsstrahlung emission by electrons in plasmas may provide a broadband light source for diagnostics.

Single-particle potential of the Λ hyperon in nuclear matter with chiral effective field theory NLO interactions including effects of Y N N three-baryon interactions

Science.gov (United States)

Kohno, M.

2018-03-01

Adopting hyperon-nucleon and hyperon-nucleon-nucleon interactions parametrized in chiral effective field theory, single-particle potentials of the Λ and Σ hyperons are evaluated in symmetric nuclear matter and in pure neutron matter within the framework of lowest-order Bruckner theory. The chiral NLO interaction bears strong Λ N -Σ N coupling. Although the Λ potential is repulsive if the coupling is switched off, the Λ N -Σ N correlation brings about the attraction consistent with empirical data. The Σ potential is repulsive, which is also consistent with empirical information. The interesting result is that the Λ potential becomes shallower beyond normal density. This provides the possibility of solving the hyperon puzzle without introducing ad hoc assumptions. The effects of the Λ N N -Λ N N and Λ N N -Σ N N three-baryon forces are considered. These three-baryon forces are first reduced to normal-ordered effective two-baryon interactions in nuclear matter and then incorporated in the G -matrix equation. The repulsion from the Λ N N -Λ N N interaction is of the order of 5 MeV at normal density and becomes larger with increasing density. The effects of the Λ N N -Σ N N coupling compensate the repulsion at normal density. The net effect of the three-baryon interactions on the Λ single-particle potential is repulsive at higher densities.

The Dark Matter of Biology.

Science.gov (United States)

Ross, Jennifer L

2016-09-06

The inside of the cell is full of important, yet invisible species of molecules and proteins that interact weakly but couple together to have huge and important effects in many biological processes. Such "dark matter" inside cells remains mostly hidden, because our tools were developed to investigate strongly interacting species and folded proteins. Example dark-matter species include intrinsically disordered proteins, posttranslational states, ion species, and rare, transient, and weak interactions undetectable by biochemical assays. The dark matter of biology is likely to have multiple, vital roles to regulate signaling, rates of reactions, water structure and viscosity, crowding, and other cellular activities. We need to create new tools to image, detect, and understand these dark-matter species if we are to truly understand fundamental physical principles of biology. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Fungal phytotoxins with potential herbicidal activity: chemical and biological characterization.

Science.gov (United States)

Cimmino, Alessio; Masi, Marco; Evidente, Marco; Superchi, Stefano; Evidente, Antonio

2015-12-19

Covering: 2007 to 2015 Fungal phytotoxins are secondary metabolites playing an important role in the induction of disease symptoms interfering with host plant physiological processes. Although fungal pathogens represent a heavy constraint for agrarian production and for forest and environmental heritage, they can also represent an ecofriendly alternative to manage weeds. Indeed, the phytotoxins produced by weed pathogenic fungi are an efficient tool to design natural, safe bioherbicides. Their use could avoid that of synthetic pesticides causing resistance in the host plants and the long term impact of residues in agricultural products with a risk to human and animal health. The isolation and structural and biological characterization of phytotoxins produced by pathogenic fungi for weeds, including parasitic plants, are described. Structure activity relationships and mode of action studies for some phytotoxins are also reported to elucidate the herbicide potential of these promising fungal metabolites.

A canonical correlation analysis-based dynamic bayesian network prior to infer gene regulatory networks from multiple types of biological data.

Science.gov (United States)

Baur, Brittany; Bozdag, Serdar

2015-04-01

One of the challenging and important computational problems in systems biology is to infer gene regulatory networks (GRNs) of biological systems. Several methods that exploit gene expression data have been developed to tackle this problem. In this study, we propose the use of copy number and DNA methylation data to infer GRNs. We developed an algorithm that scores regulatory interactions between genes based on canonical correlation analysis. In this algorithm, copy number or DNA methylation variables are treated as potential regulator variables, and expression variables are treated as potential target variables. We first validated that the canonical correlation analysis method is able to infer true interactions in high accuracy. We showed that the use of DNA methylation or copy number datasets leads to improved inference over steady-state expression. Our results also showed that epigenetic and structural information could be used to infer directionality of regulatory interactions. Additional improvements in GRN inference can be gleaned from incorporating the result in an informative prior in a dynamic Bayesian algorithm. This is the first study that incorporates copy number and DNA methylation into an informative prior in dynamic Bayesian framework. By closely examining top-scoring interactions with different sources of epigenetic or structural information, we also identified potential novel regulatory interactions.

Single-Molecule Sensing with Nanopore Confinement: from Chemical Reactions to Biological Interactions.

Science.gov (United States)

Lin, Yao; Ying, Yi-Lun; Gao, Rui; Long, Yi-Tao

2018-03-25

The nanopore can generate an electrochemical confinement for single-molecule sensing which help understand the fundamental chemical principle in nanoscale dimensions. By observing the generated ionic current, individual bond-making and bond-breaking steps, single biomolecule dynamic conformational changes and electron transfer processes that occur within pore can be monitored with high temporal and current resolution. These single-molecule studies in nanopore confinement are revealing information about the fundamental chemical and biological processes that cannot be extracted from ensemble measurements. In this concept, we introduce and discuss the electrochemical confinement effects on single-molecule covalent reactions, conformational dynamics of individual molecules and host-guest interactions in protein nanopores. Then, we extend the concept of nanopore confinement effects to confine electrochemical redox reactions in solid-state nanopores for developing new sensing mechanisms. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interaction of a pulsed alexandrite laser with hard and soft biological tissue

Science.gov (United States)

Paterson, Lorna M.; Dickinson, Mark R.; King, Terence A.; Watts, David C.

1994-02-01

An alexandrite laser has been used in the fixed-Q and Q-switched modes, at the fundamental and frequency doubled wavelengths on a selection of hard and soft tissue. In an investigation into the potential use of the laser for the removal of deep lying lesions such as cutaneous vascular lesions and tatoos, studies have been carried out to characterize the depth and extent of the laser/tissue interaction in samples of tissue which greatly absorb the 750 nm radiation. The interaction of the laser radiation with extracted teeth was investigated looking at healthy enamel and dentine, and caries. Surface profile measurements of the enamel and dentine before and after irradiation show little physical effect of the laser irradiation, whereas caries appear to be ablated.

Biological and Docking Studies of Sulfonamide Derivatives of 4-Aminophenazone

International Nuclear Information System (INIS)

Akhtar, M.S.; Ismail, A.; Murtaza, S.; Shamim, S.; Tahir, M.N.; Usman Ali Rana, U.A.

2016-01-01

Sulfonamide derivatives of 4-aminophenazone (4APZ) were synthesized and accordingly characterized by spectroscopic techniques. These newly synthesized compounds were examined for their biological activities such as enzyme inhibition, analgesic, antibacterial, antioxidant and DNA interaction. A direct correlation between enzyme inhibition activity and concentration of the compounds was observed both by experimental and molecular docking studies. Analgesic activity of the compounds was investigated by formalin-induced paw licking (FIPL), acetic acid-induced writhing (AIW) and heat conduction methods in mice. Membrane stabilization effect was determined by hypotonicity-induced hemolysis. Bacterial strains, S. aureus, S. epidermidis, B. subtilis, E. coli, P. aeruginosa, S. mutans and A. odontolyticus were used for investigating the antibacterial potential of the compounds. Antioxidant potential was investigated by Ferric Reducing Antioxidant Power assay (FRAP) and DPPH free radical scavenging method. DNA interaction studies of the synthesized compounds showed weak interaction. Hyperchromic effect was observed along the series and large positive K values were obtained for most of the compounds. (author)

Interaction potentials for multiquark states from instantons and other background gauge field configurations

International Nuclear Information System (INIS)

Warner, R.C.; Joshi, G.C.

1979-01-01

A simple rule is presented for calculating the contributions to the interaction potentials between constituent particles for a family of multiquark states, due to the presence of a semi-classical gauge field configuration which exists in a single SU(2) subgroup of colour SU(3). In multiquark states beyond the baryon many-body potential terms are found. The static (Wilson loop) limit is sufficient to elucidate the dependence of the potential on the colour structure of the multiquark state

The potential roles of biological soil crusts in dryland hydrologic cycles

Science.gov (United States)

Belnap, J.

