WorldWideScience

Sample records for membrane biophysics

  1. Membrane Biophysics

    CERN Document Server

    Ashrafuzzaman, Mohammad

    2013-01-01

    Physics, mathematics and chemistry all play a vital role in understanding the true nature and functioning of biological membranes, key elements of living processes. Besides simple spectroscopic observations and electrical measurements of membranes we address in this book the phenomena of coexistence and independent existence of different membrane components using various theoretical approaches. This treatment will be helpful for readers who want to understand biological processes by applying both simple observations and fundamental scientific analysis. It provides a deep understanding of the causes and effects of processes inside membranes, and will thus eventually open new doors for high-level pharmaceutical approaches towards fighting membrane- and cell-related diseases.

  2. Biophysics

    CERN Document Server

    Glaser, Roland

    1999-01-01

    The message of this book is that biophysics is the science of physical principles underlying the "phenomenon life" on all levels of organization. Rather than teaching "physics for biologists" or "physical methods applied to biology", it regards its subject as a defined discipline with its own network of ideas and approaches. The book starts by explaining molecular structures of biological systems, various kinds of atomic, molecular and ionic interactions, movements, energy transfer, self organization of supramolecular structures and dynamic properties of biological membranes. It then goes on to introduce the biological organism as a non-equilibrium system, before treating thermodynamic concepts of osmotic and electrolyte equilibria as well as currents and potential profiles. It continues with topics of environmental biophysics and such medical aspects as the influence of electromagnetic fields or radiation on living systems and the biophysics of hearing and noice protection. The book concludes with a discussi...

  3. Biophysical studies of membrane channel polypeptides

    CERN Document Server

    Galbraith, T P

    2001-01-01

    Membrane channels facilitate the flow of ions across biological membranes, a process which is important in numerous cellular functions. The study of large integral membrane proteins is made difficult by identification, production and purification problems, and detailed knowledge of their three-dimensional structures is relatively scarce. The study of simple 'model' membrane proteins has given valuable insight into the structures and dynamics of membrane proteins in general. The bacterial peptide gramicidin has been the subject of intense study for many years, and has provided important information into the structural basis of channel function. Peptaibols, a class of fungal membrane peptides which includes alamethicin and antiamoebin, have also been useful in relating structural details to molecular ion transport processes. Gramicidin crystals were grown in the presence of phospholipids with various headgroups and acyl chains. The diffraction patterns of the crystals obtained were processed, but found to be in...

  4. Chemical synthesis and biophysical applications of membrane proteins.

    Science.gov (United States)

    Zuo, Chao; Tang, Shan; Zheng, Ji-Shen

    2015-07-01

    Chemical synthesis or semi-synthesis of membrane proteins can provide unique molecular tools, such as site-specific isotope labeling or post-translationally modified membrane proteins to gain insight into their biophysical and functional characteristics. However, during preparation, purification, and ligation of transmembrane peptides, tremendous challenges are encountered owing to their hydrophobic nature. This review focuses on the recent advances in chemical synthesis strategies of membrane proteins. These strategies help to solubilize the hydrophobic transmembrane peptide sequences under standard purification and chemical ligation conditions to improve their handling properties. Biophysical and functional studies of synthetic membrane proteins are reviewed as well. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.

  5. Systems biology of cellular membranes: a convergence with biophysics.

    Science.gov (United States)

    Chabanon, Morgan; Stachowiak, Jeanne C; Rangamani, Padmini

    2017-09-01

    Systems biology and systems medicine have played an important role in the last two decades in shaping our understanding of biological processes. While systems biology is synonymous with network maps and '-omics' approaches, it is not often associated with mechanical processes. Here, we make the case for considering the mechanical and geometrical aspects of biological membranes as a key step in pushing the frontiers of systems biology of cellular membranes forward. We begin by introducing the basic components of cellular membranes, and highlight their dynamical aspects. We then survey the functions of the plasma membrane and the endomembrane system in signaling, and discuss the role and origin of membrane curvature in these diverse cellular processes. We further give an overview of the experimental and modeling approaches to study membrane phenomena. We close with a perspective on the converging futures of systems biology and membrane biophysics, invoking the need to include physical variables such as location and geometry in the study of cellular membranes. WIREs Syst Biol Med 2017, 9:e1386. doi: 10.1002/wsbm.1386 For further resources related to this article, please visit the WIREs website. © 2017 Wiley Periodicals, Inc.

  6. EDTA-induced membrane fluidization and destabilization: biophysical studies on artificial lipid membranes.

    Science.gov (United States)

    Prachayasittikul, Virapong; Isarankura-Na-Ayudhya, Chartchalerm; Tantimongcolwat, Tanawut; Nantasenamat, Chanin; Galla, Hans-Joachim

    2007-11-01

    The molecular mechanism of ethylenediaminetetraacetic acid (EDTA)-induced membrane destabilization has been studied using a combination of four biophysical techniques on artificial lipid membranes. Data from Langmuir film balance and epifluorescence microscopy revealed the fluidization and expansion effect of EDTA on phase behavior of monolayers of either 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) or mixtures of DPPC and metal-chelating lipids, such as N(alpha),N(alpha)-Bis[carboxymethyl]-N(epsilon)-[(dioctadecylamino)succinyl]-L-lysine or 1,2-dioleoyl-sn-glycero-3-[N-(5-amino-1-carboxypentyl iminodiacetic acid) succinyl]. A plausible explanation could be drawn from the electrostatic interaction between negatively charged groups of EDTA and the positively charged choline head group of DPPC. Intercalation of EDTA into the lipid membrane induced membrane curvature as elucidated by atomic force microscopy. Growth in size and shape of the membrane protrusion was found to be time-dependent upon exposure to EDTA. Further loss of material from the lipid membrane surface was monitored in real time using a quartz crystal microbalance. This indicates membrane restabilization by exclusion of the protrusions from the surface. Loss of lipid components facilitates membrane instability, leading to membrane permeabilization and lysis.