2006-01-01

Biological soil crusts (BSCs) are the dominant living cover in many drylands of the world. They possess many features that can influence different aspects of local hydrologic cycles, including soil porosity, absorptivity, roughness, aggregate stability, texture, pore formation, and water retention. The influence of biological soil crusts on these factors depends on their internal and external structure, which varies with climate, soil, and disturbance history. This paper presents the different types of biological soil crusts, discusses how crust type likely influences various aspects of the hydrologic cycle, and reviews what is known and not known about the influence of biological crusts on sediment production and water infiltration versus runoff in various drylands around the world. Most studies examining the effect of biological soil crusts on local hydrology are done by comparing undisturbed sites with those recently disturbed by the researchers. Unfortunately, this greatly complicates interpretation of the results. Applied disturbances alter many soil features such as soil texture, roughness, aggregate stability, physical crusting, porosity, and bulk density in ways that would not necessarily be the same if crusts were not naturally present. Combined, these studies show little agreement on how biological crusts affect water infiltration or runoff. However, when studies are separated by biological crust type and utilize naturally occurring differences among these types, results indicate that biological crusts in hyperarid regions reduce infiltration and increase runoff, have mixed effects in and regions, and increase infiltration and reduce runoff in semiarid cool and cold drylands. However, more studies are needed before broad generalizations can be made on how biological crusts affect infiltration and runoff. We especially need studies that control for sub-surface soil features such as bulk density, micro- and macropores, and biological crust structure. Unlike

Systems Biology and Health Systems Complexity in;

NARCIS (Netherlands)

Donald Combs, C.; Barham, S.R.; Sloot, P.M.A.

2016-01-01

Systems biology addresses interactions in biological systems at different scales of biological organization, from the molecular to the cellular, organ, organism, societal, and ecosystem levels. This chapter expands on the concept of systems biology, explores its implications for individual patients

Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity

DEFF Research Database (Denmark)

Green, Sara; Serban, Maria; Scholl, Raphael

2018-01-01

of biological networks using tools from graph theory to the application of dynamical systems theory to understand the behavior of complex biological systems. We show how network approaches support and extend traditional mechanistic strategies but also offer novel strategies for dealing with biological...... strategies? When and how can network and mechanistic approaches interact in productive ways? In this paper we address these questions by focusing on how biological networks are represented and analyzed in a diverse class of case studies. Our examples span from the investigation of organizational properties...

Neutron interactions with biological tissue. Progress report, December 1, 1993--November 30, 1994

International Nuclear Information System (INIS)

1994-01-01

An attempt is made to obtain information about the physical stage of neutron interactions with tissue through secondary charged particles. The authors use theoretical calculations whose input includes neutron cross section data; range, stopping power, ion yield, and straggling information; and geometrical properties. Outputs are initial and slowing-down spectra of charged particles, kerma factors, average values of quality factors, microdosimetric spectra, and integral microdosimetric parameters such as bar y F , bar y D , y * . Since it has become apparent that nanometer site sizes are more relevant to radiobiological effects, the calculations of event size spectra and their parameters have been extended to these smaller diameters. This information is basic to radiological physics, radiation biology, radiation protection of workers, and standards for neutron dose measurement

Intermolecular interaction potentials of the methane dimer from the local density approximation

International Nuclear Information System (INIS)

Chen Xiangrong; Bai Yulin; Zhu Jun; Yang Xiangdong

2004-01-01

The intermolecular interaction potentials of methane (CH 4 ) dimer are calculated within the density functional theory in the local density approximation (LDA). It is found that the calculated potentials have minima when the intermolecular distance of CH 4 dimer is about 7.0 a.u., which is in good agreement with the experiment. The depth of the potential is 0.017 eV. The results obtained by our LDA calculations seem to agree well with those obtained by MP2, MP3, and CCSD from the Moeller-Plesset and coupled cluster methods by Tsuzuki et al. and with the experimental data

Influence of Solvent-Solvent and Solute-Solvent Interaction Properties on Solvent-Mediated Potential

International Nuclear Information System (INIS)

Zhou Shiqi

2005-01-01

A recently proposed universal calculational recipe for solvent-mediated potential is applied to calculate excess potential of mean force between two large Lennard-Jones (LJ) or hard core attractive Yukawa particles immersed in small LJ solvent bath at supercritical state. Comparison between the present prediction with a hypernetted chain approximation adopted for solute-solute correlation at infinitely dilute limit and existing simulation data shows high accuracy for the region with large separation, and qualitative reliability for the solute particle contact region. The calculational simplicity of the present recipe allows for a detailed investigation on the effect of the solute-solvent and solvent-solvent interaction details on the excess potential of mean force. The resultant conclusion is that gathering of solvent particles near a solute particle leads to repulsive excess PMF, while depletion of solvent particles away from the solute particle leads to attractive excess PMF, and minor change of the solvent-solvent interaction range has large influence on the excess PMF.

Adverse event potentially due to an interaction between ibrutinib and verapamil: a case report.

Science.gov (United States)

Lambert Kuhn, E; Levêque, D; Lioure, B; Gourieux, B; Bilbault, P

2016-02-01

Ibrutinib is a recently approved oral anticancer agent with pharmacokinetics that is very sensitive to metabolic inhibition. We report a serious side effect of ibrutinib potentially attributable to interaction with the moderate CYP3A4 inhibitor verapamil. A patient with mantle cell lymphoma was admitted to our emergency department with severe diarrhoea. During a prescription review, the clinical pharmacist identified a potential drug interaction between ibrutinib and verapamil present in a branded combination product also containing trandolapril. Ibrutinib was discontinued for 5 days, and verapamil was stopped. Lercanidipine 10 mg daily was prescribed as an alternative antihypertensive drug. The patient was discharged after 3 days with symptomatic treatment for his diarrhoea. Three months later, the patient maintained control with ibrutinib and olmesartan, but without verapamil. This is the first description of a serious side effect of ibrutinib likely due to an interaction with the CYP3A4 inhibitor verapamil. Prescriptions of ibrutinib must be carefully checked to identify possible interactions with CYP3A4 inhibitors and patients monitored accordingly. © 2016 John Wiley & Sons Ltd.

Biological General Repository for Interaction Datasets (BioGRID)

Data.gov (United States)

U.S. Department of Health & Human Services — BioGRID is an online interaction repository with data on raw protein and genetic interactions from major model organism species. All interaction data are freely...

Assessing the Soil Physiological Potential Using Pedo-Biological Diagnosis Under Minimum-Tillage System and Mineral Fertilization

Directory of Open Access Journals (Sweden)

Lazar Bireescu

2014-11-01

Full Text Available The main objective of sustainable agriculture is the protection of environment and natural vegetal and soil resources. Accordingly, the objective of this research was to assess the impact of technological systems by minimum tillage on soil biological activity, using the Pedo-Biological Diagnosis of Soil Resources. Our research was conducted on haplic chernozem from Experimental Station of UASVM of Iasi, Romania, during the seasonal dynamic, to the soybean crop, on unfertilized and fertilized agrofond, using moderate mineral doses (N80P80 as average of 2009–2010 period, under minimum tillage (2x disk, paraplow, chisel compared to conventional (plugging at 20 cm and 30 cm. In the case of soil works with chisel and paraplow without return of furrow, the Pedo-Biological Diagnosis highlights an increase of soil physiological potential, in the both variants (unfertilized and fertilized, unlike the method of alternating the depth of plugging that proved to be ineffective.

Molecular and biological interactions in colorectal cancer

NARCIS (Netherlands)

Heer, Pieter de

2007-01-01

The current thesis discusses the use of molecular and biological tumor markers to predict clinical outcome. By studying several key processes in the develepment of cancer as regulation of cell motility (non-receptor protein tyrosin adesion kinases, FAK, Src and paxillin, Apoptosis (caspase-3

Mutagenic potential scale developed for relative evaluation of biological system response to environments presenting different gamma exposure rates

International Nuclear Information System (INIS)

Nouailhetas, Yannick; Almeida, Carlos E. Bonacossa de; Mezrahi, Arnaldo; Shu, Jane; Xavier, Ana Maria

1999-01-01

The elaboration of a mutagenic potential scale (MPS) will be accomplished through the evaluation of the frequency of induced mutations in a plant biological system in different sites. The selection of these sites will be based on general public perception of risk to health. In this selection, it will include areas such ecological paradises and also neighborhoods of nuclear reactors and uranium mining and milling industry with potential radiological impact. The developed project foresees the contribution of other research groups that will also provide data from different sites. The referred scale will be built based on the response of the genetic system that gives color to the cells of Tradescantia (BNL 4430) stamen hair to mutagenic agents. Methodological improvements has been developed aiming the computerization of mutagenic events evaluation and statistical analysis of data that will significantly increase the efficiency of the system and obtention of results. Other biological systems of environmental quality are being added to the project, for future use. MPS should facilitate the general public and professionals of the nuclear area to understand risks, on a biological basis, of exposure from radiologically impacted environments. (author)

Tunable interactions between paramagnetic colloidal particles driven in a modulated ratchet potential.

Science.gov (United States)

Straube, Arthur V; Tierno, Pietro

2014-06-14

We study experimentally and theoretically the interactions between paramagnetic particles dispersed in water and driven above the surface of a stripe patterned magnetic garnet film. An external rotating magnetic field modulates the stray field of the garnet film and generates a translating potential landscape which induces directed particle motion. By varying the ellipticity of the rotating field, we tune the inter-particle interactions from net repulsive to net attractive. For attractive interactions, we show that pairs of particles can approach each other and form stable doublets which afterwards travel along the modulated landscape at a constant mean speed. We measure the strength of the attractive force between the moving particles and propose an analytically tractable model that explains the observations and is in quantitative agreement with experiment.

Astronomy education through interactive materials

Science.gov (United States)

Voelzke, Marcos Rincon; Antunes de Macêdo, Josué

2015-08-01

This study presents results of a survey conducted at the Federal Institution of Education, Science and Technology in the North of Minas Gerais (IFNMG), and aimed to investigate the potentialities of the use of interactive materials in the teaching of astronomy. An advanced training course with involved learning activities about basic concepts of astronomy was offered to thirty-two Licenciate students in Physics, Mathematics and Biological Sciences, using the mixed methodology, combined with the three pedagogical moments. Among other aspects, the viability of the use of resources was noticed, involving digital technologies and interactive materials on teaching of astronomy, which may contribute to the broadening of methodological options for future teachers and meet their training needs.

Frequency of potential interactions between drugs in medical prescriptions in a city in southern Brazil

Directory of Open Access Journals (Sweden)

Genici Weyh Bleich

Full Text Available CONTEXT AND OBJECTIVE: Drug interactions form part of current clinical practice and they affect between 3 and 5% of polypharmacy patients. The aim of this study was to identify the frequency of potential drug-drug interactions in prescriptions for adult and elderly patients. TYPE OF STUDY AND SETTING: Cross-sectional pharmacoepidemiological survey in the Parque Verde housing project, municipality of Cascavel, Paraná, Brazil, between December 2006 and February 2007. METHODS: Stratified cluster sampling, proportional to the total number of homes in the housing project, was used. The sample consisted of 95 homes and 96 male or female patients aged 19 or over, with medical prescriptions for at least two pharmaceutical drugs. Interactions were identified using DrugDigest, Medscape and Micromedex softwares. RESULTS: Most of the patients were female (69.8%, married (59.4% and in the age group of 60 years or over (56.3%, with an income less than or equal to three minimum monthly salaries (81.3% and less than eight years of schooling (69.8%; 90.6% of the patients were living with another person. The total number of pharmaceutical drugs was 406 (average of 4.2 medications per patient. The drugs most prescribed were antihypertensives (47.5%. The frequency of drug interactions was 66.6%. Among the 154 potential drug interactions, 4.6% were classified as major, 65.6% as moderate and 20.1% as minor. CONCLUSION: The high frequency of drug prescriptions with a potential for differentiated interactions indicates a situation that has so far been little explored, albeit a reality in household surveys.

The Prevalence of Potential Drug Interactions Among Critically Ill Elderly Patients in the Intensive Care Unit (ICU

Directory of Open Access Journals (Sweden)

Hossein Rafiei

2012-01-01

Full Text Available Objectives: The aim of the research was to determine prevalence of potential drug interactions among elderly patients in the Shahid Bahonar ICU in Kerman. Methods & Materials: In this cross sectional study, data about all elderly patients who were admitted in the intensive care unit from 1/4/2009 to 1/4/2010 were retrieved from medical records and evaluated with regard to the number and type of drug interactions, the number of drugs administered, age, sex, length of stay in the ICU, and the number of doctors prescribing medications of medications administered. The extent and number of drug interactions were investigated based on the reference textbook Drug Interaction Facts and in order to analyze the data collected, using SPSS 18 and according to study goals, a descriptive test, Pierson's correlation test, an independent T-test and a one-way ANOVA were used. Results: In total, 77 types of drugs and 394 drugs were prescribed with a mean of 5.6(SD=1.5 drugs per patient. A total of 108 potential drug interactions were found related to drugs prescribed during the first twenty-four hours. In terms of the type of drug interactions, delayed, moderate and possible types comprised the highest proportion of drug interactions. The four major interactions were between cimetidine and methadone, furosemide and amikacine, phenytoin and dopamine, and heparin and aspirin. The results of Pierson's correlation test were inicative of a positive correlation between the number of potential drug interactions and that of the drugs prescribed (r=0.563, P<0.05. Results of a one-way ANOVA showed that the mean number of potential drug interaction were significantly higher in those who died than in other patients (P<0.05. Conclusion: Elderly patients who are admitted to the intensive care unit are at a high risk of developing drug interactions and better care must be taken by medical team members.

Potential herb-drug interactions found in a community pharmacy patients

OpenAIRE

C. Batista; C. Pinho; M. Castel-Branco; M. Caramona; I. Figueiredo

2015-01-01

Phytotherapy has always played a leading role in therapeutics. However, a strong knowledge of the risk-benefit relationship of herbal products by patients and health professionals is necessary. The goals of this study were to characterize the consumption pattern of medicinal plants in patients in a community pharmacy, identify potential herb-drug interactions, and establish a list of recommendations for health professionals and/or patients in order to prevent/minimize negative outcomes arisin...

First Evaluation of the Biologically Active Substances and Antioxidant Potential of Regrowth Velvet Antler by means of Multiple Biochemical Assays

Directory of Open Access Journals (Sweden)

Yujiao Tang

2015-01-01

Full Text Available We investigated the biologically active substances contained in RVA (regrowth velvet antler by comparing the composition of biologically active substances and antioxidant potential of different antler segments. RVA was subjected to extraction using DW (distilled water. RVA was divided into 3 segments: T-RVA (top RVA, M-RVA (middle RVA, and B-RVA (base RVA. The T-RVA section possessed the greatest amounts of uronic acid (36.251 mg/g, sulfated GAGs (sulfated glycosaminoglycans (555.76 mg/g, sialic acid (111.276 mg/g, uridine (0.957 mg/g, uracil (1.084 mg/g, and hypoxanthine (1.2631 mg/g. In addition, the T-RVA section possessed the strongest antioxidant capacity as determined by DPPH, H2O2 (hydrogen peroxide, hydroxyl, and ABTS (2,2′-azinobis-3-ethylbenzthiazoline-6-sulphonate radical scavenging activity as well as FRAP (ferric reducing antioxidant power and ORAC (oxygen radical absorbance capacity. The values of those were 53.44, 23.09, 34.12, 60.31, and 35.81 TE/μM at 1 mg/mL and 113.57 TE/μM at 20 μg/mL. These results indicate that the T-RVA section possesses the greatest amount of biologically active substances and highest antioxidant potential. This is the first report on the biologically active substances and antioxidant potential of RVA.

Charged patchy particle models in explicit salt: Ion distributions, electrostatic potentials, and effective interactions.