  7. Biophysics of Cell Membrane Lipids in Cancer Drug Resistance: Implications for Drug Transport and Drug Delivery with Nanoparticles

    Science.gov (United States)

    Peetla, Chiranjeevi; Vijayaraghavalu, Sivakumar; Labhasetwar, Vinod

    2013-01-01

    In this review, we focus on the biophysics of cell membrane lipids, particularly when cancers develop acquired drug resistance, and how biophysical changes in resistant cell membrane influence drug transport and nanoparticle-mediated drug delivery. Recent advances in membrane lipid research show the varied roles of lipids in regulating membrane P-glycoprotein function, membrane trafficking, apoptotic pathways, drug transport, and endocytic functions, particularly endocytosis, the primary mechanism of cellular uptake of nanoparticle-based drug delivery systems. Since acquired drug resistance alters lipid biosynthesis, understanding the role of lipids in cell membrane biophysics and its effect on drug transport is critical for developing effective therapeutic and drug delivery approaches to overcoming drug resistance. Here we discuss novel strategies for (a) modulating the biophysical properties of membrane lipids of resistant cells to facilitate drug transport and regain endocytic function and (b) developing effective nanoparticles based on their biophysical interactions with membrane lipids to enhance drug delivery and overcome drug resistance. PMID:24055719

  8. Editorial: Molecular Organization of Membranes: Where Biology Meets Biophysics

    Czech Academy of Sciences Publication Activity Database

    Cebecauer, Marek; Holowka, D.

    2017-01-01

    Roč. 5, č. 113 (2017), s. 1-3 ISSN 2296-634X Institutional support: RVO:61388955 Keywords : nanodomains * membrane properties * cell membrane Subject RIV: CE - Biochemistry OBOR OECD: Biochemistry and molecular biology

  9. Biophysics

    International Nuclear Information System (INIS)

    Danyluk, S.S.

    1975-01-01

    Research is reported on magnetic resonance spectroscopy of biological molecules, development of clinical applications of stable isotopes, circadian cybernetics, and X-ray crystallography of immunoglobulins. Biological processes occur in fluid media, and ultimately our knowledge of their mechanisms requires detailed information for chemical and molecular structural properties in biological fluids. Magnetic resonance spectroscopy has unique advantages over other approaches in this area that are being exploited in studies currently underway in the group. The program continues to develop along three interrelated lines, measurement and analysis of high resolution spectra for biological molecules (especially nucleic acid constituents and drugs), synthesis of selectively labeled nucleic acid fragments essential for complete spectral assignments, and computation of conformational properties from NMR parameters. This coordinated approach enabled the first complete conformation analysis for a dinucleoside monophosphate, ApA, in aqueous solution. It was found that the conformation is actually a time-average of right helical, loop, and extended conformations, the interchange being extremely rapid on an NMR time scale. Spectral analyses were also completed for all possible ribonucleotide dimers, the assignments again relying heavily on synthesis of appropriate deuterated counterparts. Studies of conformational flexibility in nucleic acid fragments showed that changes in hydrogen ion concentration and temperature produce correlated conformational changes specific for each nucleotidyl unit. Studies were also initiated in three new projects dealing with the effect of hapten binding on antibody structure, counter ion influence on nucleic acid free radicals, and membrane differences between normal and sickled erythrocytes

  10. 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.

  11. Plant membranes a biophysical approach to structure, development and senescence

    CERN Document Server

    Leshem, Ya’Acov Y

    1992-01-01

    The plasma membrane is at once the window through which the cell senses the environment and the portal through which the environment influences the structure and activities of the cell. Its importance in cellular physiology can thus hardly be overestimated, since constant flow of materials between cell and environment is essential to the well-being of any biological system. The nature of the materials mov­ ing into the cell is also critical, since some substances are required for maintenance and growth, while others, because of their toxicity, must either be rigorously excluded or permitted to enter only after chemical alteration. Such alteration frequently permits the compounds to be sequestered in special cellular compartments having different types of membranes. This type of homogeneity, plus the fact that the wear and tear of transmembrane molecular traffic compels the system to be constantly monitored and repaired, means that the membrane system of any organism must be both structurally complex and dy­...

  12. Biophysical characterization of membrane protein-small molecule interactions

    NARCIS (Netherlands)

    Chen, Dan

    2015-01-01

    Membrane proteins are account for up to two thirds of known druggable targets. Traditionally, new drugs against this class of proteins have been discovered through HTS. However, not all GPCRs are amenable to traditional screening methods. Recently, fragment-based drug discovery (FBDD) has emerged as

  13. Energy efficient neural stimulation: coupling circuit design and membrane biophysics.

    Directory of Open Access Journals (Sweden)

    Thomas J Foutz

    Full Text Available The delivery of therapeutic levels of electrical current to neural tissue is a well-established treatment for numerous indications such as Parkinson's disease and chronic pain. While the neuromodulation medical device industry has experienced steady clinical growth over the last two decades, much of the core technology underlying implanted pulse generators remain unchanged. In this study we propose some new methods for achieving increased energy-efficiency during neural stimulation. The first method exploits the biophysical features of excitable tissue through the use of a centered-triangular stimulation waveform. Neural activation with this waveform is achieved with a statistically significant reduction in energy compared to traditional rectangular waveforms. The second method demonstrates energy savings that could be achieved by advanced circuitry design. We show that the traditional practice of using a fixed compliance voltage for constant-current stimulation results in substantial energy loss. A portion of this energy can be recuperated by adjusting the compliance voltage to real-time requirements. Lastly, we demonstrate the potential impact of axon fiber diameter on defining the energy-optimal pulse-width for stimulation. When designing implantable pulse generators for energy efficiency, we propose that the future combination of a variable compliance system, a centered-triangular stimulus waveform, and an axon diameter specific stimulation pulse-width has great potential to reduce energy consumption and prolong battery life in neuromodulation devices.