Science.gov (United States)

Yigit, Cemil; Heyda, Jan; Dzubiella, Joachim

2015-08-14

We introduce a set of charged patchy particle models (CPPMs) in order to systematically study the influence of electrostatic charge patchiness and multipolarity on macromolecular interactions by means of implicit-solvent, explicit-ion Langevin dynamics simulations employing the Gromacs software. We consider well-defined zero-, one-, and two-patched spherical globules each of the same net charge and (nanometer) size which are composed of discrete atoms. The studied mono- and multipole moments of the CPPMs are comparable to those of globular proteins with similar size. We first characterize ion distributions and electrostatic potentials around a single CPPM. Although angle-resolved radial distribution functions reveal the expected local accumulation and depletion of counter- and co-ions around the patches, respectively, the orientation-averaged electrostatic potential shows only a small variation among the various CPPMs due to space charge cancellations. Furthermore, we study the orientation-averaged potential of mean force (PMF), the number of accumulated ions on the patches, as well as the CPPM orientations along the center-to-center distance of a pair of CPPMs. We compare the PMFs to the classical Derjaguin-Verwey-Landau-Overbeek theory and previously introduced orientation-averaged Debye-Hückel pair potentials including dipolar interactions. Our simulations confirm the adequacy of the theories in their respective regimes of validity, while low salt concentrations and large multipolar interactions remain a challenge for tractable theoretical descriptions.

Global mapping of miRNA-target interactions in cattle (Bos taurus)

DEFF Research Database (Denmark)

Scheel, Troels K H; Moore, Michael J; Luna, Joseph M

2017-01-01

With roles in development, cell proliferation and disease, micro-RNA (miRNA) biology is of great importance and a potential therapeutic target. Here we used cross-linking immunoprecipitation (CLIP) and ligation of miRNA-target chimeras on the Argonaute (AGO) protein to globally map miRNA interact...

Gene-environment interaction in Major Depression: focus on experience-dependent biological systems

Directory of Open Access Journals (Sweden)

Nicola eLopizzo

2015-05-01

Full Text Available Major Depressive Disorder (MDD is a multifactorial and polygenic disorder, where multiple and partially overlapping sets of susceptibility genes interact each other and with the environment, predisposing individuals to the development of the illness. Thus, MDD results from a complex interplay of vulnerability genes and environmental factors that act cumulatively throughout individual's lifetime. Among these environmental factors, stressful life experiences, especially those occurring early in life, have been suggested to exert a crucial impact on brain development, leading to permanent functional changes that may contribute to life long risk for mental health outcomes. In this review we will discuss how genetic variants (polymorphisms, SNPs within genes operating in neurobiological systems that mediate stress response and synaptic plasticity, can impact, by themselves, the vulnerability risk for MDD; we will also consider how this MDD risk can be further modulated when gene X environment interaction is taken into account. Finally, we will discuss the role of epigenetic mechanisms, and in particular of DNA methylation and miRNAs expression changes, in mediating the effect of the stress on the vulnerability risk to develop MDD. Taken together, in this review we aim to underlie the role of genetic and epigenetic processes involved in stress and neuroplasticity related biological systems on development of MDD after exposure to early life stress, thereby building the basis for future research and clinical interventions.

Reconstruction of the Tip-Surface Interaction Potential by Analysis of the Brownian Motion of an Atomic Force Microscope Tip

NARCIS (Netherlands)

Willemsen, O.H.; Kuipers, L.; van der Werf, Kees; de Grooth, B.G.; Greve, Jan

2000-01-01

The thermal movement of an atomic force microscope (AFM) tip is used to reconstruct the tip-surface interaction potential. If a tip is brought into the vicinity of a surface, its movement is governed by the sum of the harmonic cantilever potential and the tip-surface interaction potential. By

The astronomy education through interactive materials

Science.gov (United States)

de Macedo, Josué Antunes; Voelzke, Marcos Rincon

2014-11-01

This study presents results of a survey conducted at the Federal Institution of Education, Science and Technology in the North of Minas Gerais (IFNMG), and aimed to investigate the potentialities of the use of interactive materials in the teaching of astronomy. An advanced training course with involved learning activities about basic concepts of astronomy was offered to thirty-two Licenciate students in Physics, Mathematics and Biological Sciences, using three pedagogical moments. Among other aspects, the viability of the use of resources was noticed, involving digital technologies and interactive materials on teaching of astronomy, which may contribute to the broadening of methodological options for future teachers and meet their training needs

MOLNs: A CLOUD PLATFORM FOR INTERACTIVE, REPRODUCIBLE, AND SCALABLE SPATIAL STOCHASTIC COMPUTATIONAL EXPERIMENTS IN SYSTEMS BIOLOGY USING PyURDME.

Science.gov (United States)

Drawert, Brian; Trogdon, Michael; Toor, Salman; Petzold, Linda; Hellander, Andreas

2016-01-01

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools and a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments.

Social traits, social networks and evolutionary biology.

Science.gov (United States)

Fisher, D N; McAdam, A G

2017-12-01

effects) provides the potential to understand how entire networks of social interactions in populations influence phenotypes and predict how these traits may evolve. By theoretical integration of social network analysis and quantitative genetics, we hope to identify areas of compatibility and incompatibility and to direct research efforts towards the most promising areas. Continuing this synthesis could provide important insights into the evolution of traits expressed in a social context and the evolutionary consequences of complex and nuanced social phenotypes. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Mean Field Limits for Interacting Diffusions in a Two-Scale Potential

Science.gov (United States)

Gomes, S. N.; Pavliotis, G. A.

2018-06-01

In this paper, we study the combined mean field and homogenization limits for a system of weakly interacting diffusions moving in a two-scale, locally periodic confining potential, of the form considered in Duncan et al. (Brownian motion in an N-scale periodic potential, arXiv:1605.05854, 2016b). We show that, although the mean field and homogenization limits commute for finite times, they do not, in general, commute in the long time limit. In particular, the bifurcation diagrams for the stationary states can be different depending on the order with which we take the two limits. Furthermore, we construct the bifurcation diagram for the stationary McKean-Vlasov equation in a two-scale potential, before passing to the homogenization limit, and we analyze the effect of the multiple local minima in the confining potential on the number and the stability of stationary solutions.

Inelastic multiple scattering of interacting bosons in weak random potentials

International Nuclear Information System (INIS)

Geiger, Tobias

2013-01-01

Within the present thesis we develop a diagrammatic scattering theory for interacting bosons in a three-dimensional, weakly disordered potential. Based on a microscopic N-body scattering theory, we identify the relevant diagrams including elastic and inelastic collision processes that are sufficient to describe quantum transport in the regime of weak disorder. By taking advantage of the statistical properties of the weak disorder potential, we demonstrate how the N-body dynamics can be reduced to a nonlinear integral equation of Boltzmann type for the single-particle diffusive flux. A presently available alternative description - based on the Gross-Pitaevskii equation - only includes elastic collisions. In contrast, we show that far from equilibrium the presence of inelastic collisions - even for weak interaction strength - must be accounted for and can induce the full thermalization of the single-particle current. In addition, we also determine the coherent corrections to the incoherent transport, leading to the effect of coherent backscattering. For the first time, we are able to analyze the influence of inelastic collisions on the coherent backscattering signal, which lead to an enhancement of the backscattered cone in a narrow spectral window, even for increasing non-linearity. With a short recollection of the presently available experimental techniques we furthermore show how an immediate implementation of our suggested setup with confined Bose-Einstein condensates can be accomplished. Thereby, the emergence of collective and/or thermodynamic behavior from fundamental, microscopic constituents can also be assessed experimentally. In a second part of this thesis, we present first results for light scattering off strongly interacting Rydberg atoms trapped in a one-dimensional, chain-like configuration. In order to monitor the time-dependence of this interacting many-body system, we devise a weak measurement scenario for which we derive a master equation for the

Cubic–quintic long-range interactions with double well potentials

International Nuclear Information System (INIS)

Tsilifis, Panagiotis A; Kevrekidis, Panayotis G; Rothos, Vassilis M

2014-01-01

In the present work, we examine the combined effects of cubic and quintic terms of the long-range type in the dynamics of a double well potential. Employing a two-mode approximation, we systematically develop two cubic–quintic ordinary differential equations and assess the contributions of the long-range interactions in each of the relevant prefactors, gauging how to simplify the ensuing dynamical system. Finally, we obtain a reduced canonical description for the conjugate variables of relative population imbalance and relative phase between the two wells and proceed to a dynamical systems analysis of the resulting pair of ordinary differential equations. While in the case of cubic and quintic interactions of the same kind (e.g. both attractive or both repulsive), only a symmetry-breaking bifurcation can be identified, a remarkable effect that emerges e.g. in the setting of repulsive cubic but attractive quintic interactions is a ‘symmetry-restoring’ bifurcation. Namely, in addition to the supercritical pitchfork that leads to a spontaneous symmetry breaking of the antisymmetric state, there is a subcritical pitchfork that eventually reunites the asymmetric daughter branch with the antisymmetric parent one. The relevant bifurcations, the stability of the branches and their dynamical implications are examined both in the reduced (ODE) and in the full (PDE) setting. The model is argued to be of physical relevance, especially so in the context of optical thermal media. (paper)

Biomaterials-based electronics: polymers and interfaces for biology and medicine.