  14. Energy efficient neural stimulation: coupling circuit design and membrane biophysics.

    Science.gov (United States)

    Foutz, Thomas J; Ackermann, D Michael; Kilgore, Kevin L; McIntyre, Cameron C

    2012-01-01

    The delivery of therapeutic levels of electrical current to neural tissue is a well-established treatment for numerous indications such as Parkinson's disease and chronic pain. While the neuromodulation medical device industry has experienced steady clinical growth over the last two decades, much of the core technology underlying implanted pulse generators remain unchanged. In this study we propose some new methods for achieving increased energy-efficiency during neural stimulation. The first method exploits the biophysical features of excitable tissue through the use of a centered-triangular stimulation waveform. Neural activation with this waveform is achieved with a statistically significant reduction in energy compared to traditional rectangular waveforms. The second method demonstrates energy savings that could be achieved by advanced circuitry design. We show that the traditional practice of using a fixed compliance voltage for constant-current stimulation results in substantial energy loss. A portion of this energy can be recuperated by adjusting the compliance voltage to real-time requirements. Lastly, we demonstrate the potential impact of axon fiber diameter on defining the energy-optimal pulse-width for stimulation. When designing implantable pulse generators for energy efficiency, we propose that the future combination of a variable compliance system, a centered-triangular stimulus waveform, and an axon diameter specific stimulation pulse-width has great potential to reduce energy consumption and prolong battery life in neuromodulation devices.

  15. Interplay of mycolic acids, antimycobacterial compounds and pulmonary surfactant membrane: a biophysical approach to disease.

    Science.gov (United States)

    Pinheiro, Marina; Giner-Casares, Juan J; Lúcio, Marlene; Caio, João M; Moiteiro, Cristina; Lima, José L F C; Reis, Salette; Camacho, Luis

    2013-02-01

    This work focuses on the interaction of mycolic acids (MAs) and two antimycobacterial compounds (Rifabutin and N'-acetyl-Rifabutin) at the pulmonary membrane level to convey a biophysical perspective of their role in disease. For this purpose, accurate biophysical techniques (Langmuir isotherms, Brewster angle microscopy, and polarization-modulation infrared reflection spectroscopy) and lipid model systems were used to mimic biomembranes: MAs mimic bacterial lipids of the Mycobacterium tuberculosis (MTb) membrane, whereas Curosurf® was used as the human pulmonary surfactant (PS) membrane model. The results obtained show that high quantities of MAs are responsible for significant changes on PS biophysical properties. At the dynamic inspiratory surface tension, high amounts of MAs decrease the order of the lipid monolayer, which appears to be a concentration dependent effect. These results suggest that the amount of MAs might play a critical role in the initial access of the bacteria to their targets. Both molecules also interact with the PS monolayer at the dynamic inspiratory surface. However, in the presence of higher amounts of MAs, both compounds improve the phospholipid packing and, therefore, the order of the lipid surfactant monolayer. In summary, this work discloses the putative protective effects of antimycobacterial compounds against the MAs induced biophysical impairment of PS lipid monolayers. These protective effects are most of the times overlooked, but can constitute an additional therapeutic value in the treatment of pulmonary tuberculosis (Tb) and may provide significant insights for the design of new and more efficient anti-Tb drugs based on their behavior as membrane ordering agents. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. Biophysics demystified

    CERN Document Server

    Goldfarb, Daniel

    2011-01-01

    Written in a step-by-step format, this practical guide begins with an introduction to the science of biophysics, covering biophysical techniques and applications. Next, you'll learn the principles of physics, biology, and chemistry required to understand biophysics, including free energy, entropy, and statistical mechanics. Biomolecules and the forces that influence their structure and conformation are also covered, as are protein, nucleic acid, and membrane biophysics. Detailed examples and concise explanations make it easy to understand the material, and end-of-chapter quizzes and a final exam help reinforce key concepts.

  17. Biophysical characterization of the Lactobacillus delbrueckii subsp. bulgaricus membrane during cold and osmotic stress and its relevance for cryopreservation.

    Science.gov (United States)

    Meneghel, Julie; Passot, Stéphanie; Dupont, Sébastien; Fonseca, Fernanda

    2017-02-01

    Freezing lactic acid bacteria often leads to cell death and loss of technological properties. Our objective was to provide an in-depth characterization of the biophysical properties of the Lactobacillus delbrueckii subsp. bulgaricus membrane in relation to its freeze resistance. Freezing was represented as a combination of cold and osmotic stress. This work investigated the relative incidence of increasing sucrose concentrations coupled or not with subzero temperatures without ice nucleation on the biological and biophysical responses of two strains with different membrane fatty acid compositions and freeze resistances. Following exposure of bacterial cells to the highest sucrose concentration, the sensitive strain exhibited a survival rate of less than 10 % and 5 h of acidifying activity loss. Similar biological activity losses were observed upon freeze-thawing and after osmotic treatment for each strain thus highlighting osmotic stress as the main source of cryoinjury. The direct measurement of membrane fluidity by fluorescence anisotropy was linked to membrane lipid organization characterized by FTIR spectroscopy. Both approaches made it possible to investigate the specific contributions of the membrane core and the bilayer external surface to cell degradation caused by cold and osmotic stress. Cold-induced membrane rigidification had no significant implication on bacterial freeze-thaw resistance. Interactions between extracellular sucrose and membrane phospholipid headgroups under osmotic stress were also observed. Such interactions were more evident in the sensitive strain and when increasing sucrose concentration, thus suggesting membrane permeabilization. The relevance of biophysical properties for elucidating mechanisms of cryoinjury and cryoprotection is discussed.

  18. Online determination of biophysical parameters of mucous membranes of a human body

    Energy Technology Data Exchange (ETDEWEB)

    Lisenko, S A; Kugeiko, M M [Belarusian State University, Minsk (Belarus)

    2013-07-31

    We have developed a method for online determination of biophysical parameters of mucous membranes (MMs) of a human body (transport scattering coefficient, scattering anisotropy factor, haemoglobin concentration, degrees of blood oxygenation, average diameter of capillaries with blood) from measurements of spectral and spatial characteristics of diffuse reflection. The method is based on regression relationships between linearly independent components of the measured light signals and the unknown parameters of MMs, obtained by simulation of the radiation transfer in the MM under conditions of its general variability. We have proposed and justified the calibration-free fibre-optic method for determining the concentration of haemoglobin in MMs by measuring the light signals diffusely reflected by the tissue in four spectral regions at two different distances from the illumination spot. We have selected the optimal wavelengths of optical probing for the implementation of the method. (laser applications in biology and medicine)

  19. Structure-function relationships in pulmonary surfactant membranes: from biophysics to therapy.

    Science.gov (United States)

    Lopez-Rodriguez, Elena; Pérez-Gil, Jesús

    2014-06-01

    Pulmonary surfactant is an essential lipid-protein complex to maintain an operative respiratory surface at the mammalian lungs. It reduces surface tension at the alveolar air-liquid interface to stabilise the lungs against physical forces operating along the compression-expansion breathing cycles. At the same time, surfactant integrates elements establishing a primary barrier against the entry of pathogens. Lack or deficiencies of the surfactant system are associated with respiratory pathologies, which treatment often includes supplementation with exogenous materials. The present review summarises current models on the molecular mechanisms of surfactant function, with particular emphasis in its biophysical properties to stabilise the lungs and the molecular alterations connecting impaired surfactant with diseased organs. It also provides a perspective on the current surfactant-based strategies to treat respiratory pathologies. This article is part of a Special Issue entitled: Membrane Structure and Function: Relevance in the Cell's Physiology, Pathology and Therapy. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Biophysical mechanism for ras-nanocluster formation and signaling in plasma membrane.

    Directory of Open Access Journals (Sweden)

    Thomas Gurry

    2009-07-01

    Full Text Available Ras GTPases are lipid-anchored G proteins, which play a fundamental role in cell signaling processes. Electron micrographs of immunogold-labeled Ras have shown that membrane-bound Ras molecules segregate into nanocluster domains. Several models have been developed in attempts to obtain quantitative descriptions of nanocluster formation, but all have relied on assumptions such as a constant, expression-level independent ratio of Ras in clusters to Ras monomers (cluster/monomer ratio. However, this assumption is inconsistent with the law of mass action. Here, we present a biophysical model of Ras clustering based on short-range attraction and long-range repulsion between Ras molecules in the membrane. To test this model, we performed Monte Carlo simulations and compared statistical clustering properties with experimental data. We find that we can recover the experimentally-observed clustering across a range of Ras expression levels, without assuming a constant cluster/monomer ratio or the existence of lipid rafts. In addition, our model makes predictions about the signaling properties of Ras nanoclusters in support of the idea that Ras nanoclusters act as an analog-digital-analog converter for high fidelity signaling.

  1. Biophysics conference 1978

    International Nuclear Information System (INIS)

    1978-01-01

    The main subject on the biophysics meeting was the biophysics of membranes with practical subjects from photosynthesis and the transfer processes on membranes. In radiation biophysics, problems of radiation sensitisation, immunological problems after radiation exposure, the oxygen effect and inhibitory processes in RNS synthesis after radiation exposure were discussed with a view to tumour therapy. (AJ) [de

  2. Optimisation of over-expression in E. coli and biophysical characterisation of human membrane protein synaptogyrin 1.

    Directory of Open Access Journals (Sweden)

    Christian Löw

    Full Text Available Progress in functional and structural studies of integral membrane proteins (IMPs is lacking behind their soluble counterparts due to the great challenge in producing stable and homogeneous IMPs. Low natural abundance, toxicity when over-expressed and potential lipid requirements of IMPs are only a few reasons for the limited progress. Here, we describe an optimised workflow for the recombinant over-expression of the human tetraspan vesicle protein (TVP synaptogyrin in Escherichia coli and its biophysical characterisation. TVPs are ubiquitous and abundant components of vesicles. They are believed to be involved in various aspects of the synaptic vesicle cycle, including vesicle biogenesis, exocytosis and endocytotic recycling. Even though TVPs are found in most cell types, high-resolution structural information for this class of membrane proteins is still missing. The optimisation of the N-terminal sequence of the gene together with the usage of the recently developed Lemo21(DE3 strain which allows the balancing of the translation with the membrane insertion rate led to a 50-fold increased expression rate compared to the classical BL21(DE3 strain. The protein was soluble and stable in a variety of mild detergents and multiple biophysical methods confirmed the folded state of the protein. Crosslinking experiments suggest an oligomeric architecture of at least four subunits. The protein stability is significantly improved in the presence of cholesteryl hemisuccinate as judged by differential light scattering. The approach described here can easily be adapted to other eukaryotic IMPs.

  3. Perfil Biofísico Fetal na Ruptura Prematura das Membranas Fetal Biophysical Profile in Premature Rupture of the Membranes

    Directory of Open Access Journals (Sweden)

    Vardeli Alves de Moraes

    2000-05-01

    modifications due to premature rupture of the membranes of variables of the fetal biophysical profile, comparing them to the ones found in pregnant women with intact membranes. In the group with premature rupture of the membranes, the association of biophysical variables with the Apgar score at the first and fifth minutes and with the occurrence or not of clinical chorioamnionitis and neonatal infection was analyzed. Patients and Methods: in a prospective study, 112 fetal biophysical profiles were established in 60 pregnant women with premature rupture of the membranes at a period between the 28th and the 40th week of pregnancy, and only the last fetal biophysical profile was analyzed and compared to other 60 fetal biophysical profiles of pregnant women with gestational ages identical to the group of study and with intact membranes. Results: statistical analysis of the results revealed that the premature rupture of the membranes diminished the reactivity, not interfering with the body movements of the fetus. It also diminished the frequency of the respiratory movements of the fetus, not determining modifications of the fetal tonus, and considerably decreasing the amniotic fluid index. In terms of prediction of chorioamnionitis and neonatal infection, the fetal biophysical profile did not show any significant statistic validity; however, when the biophysical variables were present, the correlation with the absence of chorioamnionitis and neonatal infection was clearly shown. The result of the last fetal biophysical profile was strongly associated with the Apgar score at the 5th minute. Conclusion: the fetal biophysical profile should be used routinely in pregnant women with premature rupture of the membranes with the purpose of evaluating fetal vitality, and in order to detect those fetuses at a higher risk of infection, specially those with gestational ages of less than 34 weeks. Regarding those fetuses it is best to use a conservative approach.