Science.gov (United States)

Muskovich, Meredith; Bettinger, Christopher J

2012-05-01

Advanced polymeric biomaterials continue to serve as a cornerstone for new medical technologies and therapies. The vast majority of these materials, both natural and synthetic, interact with biological matter in the absence of direct electronic communication. However, biological systems have evolved to synthesize and utilize naturally-derived materials for the generation and modulation of electrical potentials, voltage gradients, and ion flows. Bioelectric phenomena can be translated into potent signaling cues for intra- and inter-cellular communication. These cues can serve as a gateway to link synthetic devices with biological systems. This progress report will provide an update on advances in the application of electronically active biomaterials for use in organic electronics and bio-interfaces. Specific focus will be granted to covering technologies where natural and synthetic biological materials serve as integral components such as thin film electronics, in vitro cell culture models, and implantable medical devices. Future perspectives and emerging challenges will also be highlighted. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Potential pharmacokinetic interactions between antiretrovirals and medicinal plants used as complementary and African traditional medicines.

Science.gov (United States)

Müller, Adrienne C; Kanfer, Isadore

2011-11-01

The use of traditional/complementary/alternate medicines (TCAMs) in HIV/AIDS patients who reside in Southern Africa is quite common. Those who use TCAMs in addition to antiretroviral (ARV) treatment may be at risk of experiencing clinically significant pharmacokinetic (PK) interactions, particularly between the TCAMs and the protease inhibitors (PIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs). Mechanisms of PK interactions include alterations to the normal functioning of drug efflux transporters, such as P-gp and/or CYP isoenzymes, such a CYP3A4 that mediate the absorption and elimination of drugs in the small intestine and liver. Specific mechanisms include inhibition and activation of these proteins and induction via the pregnane X receptor (PXR). Several clinical studies and case reports involving ARV-herb PK interactions have been reported. St John's Wort, Garlic and Cat's Claw exhibited potentially significant interactions, each with a PI or NNRTI. The potential for these herbs to induce PK interactions with drugs was first identified in reports of in vitro studies. Other in vitro studies have shown that several African traditional medicinal (ATM) plants and extracts may also demonstrate PK interactions with ARVs, through effects on CYP3A4, P-gp and PXR. The most complex effects were exhibited by Hypoxis hemerocallidea, Sutherlandia frutescens, Cyphostemma hildebrandtii, Acacia nilotica, Agauria salicifolia and Elaeodendron buchananii. Despite a high incidence of HIV/AIDs in the African region, only one clinical study, between efavirenz and Hypoxis hemerocallidea has been conducted. However, several issues/concerns still remain to be addressed and thus more studies on ATMs are warranted in order for more meaningful data to be generated and the true potential for such interactions to be determined. Copyright © 2011 John Wiley & Sons, Ltd.

Interactions between mammalian cells and nano- or micro-sized wear particles: physico-chemical views against biological approaches.

Science.gov (United States)

Prokopovich, Polina

2014-11-01

Total joint arthroplasty (TJA) is a more and more frequent approach for the treatment of end-stage osteoarthritis in young and active adults; it successfully relieves joint pain and improves function significantly enhancing the health-related quality of life. Aseptic loosening and other wear-related complications are some of the most recurrent reasons for revision of TJA. This review focuses on current understanding of the biological reactions to prosthetic wear debris comparing in vivo and in vitro results. Mechanisms of interactions of various types of cells with metal, polymeric and ceramic wear particles are summarised. Alternative views based on multidisciplinary approaches are proposed to consider physico-chemical, surface parameters of wear particles (such as: particle size, geometry and charge) and material (particle chemical composition and its nature) with biological effects (cellular responses). Copyright © 2014 Elsevier B.V. All rights reserved.

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

OpenAIRE

Yamniuk, Aaron

2013-01-01

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

Potential of chicken by-products as sources of useful biological resources

International Nuclear Information System (INIS)

Lasekan, Adeseye; Abu Bakar, Fatimah; Hashim, Dzulkifly

2013-01-01

By-products from different animal sources are currently being utilised for beneficial purposes. Chicken processing plants all over the world generate large amount of solid by-products in form of heads, legs, bones, viscera and feather. These wastes are often processed into livestock feed, fertilizers and pet foods or totally discarded. Inappropriate disposal of these wastes causes environmental pollution, diseases and loss of useful biological resources like protein, enzymes and lipids. Utilisation methods that make use of these biological components for producing value added products rather than the direct use of the actual waste material might be another viable option for dealing with these wastes. This line of thought has consequently led to researches on these wastes as sources of protein hydrolysates, enzymes and polyunsaturated fatty acids. Due to the multi-applications of protein hydrolysates in various branches of science and industry, and the large body of literature reporting the conversion of animal wastes to hydrolysates, a large section of this review was devoted to this subject. Thus, this review reports the known functional and bioactive properties of hydrolysates derived from chicken by-products as well their utilisation as source of peptone in microbiological media. Methods of producing these hydrolysates including their microbiological safety are discussed. Based on the few references available in the literature, the potential of some chicken by-product as sources of proteases and polyunsaturated fatty acids are pointed out along with some other future applications

Potential of chicken by-products as sources of useful biological resources

Energy Technology Data Exchange (ETDEWEB)

Lasekan, Adeseye [Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor (Malaysia); Abu Bakar, Fatimah, E-mail: fatim@putra.upm.edu.my [Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor (Malaysia); Halal Products Research Institute, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor (Malaysia); Hashim, Dzulkifly [Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor (Malaysia); Halal Products Research Institute, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor (Malaysia)

2013-03-15

By-products from different animal sources are currently being utilised for beneficial purposes. Chicken processing plants all over the world generate large amount of solid by-products in form of heads, legs, bones, viscera and feather. These wastes are often processed into livestock feed, fertilizers and pet foods or totally discarded. Inappropriate disposal of these wastes causes environmental pollution, diseases and loss of useful biological resources like protein, enzymes and lipids. Utilisation methods that make use of these biological components for producing value added products rather than the direct use of the actual waste material might be another viable option for dealing with these wastes. This line of thought has consequently led to researches on these wastes as sources of protein hydrolysates, enzymes and polyunsaturated fatty acids. Due to the multi-applications of protein hydrolysates in various branches of science and industry, and the large body of literature reporting the conversion of animal wastes to hydrolysates, a large section of this review was devoted to this subject. Thus, this review reports the known functional and bioactive properties of hydrolysates derived from chicken by-products as well their utilisation as source of peptone in microbiological media. Methods of producing these hydrolysates including their microbiological safety are discussed. Based on the few references available in the literature, the potential of some chicken by-product as sources of proteases and polyunsaturated fatty acids are pointed out along with some other future applications.

Mach-Zehnder interferometry with interacting Bose-Einstein condensates in a double-well potential

International Nuclear Information System (INIS)

Berrada, T.

2014-01-01

Mach-Zehnder interferometry with interacting Bose-Einstein condensates in a double-well potential Particle-wave duality has enabled the construction of interferometers for massive particles such as electrons, neutrons, atoms or molecules. Implementing atom interferometry has required the development of analogues to the optical beam-splitters, phase shifters or recombiners to enable the coherent, i.e. phase-preserving manipulation of quantum superpositions. While initially demonstrating the wave nature of particles, atom interferometers have evolved into some of the most advanced devices for precision measurement, both for technological applications and tests of the fundamental laws of nature. Bose- Einstein condensates (BEC) of ultracold atoms are particular matter waves: they exhibit a collective many-body wave function and macroscopic coherence properties. As such, they have often been considered as an analogue to optical laser elds and it is natural to wonder whether BECs can provide to atom interferometry a similar boost as the laser brought to optical interferometry. One fundamental dierence between atomic BECs and lasers elds is the presence of atomic interactions, yielding an intrinsic non-linearity. On one hand, interactions can lead to eects destroying the phase coherence and limiting the interrogation time of trapped BEC interferometers. On the other hand, they can be used to generate nonclassical (e.g. squeezed) states to improve the sensitivity of interferometric measurements beyond the standard quantum limit (SQL). In this thesis, we present the realization of a full Mach-Zehnder interferometric sequence with trapped, interacting BECs con ned on an atom chip. Our interferometer relies on the coherent manipulation of a BEC in a magnetic double-well potential. For this purpose, we developed a novel type of matter-wave recombiner, an element which so far was missing in BEC atom optics. We have been able to exploit interactions to generate a squeezed

DeepPIV: Measuring in situ Biological-Fluid Interactions from the Surface to Benthos

Science.gov (United States)

Katija, K.; Sherman, A.; Graves, D.; Kecy, C. D.; Klimov, D.; Robison, B. H.