  4. Biophysical parameters of erythrocyte membranes and mechanisms of interaction with non-opioid analgesics under acute pain syndrome

    Directory of Open Access Journals (Sweden)

    Yu. I. Gubskyi

    2014-06-01

    Full Text Available Methods of fluorescent probing, spectrophotometry and microcalorimetry were applied to investigate the alterations in biophysical parameters of erythrocytes membranes, and specifically microviscosity, surface charge, molecular organization of lipid bilayer and lipid-protein interactions under conditions of acute pain syndrome produced by experimental chemical lesion. The distinctive features of non-opiod analgesics interactions and binding to the erythrocytes membranes of rats subjected to acute nociceptive pain accompanied with oxidative stress development were investigated. The abilities of analgesics under research, and namely paracetamol, aspirin, phenazone, ketorolac, pyrodazole, ketoprofenum, natrium mefenaminate, indometacin, nimesulide to make up physico-chemical complexes with lipoperoxidation modified erythrocytes surface and protein-lipid bilayer showed marked changes. The significance of oxidative damage of biophase under conditions of acute pain syndrome for analgesics effective pharmacodynamics and pharmacokinetics realization is under consideration.

  5. Mathematical biophysics

    CERN Document Server

    Rubin, Andrew

    2014-01-01

    This book presents concise descriptions and analysis of the classical and modern models used in mathematical biophysics. The authors ask the question "what new information can be provided by the models that cannot be obtained directly from experimental data?" Actively developing fields such as regulatory mechanisms in cells and subcellular systems and electron transport and energy transport in membranes are addressed together with more classical topics such as metabolic processes, nerve conduction and heart activity, chemical kinetics, population dynamics, and photosynthesis. The main approach is to describe biological processes using different mathematical approaches necessary to reveal characteristic features and properties of simulated systems. With the emergence of powerful mathematics software packages such as MAPLE, Mathematica, Mathcad, and MatLab, these methodologies are now accessible to a wide audience. Provides succinct but authoritative coverage of a broad array of biophysical topics and models Wr...

  6. Translocation mechanism(s) of cell-penetrating peptides: biophysical studies using artificial membrane bilayers.

    Science.gov (United States)

    Di Pisa, Margherita; Chassaing, Gérard; Swiecicki, Jean-Marie

    2015-01-20

    The ability of cell-penetrating peptides (CPPs) to cross cell membranes has found numerous applications in the delivery of bioactive compounds to the cytosol of living cells. Their internalization mechanisms have been questioned many times, and after 20 years of intense debate, it is now widely accepted that both energy-dependent and energy-independent mechanisms account for their penetration properties. However, the energy-independent mechanisms, named "direct translocation", occurring without the requirement of the cell internalization machinery, remain to be fully rationalized at the molecular level. Using artificial membrane bilayers, recent progress has been made toward the comprehension of the direct translocation event. This review summarizes our current understanding of the translocation process, starting from the adsorption of the CPP on the membrane to the membrane crossing itself. We describe the different key steps occurring before direct translocation, because each of them can promote and/or hamper translocation of the CPP through the membrane. We then dissect the modification to the membranes induced by the presence of the CPPs. Finally, we focus on the latest studies describing the direct translocation mechanisms. These results provide an important framework within which to design new CPPs and to rationalize an eventual selectivity of CPPs in their penetration ability.

  7. Life as a matter of fat : lipids in a membrane biophysics perspective

    CERN Document Server

    Mouritsen, Ole G

    2016-01-01

    The present book gives a multi-disciplinary perspective on the physics of life and the particular role played by lipids (fats) and the lipid-bilayer component of cell membranes. The emphasis is on the physical properties of lipid membranes seen as soft and molecularly structured interfaces. By combining and synthesizing insights obtained from a variety of recent studies, an attempt is made to clarify what membrane structure is and how it can be quantitatively described. Furthermore, it is shown how biological function mediated by membranes is controlled by lipid membrane structure and organization on length scales ranging from the size of the individual molecule, across molecular assemblies of proteins and lipid domains in the range of nanometers, to the size of whole cells. Applications of lipids in nanotechnology and biomedicine are also described.   The first edition of the present book was published in 2005 when lipidomics was still very much an emerging science and lipids about to be recognized as being...

  8. Biophysical study of resin acid effects on phospholipid membrane structure and properties

    DEFF Research Database (Denmark)

    Jagalski, Vivien; Barker, Robert; Topgaard, Daniel

    2016-01-01

    Hydrophobic resin acids (RAs) are synthesized by conifer trees as part of their defense mechanisms. One of the functions of RAs in plant defense is suggested to be the perturbation of the cellular membrane. However, there is a vast diversity of chemical structures within this class of molecules......, and there are no clear correlations to the molecular mechanisms behind the RA's toxicity. In this study we unravel the molecular interactions of the three closely related RAs dehydroabietic acid, neoabietic acid, and the synthetic analogue dichlorodehydroabietic acid with dipalmitoylphosphatidylcholine (DPPC) model...... are correlated with the physical chemical properties of the RA and their toxicity....

  9. Exploring the Underlying Biophysics of Eukaryotic Plasma Membrane Asymmetry by Sum-Frequency Vibrational Spectroscopy

    Science.gov (United States)

    Conboy, John

    2010-03-01

    A central issue in molecular biology is the movement of lipids across the cellular membrane. The translocation of lipids is involved in cell apoptosis, the viral infection of living cells, the functioning of antibiotics, antiseptics and drugs, and the regulation and growth of cells. There have been a number of studies attempting to find the putative proteins responsive for lipid transbilayer movement in eukaryotic cells. This has led to a large number of theories about the mechanism of transbilayer movement of lipids in cellular systems and the physical process by which lipid compositional asymmetry in the plasma membrane of eukaryotic cells is maintained. Using methods of classical surface chemistry coupled with nonlinear optical methods, we have developed a novel analytical approach, using sum-frequency vibrational spectroscopy (SFVS), to selectively probe lipid compositional asymmetry in a planar supported lipid bilayer. This new method allows for the detection of lipid flip-flop kinetics and compositional asymmetry without the need for a fluorescent or spin-labeled lipid species. The effect of lipid composition, headgroup and fatty acid chemical structure, on the rate and thermodynamics of lipid transbilayer migration and the electrostatic induction of lipid asymmetry will be discussed.

  10. Binding of human myeloperoxidase to red blood cells: Molecular targets and biophysical consequences at the plasma membrane level.

    Science.gov (United States)

    Gorudko, Irina V; Sokolov, Alexey V; Shamova, Ekaterina V; Grigorieva, Daria V; Mironova, Elena V; Kudryavtsev, Igor V; Gusev, Sergey A; Gusev, Alexander A; Chekanov, Andrey V; Vasilyev, Vadim B; Cherenkevich, Sergey N; Panasenko, Oleg M; Timoshenko, Alexander V

    2016-02-01

    Myeloperoxidase (MPO) is an oxidant-producing enzyme that can also bind to cellular surface proteins. We found that band 3 protein and glycophorins A and B were the key MPO-binding targets of human red blood cells (RBCs). The interaction of MPO with RBC proteins was mostly electrostatic in nature because it was inhibited by desialation, exogenic sialic acid, high ionic strength, and extreme pH. In addition, MPO failed to interfere with the lectin-induced agglutination of RBCs, suggesting a minor role of glycan-recognizing mechanisms in MPO binding. Multiple biophysical properties of RBCs were altered in the presence of native (i.e., not hypochlorous acid-damaged) MPO. These changes included transmembrane potential, availability of intracellular Ca(2+), and lipid organization in the plasma membrane. MPO-treated erythrocytes became larger in size, structurally more rigid, and hypersensitive to acidic and osmotic hemolysis. Furthermore, we found a significant correlation between the plasma MPO concentration and RBC rigidity index in type-2 diabetes patients with coronary heart disease. These findings suggest that MPO functions as a mediator of novel regulatory mechanism in microcirculation, indicating the influence of MPO-induced abnormalities on RBC deformability under pathological stress conditions. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. How to Study Basement Membrane Stiffness as a Biophysical Trigger in Prostate Cancer and Other Age-related Pathologies or Metabolic Diseases

    OpenAIRE

    Rodriguez-Teja, Mercedes; Breit, Claudia; Clarke, Mitchell; Talar, Kamil; Wang, Kai; Mohammad, Mohammad A.; Pickwell, Sage; Etchandy, Guillermina; Stasiuk, Graeme J.; Sturge, Justin

    2016-01-01

    Here we describe a protocol that can be used to study the biophysical microenvironment related to increased thickness and stiffness of the basement membrane (BM) during age-related pathologies and metabolic disorders (e.g. cancer, diabetes, microvascular disease, retinopathy, nephropathy and neuropathy). The premise of the model is non-enzymatic crosslinking of reconstituted BM (rBM) matrix by treatment with glycolaldehyde (GLA) to promote advanced glycation endproduct (AGE) generation via th...

  12. Radiation biophysics

    International Nuclear Information System (INIS)

    Anon.

    1979-01-01

    Summaries of research projects conducted during 1978 and 1979 are presented. The overall thrust of the research is aimed at understanding the effects of radiation on organisms. Specific subject areas include: the effects of heavy-particle beam nuclear interactions in tissue on dosimetry; tracer studies with radioactive fragments of heavy-ion beams; the effects of heavy/ions on human kidney cells and Chinese hamster cells; the response of a rhabdomyosarcoma tumor system in rats to heavy-ion beams; the use of heavy charged particles in radiotherapy of human cancer; heavy-ion radiography; the biological effects of high magnetic fields; central nervous system neurotoxicity; and biophysical studies on cell membranes

  13. Biophysics An Introduction

    CERN Document Server

    Glaser, Roland

    2012-01-01

    Biophysics is the science of physical principles underlying all processes of life, including the dynamics and kinetics of biological systems. This fully revised 2nd English edition is an introductory text that spans all steps of biological organization, from the molecular, to the organism level, as well as influences of environmental factors. In response to the enormous progress recently made, especially in theoretical and molecular biophysics, the author has updated the text, integrating new results and developments concerning protein folding and dynamics, molecular aspects of membrane assembly and transport, noise-enhanced processes, and photo-biophysics. The advances made in theoretical biology in the last decade call for a fully new conception of the corresponding sections. Thus, the book provides the background needed for fundamental training in biophysics and, in addition, offers a great deal of advanced biophysical knowledge.

  14. Proof of pore formation and biophysical perturbations through a 2D amoxicillin-lipid membrane interaction approach.

    Science.gov (United States)

    Lopes, Daniela; Nunes, Cláudia; Fontaine, Philippe; Sarmento, Bruno; Reis, Salette

    2017-05-01

    Amoxicillin is a worldwide used antibiotic, and it is classified as a first-line drug against Helicobacter pylori gastric infections. However, the current treatment of these infections has several limitations, such as the side effects and the low therapeutic compliance. Amoxicillin has been associated with gastrointestinal and renal side effects, with higher toxicity when the pH is lower. By considering this association and the well-known pH gradient of the gastric mucosa, this work aims to evaluate the influence of pH on the toxicity of amoxicillin. For that purpose, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) monolayers were used since phosphatidylcholines are the most common phospholipid headgroup of biological membranes. To have insight of the effects of amoxicillin, different techniques were employed, namely, isotherm measurements, infrared reflection-absorption spectroscopy, grazing incident X-ray diffraction and Brewster angle microscopy. The monolayers of DPPC spread onto different buffer solutions (pH1.2, pH5 and pH7.4) showed different structural and packing properties. The interaction with amoxicillin also depended on the pH. At pH7.4, the highest effect was visualized at lower pressures, with partial restoration of the biophysical properties of the monolayer at 30 mN.m -1 . A higher perturbation is shown at acidic pH, in which pores were visualized by Brewster angle microscopy. These perturbations may ultimately be related with amoxicillin toxicity. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Encyclopedia of biophysics

    CERN Document Server

    2013-01-01

    The Encyclopedia of Biophysics is envisioned both as an easily accessible source of information and as an introductory guide to the scientific literature. It includes entries describing both Techniques and Systems.  In the Techniques entries, each of the wide range of methods which fall under the heading of Biophysics are explained in detail, together with the value and the limitations of the information each provides. Techniques covered range from diffraction (X-ray, electron and neutron) through a wide range of spectroscopic methods (X-ray, optical, EPR, NMR) to imaging (from electron microscopy to live cell imaging and MRI), as well as computational and simulation approaches. In the Systems entries, biophysical approaches to specific biological systems or problems – from protein and nucleic acid structure to membranes, ion channels and receptors – are described. These sections, which place emphasis on the integration of the different techniques, therefore provide an inroad into Biophysics from a biolo...