2015-12-01

The midwater region of the ocean (below the euphotic zone and above the benthos) is one of the largest ecosystems on our planet, yet it remains one of the least explored. Little known marine organisms that inhabit midwater have developed strategies for swimming and feeding that ultimately contributes to their evolutionary success, and may inspire engineering solutions for societally relevant challenges. Fluid mechanics governs the interactions that midwater organisms have with their physical environment, but limited access to midwater depths and lack of non-invasive methods to measure in situ small-scale fluid motions prevent these interactions from being better understood. Significant advances in underwater vehicle technologies have only recently improved access to midwater. Unfortunately, in situ small-scale fluid mechanics measurement methods are still lacking in the oceanographic community. Here we present DeepPIV, an instrumentation package that can be affixed to remotely operated underwater vehicles that quantifies small-scale fluid motions from the surface of the ocean down to 4000 m depths. Utilizing ambient, suspended particulate in the coastal regions of Monterey Bay, fluid-structure interactions are evaluated on a range of marine organisms in midwater. Initial science targets include larvaceans, biological equivalents of flapping flexible foils, that create mucus houses to filter food. Little is known about the structure of these mucus houses and the function they play in selectively filtering particles, and these dynamics can serve as particle-mucus models for human health. Using DeepPIV, we reveal the complex structures and flows generated within larvacean mucus houses, and elucidate how these structures function.

Calculation of Rydberg interaction potentials

DEFF Research Database (Denmark)

Weber, Sebastian; Tresp, Christoph; Menke, Henri

2017-01-01

The strong interaction between individual Rydberg atoms provides a powerful tool exploited in an ever-growing range of applications in quantum information science, quantum simulation and ultracold chemistry. One hallmark of the Rydberg interaction is that both its strength and angular dependence...... for calculating the required electric multipole moments and the inclusion of electromagnetic fields with arbitrary direction. We focus specifically on symmetry arguments and selection rules, which greatly reduce the size of the Hamiltonian matrix, enabling the direct diagonalization of the Hamiltonian up...

Cellulose-Hemicellulose Interactions at Elevated Temperatures Increase Cellulose Recalcitrance to Biological Conversion

Energy Technology Data Exchange (ETDEWEB)

Mittal, Ashutosh [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Himmel, Michael E [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Kumar, Rajeev [University of California, Riverside; Oak Ridge National Laboratory; ; Smith, Micholas Dean [Oak Ridge National Laboratory; University of Tennessee; Petridis, Loukas [Oak Ridge National Laboratory; University of Tennessee; Ong, Rebecca G. [Michigan Technological University; Cai, Charles M. [University of California, Riverside; Oak Ridge National Laboratory; Balan, Venkatesh [University of Houston; Dale, Bruce E. [Michigan State University; Ragauskas, Arthur J. [Oak Ridge National Laboratory; University of Tennessee; Smith, Jeremy C. [Oak Ridge National Laboratory; University of Tennessee; Wyman, Charles E. [University of California, Riverside; Oak Ridge National Laboratory

2018-01-23

It has been previously shown that cellulose-lignin droplets' strong interactions, resulting from lignin coalescence and redisposition on cellulose surface during thermochemical pretreatments, increase cellulose recalcitrance to biological conversion, especially at commercially viable low enzyme loadings. However, information on the impact of cellulose-hemicellulose interactions on cellulose recalcitrance following relevant pretreatment conditions are scarce. Here, to investigate the effects of plausible hemicellulose precipitation and re-association with cellulose on cellulose conversion, different pretreatments were applied to pure Avicel(R) PH101 cellulose alone and Avicel mixed with model hemicellulose compounds followed by enzymatic hydrolysis of resulting solids at both low and high enzyme loadings. Solids produced by pretreatment of Avicel mixed with hemicelluloses (AMH) were found to contain about 2 to 14.6% of exogenous, precipitated hemicelluloses and showed a remarkably much lower digestibility (up to 60%) than their respective controls. However, the exogenous hemicellulosic residues that associated with Avicel following high temperature pretreatments resulted in greater losses in cellulose conversion than those formed at low temperatures, suggesting that temperature plays a strong role in the strength of cellulose-hemicellulose association. Molecular dynamics simulations of hemicellulosic xylan and cellulose were found to further support this temperature effect as the xylan-cellulose interactions were found to substantially increase at elevated temperatures. Furthermore, exogenous, precipitated hemicelluloses in pretreated AMH solids resulted in a larger drop in cellulose conversion than the delignified lignocellulosic biomass containing comparably much higher natural hemicellulose amounts. Increased cellulase loadings or supplementation of cellulase with xylanases enhanced cellulose conversion for most pretreated AMH solids; however, this approach

Connecting Biology to Electronics: Molecular Communication via Redox Modality.

Science.gov (United States)

Liu, Yi; Li, Jinyang; Tschirhart, Tanya; Terrell, Jessica L; Kim, Eunkyoung; Tsao, Chen-Yu; Kelly, Deanna L; Bentley, William E; Payne, Gregory F

2017-12-01

Biology and electronics are both expert at for accessing, analyzing, and responding to information. Biology uses ions, small molecules, and macromolecules to receive, analyze, store, and transmit information, whereas electronic devices receive input in the form of electromagnetic radiation, process the information using electrons, and then transmit output as electromagnetic waves. Generating the capabilities to connect biology-electronic modalities offers exciting opportunities to shape the future of biosensors, point-of-care medicine, and wearable/implantable devices. Redox reactions offer unique opportunities for bio-device communication that spans the molecular modalities of biology and electrical modality of devices. Here, an approach to search for redox information through an interactive electrochemical probing that is analogous to sonar is adopted. The capabilities of this approach to access global chemical information as well as information of specific redox-active chemical entities are illustrated using recent examples. An example of the use of synthetic biology to recognize external molecular information, process this information through intracellular signal transduction pathways, and generate output responses that can be detected by electrical modalities is also provided. Finally, exciting results in the use of redox reactions to actuate biology are provided to illustrate that synthetic biology offers the potential to guide biological response through electrical cues. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis and Characterization of Rhodamine B-ethylenediamine-hyaluronan Acid as Potential Biological Functional Materials

Science.gov (United States)

Li, Y. L.; Wang, W. X.; Wang, Y.; Zhang, W. B.; Gong, H. M.; Liu, M. X.

2018-05-01

The purpose of this study is to synthesize and characterize fluorescent polymers, rhodamine B-ethylenediamine-hyaluronan acid (RhB-EA-HA). RhB-EA-HA was successfully synthesized by ester ammonolysis reaction and amidation reaction. Moreover, the structural properties of RhB-EA-HA were characterized by 1H-NMR spectra, UV-vis spectrometry and Fourier transform infrared spectroscopy (FT-IR). RhB-EA-HA can be grafted on the surface of silica nanomaterials, which may be potential biological functional materials for drug delivery system.

Collision kernels in the eikonal approximation for Lennard-Jones interaction potential

International Nuclear Information System (INIS)

Zielinska, S.

1985-03-01

The velocity changing collisions are conveniently described by collisional kernels. These kernels depend on an interaction potential and there is a necessity for evaluating them for realistic interatomic potentials. Using the collision kernels, we are able to investigate the redistribution of atomic population's caused by the laser light and velocity changing collisions. In this paper we present the method of evaluating the collision kernels in the eikonal approximation. We discuss the influence of the potential parameters Rsub(o)sup(i), epsilonsub(o)sup(i) on kernel width for a given atomic state. It turns out that unlike the collision kernel for the hard sphere model of scattering the Lennard-Jones kernel is not so sensitive to changes of Rsub(o)sup(i) as the previous one. Contrary to the general tendency of approximating collisional kernels by the Gaussian curve, kernels for the Lennard-Jones potential do not exhibit such a behaviour. (author)

Unified Deep Learning Architecture for Modeling Biology Sequence.

Science.gov (United States)

Wu, Hongjie; Cao, Chengyuan; Xia, Xiaoyan; Lu, Qiang

2017-10-09

Prediction of the spatial structure or function of biological macromolecules based on their sequence remains an important challenge in bioinformatics. When modeling biological sequences using traditional sequencing models, characteristics, such as long-range interactions between basic units, the complicated and variable output of labeled structures, and the variable length of biological sequences, usually lead to different solutions on a case-by-case basis. This study proposed the use of bidirectional recurrent neural networks based on long short-term memory or a gated recurrent unit to capture long-range interactions by designing the optional reshape operator to adapt to the diversity of the output labels and implementing a training algorithm to support the training of sequence models capable of processing variable-length sequences. Additionally, the merge and pooling operators enhanced the ability to capture short-range interactions between basic units of biological sequences. The proposed deep-learning model and its training algorithm might be capable of solving currently known biological sequence-modeling problems through the use of a unified framework. We validated our model on one of the most difficult biological sequence-modeling problems currently known, with our results indicating the ability of the model to obtain predictions of protein residue interactions that exceeded the accuracy of current popular approaches by 10% based on multiple benchmarks.

A Classical Potential to Model the Adsorption of Biological Molecules on Oxidized Titanium Surfaces.

Science.gov (United States)

Schneider, Julian; Ciacchi, Lucio Colombi

2011-02-08

The behavior of titanium implants in physiological environments is governed by the thin oxide layer that forms spontaneously on the metal surface and mediates the interactions with adsorbate molecules. In order to study the adsorption of biomolecules on titanium in a realistic fashion, we first build up a model of an oxidized Ti surface in contact with liquid water by means of extensive first-principles molecular dynamics simulations. Taking the obtained structure as reference, we then develop a classical potential to model the Ti/TiOx/water interface. This is based on the mapping with Coulomb and Lennard-Jones potentials of the adsorption energy landscape of single water and ammonia molecules on the rutile TiO2(110) surface. The interactions with arbitrary organic molecules are obtained via standard combination rules to established biomolecular force fields. The transferability of our potential to the case of organic molecules adsorbing on the oxidized Ti surface is checked by comparing the classical potential energy surfaces of representative systems to quantum mechanical results at the level of density functional theory. Moreover, we calculate the heat of immersion of the TiO2 rutile surface and the detachment force of a single tyrosine residue from steered molecular dynamics simulations, finding good agreement with experimental reference data in both cases. As a first application, we study the adsorption behavior of the Arg-Gly-Asp (RGD) peptide on the oxidized titanium surface, focusing particularly on the calculation of the free energy of desorption.

Factors Associated with Potential Food-Drug Interaction in Hospitalized Patients: A Cross-Sectional Study in Northeast Iran

Directory of Open Access Journals (Sweden)

Mostafa Abdollahi

2018-04-01

Full Text Available Background: The minimization of adverse food-drug interactions will improve patient care by optimizing the therapeutic effects and maintaining proper nutritional status. Aim: The aim of the present study was to find the main factors that may place the hospitalized patients at risk of potential food-drug interactions. Method: This cross-sectional, descriptive study was conducted on 400 inpatients admitted to the Department of Internal Medicine of a teaching hospital in Mashhad, Northeast Iran, within 20 March 2013 to 20 April 2013. The potential food-drug interactions were evaluated for 19 commonly prescribed medications. The main factors (e.g., age, gender, education level, number of medications, and duration of the disease that may place the patients at risk of potential food-drug interactions were analyzed for each patient. Results: Out of the 19 commonly prescribed medications, 17 drugs (89% were not properly used with respect to meal. Furthermore, 14 commonly prescribed drugs were found to have a high frequency (≥50% of potential food-drug interactions. Most of the patients (n=359, 89.8% consumed their medicines at inappropriate time with respect to meals. The results of a multiple logistic regression after adjustment for confounders revealed that the age [β=0.005, CI: 0.0-0.01; P=033], number of medications [β=0.1, CI: 0.083-0.117; P

Consensus validation of the POSAMINO (POtentially Serious Alcohol-Medication INteractions in Older adults) criteria.

LENUS (Irish Health Repository)

Holton, Alice E

2017-11-08

Older adults are particularly vulnerable to adverse effects from concurrent alcohol and medication use. However, there is limited evidence regarding the prevalence of these adverse outcomes among older adults, and there is a lack of consensus regarding what constitutes an alcohol-interactive medicine. The objective of this study was to develop an explicit list of potentially serious alcohol-medication interactions for use in older adults.

Whitebark pine facilitation at treeline: potential interactions for disruption by an invasive pathogen.

Science.gov (United States)

Tomback, Diana F; Blakeslee, Sarah C; Wagner, Aaron C; Wunder, Michael B; Resler, Lynn M; Pyatt, Jill C; Diaz, Soledad

2016-08-01

In stressful environments, facilitation often aids plant establishment, but invasive plant pathogens may potentially disrupt these interactions. In many treeline communities in the northern Rocky Mountains of the U.S. and Canada, Pinus albicaulis, a stress-tolerant pine, initiates tree islands at higher frequencies than other conifers - that is, leads to leeward tree establishment more frequently. The facilitation provided by a solitary (isolated) P. albicaulis leading to tree island initiation may be important for different life-history stages for leeward conifers, but it is not known which life-history stages are influenced and protection provided. However, P. albicaulis mortality from the non-native pathogen Cronartium ribicola potentially disrupts these facilitative interactions, reducing tree island initiation. In two Rocky Mountain eastern slope study areas, we experimentally examined fundamental plant-plant interactions which might facilitate tree island formation: the protection offered by P. albicaulis to leeward seed and seedling life-history stages, and to leeward krummholz conifers. In the latter case, we simulated mortality from C. ribicola for windward P. albicaulis to determine whether loss of P. albicaulis from C. ribicola impacts leeward conifers. Relative to other common solitary conifers at treeline, solitary P. albicaulis had higher abundance. More seeds germinated in leeward rock microsites than in conifer or exposed microsites, but the odds of cotyledon seedling survival during the growing season were highest in P. albicaulis microsites. Planted seedling survival was low among all microsites examined. Simulating death of windward P. albicaulis by C. ribicola reduced shoot growth of leeward trees. Loss of P. albicaulis to exotic disease may limit facilitation interactions and conifer community development at treeline and potentially impede upward movement as climate warms.

Mixed effects of organic farming and landscape compexity on farmland biodiversity and biological control potential across Europe

NARCIS (Netherlands)

Winqvist, C.; Bengtsson, J.; Aavik, T.; Berendse, F.; Clement, L.W.; Eggers, S.; Fischer, C.; Flohre, A.; Geiger, F.; Liira, J.

2011-01-01

1. Organic farming in Europe has been shown to enhance biodiversity locally, but potential interactions with the surrounding landscape and the potential effects on ecosystem services are less well known. 2. In cereal fields on 153 farms in five European regions, we examined how the species richness

Preliminary nutritional and biological potential of Artocarpus heterophyllus L. shell powder.

Science.gov (United States)

Sharma, Anubhuti; Gupta, Priti; Verma, A K

2015-03-01

Artocarpus heterophyllus shell powder was investigated in terms of its nutritional and biological potential. A thorough examination of shell powder demonstrated its potential as a source of minerals, β carotene and dietary fiber, which were assessed gravimetrically & spectrophotometrically. This showed 3.05 ± 0.19 g 100 g(-1) DW of alkaloids followed by saponins and tannins. Three different extracts; acetone, methanol, & mix solvent were used to evaluate phenolic & flavonoid content, antioxidant & antimicrobial activity, GC/MS screening and quantitative analysis of polyphenols. Among all, the methanol extract showed highest antioxidant activity evaluated by DPPH, FRAP & ABTS assays and was significantly correlated with phenolic and flavonoid contents. Phenolic & flavonoid content was found to be 158 ± 0.34 mg (GAE) and 10.0 ± 0.64 mg (CE) respectively. The results of antimicrobial activity showed that L. monocytogenes was more susceptible to all extracts followed by other microorganisms. Catechin, ascorbic & chlorogenic acids were identified as major polyphenols analyzed by LC-MS/MS. GC/MS analysis showed that it contains a variety of compounds with different therapeutic activities. The study revealed that A. heterophyllus shell is a good source of natural antioxidants & other bioactive compounds and can be used in cosmetics, medicines and functional food application.