  16. Melatonin reverses the enhanced oxidative damage to membrane lipids and improves skin biophysical characteristics in former-smokers - A study in postmenopausal women.

    Science.gov (United States)

    Sagan, Dorota; Stepniak, Jan; Gesing, Adam; Lewinski, Andrzej; Karbownik-Lewinska, Malgorzata

    2017-12-23

    Protective antioxidative effects of melatonin have been repeatedly documented in experimental and clinical studies. One of the most spectacular exogenous prooxidative agents is cigarette smoking. The aim of the study was to evaluate the level of oxidative damage to membrane lipids (lipid peroxidation; LPO) in blood serum, and in epidermis exfoliated during microdermabrasion collected from former-smokers who were treated with melatonin. The study was performed in postmenopausal women. Ninety (90) female volunteers, aged 46-67 years, were enrolled. Two major groups, i.e. never-smokers (n=44) and former-smokers (n=46), were divided into: Control, melatonin topical skin application, Restructurer (containing antioxidants) topical skin application, and melatonin oral treatment. Microdermabrasion was performed at point '0', after 2 weeks, and after 4 weeks of treatment. The following parameters were measured: LPO in blood serum, LPO in epidermis exfoliated during microdermabrasion, and skin biophysical characteristics, such as sebum, moisture, elasticity, and pigmentation. Malondialdehyde+4-hydroxyalkenals level (LPO index) was measured spectrophotometrically. Melatonin oral treatment significantly reversed the increased serum LPO level in former-smokers already after 2 weeks of treatment. In a univariate regression model, LPO blood level constituted the only independent factor negatively associated with melatonin oral treatment. After 4 weeks of treatment, melatonin given orally increased skin sebum, moisture and elasticity levels, and melatonin applied topically increased sebum level. Exogenous melatonin reverses the enhanced oxidative damage to membrane lipids and improves skin biophysical characteristics in former-smokers.

  17. Biophysical and biochemical strategies to understand membrane binding and pore formation by sticholysins, pore-forming proteins from a sea anemone.

    Science.gov (United States)

    Alvarez, Carlos; Ros, Uris; Valle, Aisel; Pedrera, Lohans; Soto, Carmen; Hervis, Yadira P; Cabezas, Sheila; Valiente, Pedro A; Pazos, Fabiola; Lanio, Maria E

    2017-10-01

    Actinoporins constitute a unique class of pore-forming toxins found in sea anemones that are able to bind and oligomerize in membranes, leading to cell swelling, impairment of ionic gradients and, eventually, to cell death. In this review we summarize the knowledge generated from the combination of biochemical and biophysical approaches to the study of sticholysins I and II (Sts, StI/II), two actinoporins largely characterized by the Center of Protein Studies at the University of Havana during the last 20 years. These approaches include strategies for understanding the toxin structure-function relationship, the protein-membrane association process leading to pore formation and the interaction of toxin with cells. The rational combination of experimental and theoretical tools have allowed unraveling, at least partially, of the complex mechanisms involved in toxin-membrane interaction and of the molecular pathways triggered upon this interaction. The study of actinoporins is important not only to gain an understanding of their biological roles in anemone venom but also to investigate basic molecular mechanisms of protein insertion into membranes, protein-lipid interactions and the modulation of protein conformation by lipid binding. A deeper knowledge of the basic molecular mechanisms involved in Sts-cell interaction, as described in this review, will support the current investigations conducted by our group which focus on the design of immunotoxins against tumor cells and antigen-releasing systems to cell cytosol as Sts-based vaccine platforms.

  18. Biophysical Profile

    Science.gov (United States)

    ... and pregnancy High-risk pregnancy Biophysical profile About Advertisement Mayo Clinic does not endorse companies or products. ... a Job Site Map About This Site Twitter Facebook Google YouTube Pinterest Mayo Clinic is a not- ...

  19. A biophysical approach to menadione membrane interactions: relevance for menadione-induced mitochondria dysfunction and related deleterious/therapeutic effects.

    Science.gov (United States)

    Monteiro, João P; Martins, André F; Nunes, Cláudia; Morais, Catarina M; Lúcio, Marlene; Reis, Salette; Pinheiro, Teresa J T; Geraldes, Carlos F G C; Oliveira, Paulo J; Jurado, Amália S

    2013-08-01

    Menadione (MEN), a polycyclic aromatic ketone, was shown to promote cell injury by imposing massive oxidative stress and has been proposed as a promising chemotherapeutic agent for the treatment of cancer diseases. The mechanisms underlying MEN-induced mitochondrial dysfunction and cell death are not yet fully understood. In this work, a systematic study was performed to unveil the effects of MEN on membrane lipid organization, using models mimicking mitochondrial membranes and native mitochondrial membranes. MEN was found to readily incorporate in membrane systems composed of a single phospholipid (phosphatidylcholine) or the lipids dioleoylphosphatidylcholine, dioleoylphosphatidylethanolamine and tetraoleoylcardiolipin at 1:1:1 molar ratio, as well as in mitochondrial membranes. Increased permeability in both membrane models, monitored by calcein release, seemed to correlate with the extent of MEN incorporation into membranes. MEN perturbed the physical properties of vesicles composed of dipalmitoylphosphatidylcholine or dipalmitoylphosphatidylethanolamine plus tetraoleoylcardiolipin (at 7:3 molar ratio), as reflected by the downshift of the lipid phase transition temperature and the emergence of a new transition peak in the mixed lipid system, detected by DSC. (31)P NMR studies revealed that MEN favored the formation of non-lamellar structures. Also, quenching studies with the fluorescent probes DPH and TMA-DPH showed that MEN distributed across the bilayer thickness in both model and native mitochondrial membranes. MEN's ability to promote alterations of membrane lipid organization was related with its reported mitochondrial toxicity and promotion of apoptosis, predictably involved in its anti-carcinogenic activity. Copyright © 2013 Elsevier B.V. All rights reserved.