Chemical Potential Dependence of the Dressed-Quark Propagator from an Effective Quark-Quark Interaction

Institute of Scientific and Technical Information of China (English)

ZONG Hong-Shi; PING Jia-Lun; SUN Wei-Min; CHANG Chao-Hsi; WANG Fan

2002-01-01

We exhibit a method for obtaining the low chemical potential dependence of the dressed quark propagatorfrom an effective quark-quark interaction model. Within this approach we explore the chemical potential dependenceof the dressed-quark propagator, which provides a means of determining the behavior of the chiral and deconfinementorder parameters. A comparison with the results of previous researches is given.

Microbial interactions with chromium: basic biological processes and applications in environmental biotechnology.

Science.gov (United States)

Gutiérrez-Corona, J F; Romo-Rodríguez, P; Santos-Escobar, F; Espino-Saldaña, A E; Hernández-Escoto, H

2016-12-01

Chromium (Cr) is a highly toxic metal for microorganisms as well as plants and animal cells. Due to its widespread industrial use, Cr has become a serious pollutant in diverse environmental settings. The hexavalent form of the metal, Cr(VI), is considered a more toxic species than the relatively innocuous and less mobile Cr(III) form. The study of the interactions between microorganisms and Cr has been helpful to unravel the mechanisms allowing organisms to survive in the presence of high concentrations of Cr(VI) and to detoxify and remove the oxyanion. Various mechanisms of interactions with Cr have been identified in diverse species of bacteria and fungi, including biosorption, bioaccumulation, reduction of Cr(VI) to Cr(III), and chromate efflux. Some of these systems have been proposed as potential biotechnological tools for the bioremediation of Cr pollution using bioreactors or by in situ treatments. In this review, the interactions of microorganisms with Cr are summarised, emphasising the importance of new research avenues using advanced methodologies, including proteomic, transcriptomic, and metabolomic analyses, as well as the use of techniques based on X-ray absorption spectroscopy and electron paramagnetic resonance spectroscopy.

Calculation of the real part of the interaction potential between two heavy ions in the sudden approximation

International Nuclear Information System (INIS)

Ngo, H.; Ngo, C.

1980-04-01

We have calculated the interaction potential between two heavy ions using the energy density formalism and Fermi distributions for the nuclear densities. The experimental fusion barriers are rather well reproduced. The conditions for the observation of fusion between two heavy ions is discussed. As far as the nuclear part of the interaction potential is concerned, the proximity scaling is investigated in details. It is found that the proximity theorem is satisfied to a good extent. However, as far as the neutron excess is concerned, a disagreement with the proximity potential is observed

Complex biological and bio-inspired systems

Energy Technology Data Exchange (ETDEWEB)

Ecke, Robert E [Los Alamos National Laboratory

2009-01-01

The understanding and characterization ofthe fundamental processes of the function of biological systems underpins many of the important challenges facing American society, from the pathology of infectious disease and the efficacy ofvaccines, to the development of materials that mimic biological functionality and deliver exceptional and novel structural and dynamic properties. These problems are fundamentally complex, involving many interacting components and poorly understood bio-chemical kinetics. We use the basic science of statistical physics, kinetic theory, cellular bio-chemistry, soft-matter physics, and information science to develop cell level models and explore the use ofbiomimetic materials. This project seeks to determine how cell level processes, such as response to mechanical stresses, chemical constituents and related gradients, and other cell signaling mechanisms, integrate and combine to create a functioning organism. The research focuses on the basic physical processes that take place at different levels ofthe biological organism: the basic role of molecular and chemical interactions are investigated, the dynamics of the DNA-molecule and its phylogenetic role are examined and the regulatory networks of complex biochemical processes are modeled. These efforts may lead to early warning algorithms ofpathogen outbreaks, new bio-sensors to detect hazards from pathomic viruses to chemical contaminants. Other potential applications include the development of efficient bio-fuel alternative-energy processes and the exploration ofnovel materials for energy usages. Finally, we use the notion of 'coarse-graining,' which is a method for averaging over less important degrees of freedom to develop computational models to predict cell function and systems-level response to disease, chemical stress, or biological pathomic agents. This project supports Energy Security, Threat Reduction, and the missions of the DOE Office of Science through its efforts to

An ontology-based search engine for protein-protein interactions.

Science.gov (United States)

Park, Byungkyu; Han, Kyungsook

2010-01-18

Keyword matching or ID matching is the most common searching method in a large database of protein-protein interactions. They are purely syntactic methods, and retrieve the records in the database that contain a keyword or ID specified in a query. Such syntactic search methods often retrieve too few search results or no results despite many potential matches present in the database. We have developed a new method for representing protein-protein interactions and the Gene Ontology (GO) using modified Gödel numbers. This representation is hidden from users but enables a search engine using the representation to efficiently search protein-protein interactions in a biologically meaningful way. Given a query protein with optional search conditions expressed in one or more GO terms, the search engine finds all the interaction partners of the query protein by unique prime factorization of the modified Gödel numbers representing the query protein and the search conditions. Representing the biological relations of proteins and their GO annotations by modified Gödel numbers makes a search engine efficiently find all protein-protein interactions by prime factorization of the numbers. Keyword matching or ID matching search methods often miss the interactions involving a protein that has no explicit annotations matching the search condition, but our search engine retrieves such interactions as well if they satisfy the search condition with a more specific term in the ontology.

Evolutionary potential games on lattices

Energy Technology Data Exchange (ETDEWEB)

Szabó, György, E-mail: szabo@mfa.kfki.hu; Borsos, István, E-mail: borsos@mfa.kfki.hu

2016-04-05

Game theory provides a general mathematical background to study the effect of pair interactions and evolutionary rules on the macroscopic behavior of multi-player games where players with a finite number of strategies may represent a wide scale of biological objects, human individuals, or even their associations. In these systems the interactions are characterized by matrices that can be decomposed into elementary matrices (games) and classified into four types. The concept of decomposition helps the identification of potential games and also the evaluation of the potential that plays a crucial role in the determination of the preferred Nash equilibrium, and defines the Boltzmann distribution towards which these systems evolve for suitable types of dynamical rules. This survey draws parallel between the potential games and the kinetic Ising type models which are investigated for a wide scale of connectivity structures. We discuss briefly the applicability of the tools and concepts of statistical physics and thermodynamics. Additionally the general features of ordering phenomena, phase transitions and slow relaxations are outlined and applied to evolutionary games. The discussion extends to games with three or more strategies. Finally we discuss what happens when the system is weakly driven out of the “equilibrium state” by adding non-potential components representing games of cyclic dominance.

Evolutionary potential games on lattices

International Nuclear Information System (INIS)

Szabó, György; Borsos, István

2016-01-01

Game theory provides a general mathematical background to study the effect of pair interactions and evolutionary rules on the macroscopic behavior of multi-player games where players with a finite number of strategies may represent a wide scale of biological objects, human individuals, or even their associations. In these systems the interactions are characterized by matrices that can be decomposed into elementary matrices (games) and classified into four types. The concept of decomposition helps the identification of potential games and also the evaluation of the potential that plays a crucial role in the determination of the preferred Nash equilibrium, and defines the Boltzmann distribution towards which these systems evolve for suitable types of dynamical rules. This survey draws parallel between the potential games and the kinetic Ising type models which are investigated for a wide scale of connectivity structures. We discuss briefly the applicability of the tools and concepts of statistical physics and thermodynamics. Additionally the general features of ordering phenomena, phase transitions and slow relaxations are outlined and applied to evolutionary games. The discussion extends to games with three or more strategies. Finally we discuss what happens when the system is weakly driven out of the “equilibrium state” by adding non-potential components representing games of cyclic dominance.

Evolutionary potential games on lattices