  20. Carbohydrate-Derived Amphiphilic Macromolecules: A Biophysical Structural Characterization and Analysis of Binding Behaviors to Model Membranes

    Directory of Open Access Journals (Sweden)

    Adriana A. T. Martin

    2015-04-01

    Full Text Available The design and synthesis of enhanced membrane-intercalating biomaterials for drug delivery or vascular membrane targeting is currently challenged by the lack of screening and prediction tools. The present work demonstrates the generation of a Quantitative Structural Activity Relationship model (QSAR to make a priori predictions. Amphiphilic macromolecules (AMs “stealth lipids” built on aldaric and uronic acids frameworks attached to poly(ethylene glycol (PEG polymer tails were developed to form self-assembling micelles. In the present study, a defined set of novel AM structures were investigated in terms of their binding to lipid membrane bilayers using Quartz Crystal Microbalance with Dissipation (QCM-D experiments coupled with computational coarse-grained molecular dynamics (CG MD and all-atom MD (AA MD simulations. The CG MD simulations capture the insertion dynamics of the AM lipophilic backbones into the lipid bilayer with the PEGylated tail directed into bulk water. QCM-D measurements with Voigt viscoelastic model analysis enabled the quantitation of the mass gain and rate of interaction between the AM and the lipid bilayer surface. Thus, this study yielded insights about variations in the functional activity of AM materials with minute compositional or stereochemical differences based on membrane binding, which has translational potential for transplanting these materials in vivo. More broadly, it demonstrates an integrated computational-experimental approach, which can offer a promising strategy for the in silico design and screening of therapeutic candidate materials.

  1. Reconstitution of the anti-apoptotic Bcl-2 protein into lipid membranes and biophysical evidence for its detergent-driven association with the pro-apoptotic Bax protein.

    Directory of Open Access Journals (Sweden)

    Marcus Wallgren

    Full Text Available The anti-apoptotic B-cell CLL/lymphoma-2 (Bcl-2 protein and its counterpart, the pro-apoptotic Bcl-2-associated X protein (Bax, are key players in the regulation of the mitochondrial pathway of apoptosis. However, how they interact at the mitochondrial outer membrane (MOM and there determine whether the cell will live or be sentenced to death remains unknown. Competing models have been presented that describe how Bcl-2 inhibits the cell-killing activity of Bax, which is common in treatment-resistant tumors where Bcl-2 is overexpressed. Some studies suggest that Bcl-2 binds directly to and sequesters Bax, while others suggest an indirect process whereby Bcl-2 blocks BH3-only proteins and prevents them from activating Bax. Here we present the results of a biophysical study in which we investigated the putative interaction of solubilized full-length human Bcl-2 with Bax and the scope for incorporating the former into a native-like lipid environment. Far-UV circular dichroism (CD spectroscopy was used to detect direct Bcl-2-Bax-interactions in the presence of polyoxyethylene-(23-lauryl-ether (Brij-35 detergent at a level below its critical micelle concentration (CMC. Additional surface plasmon resonance (SPR measurements confirmed this observation and revealed a high affinity between the Bax and Bcl-2 proteins. Upon formation of this protein-protein complex, Bax also prevented the binding of antimycin A2 (a known inhibitory ligand of Bcl-2 to the Bcl-2 protein, as fluorescence spectroscopy experiments showed. In addition, Bcl-2 was able to form mixed micelles with Triton X-100 solubilized neutral phospholipids in the presence of high concentrations of Brij-35 (above its CMC. Following detergent removal, the integral membrane protein was found to have been fully reconstituted into a native-like membrane environment, as confirmed by ultracentrifugation and subsequent SDS-PAGE experiments.

  2. Biophysical studies of the interaction of squalamine and other cationic amphiphilic molecules with bacterial and eukaryotic membranes: importance of the distribution coefficient in membrane selectivity.

    Science.gov (United States)

    Di Pasquale, Eric; Salmi-Smail, Chanaz; Brunel, Jean-Michel; Sanchez, Patrick; Fantini, Jacques; Maresca, Marc

    2010-02-01

    The interaction of squalamine (SQ) with eukaryotic and prokaryotic membranes was studied and compared with the interaction of two other cationic amphipathic antimicrobials (CAAs), i.e. the antibiotic polymyxin B (PMB) and the detergent hexadecyltrimethylammonium bromide (CTAB). Whole cell experiments showed that the three CAA have in common the ability to interact with lipopolysaccharide-containing membranes through a divalent cation sensitive process. Differences were found regarding their kinetics of membrane permeabilisation and their selectivity for bacteria, with a preferential permeabilisation of bacteria by PMB>SQ and no selectivity for CTAB. Experiments with lipid monolayers and bilayers showed that this selectivity did not correlate with a preferential interaction of the CAAs with lipids but rather relies on differences in their ability to penetrate lipid bilayers and to cause electrically active lesions. Incidentally, our results also suggest that the distribution coefficient of CAAs could be used to predict their selectivity for bacteria.

  3. High- and low-affinity sites for sodium in delta-OR-G(i)1 alpha (Cys(351)-Ile(351)) fusion protein stably expressed in HEK293 cells; functional significance and correlation with biophysical state of plasma membrane

    Czech Academy of Sciences Publication Activity Database

    Vošahlíková, Miroslava; Jurkiewicz, Piotr; Roubalová, Lenka; Hof, Martin; Svoboda, Petr

    2014-01-01

    Roč. 387, č. 5 (2014), s. 487-502 ISSN 0028-1298 R&D Projects: GA ČR(CZ) GAP207/12/0919; GA ČR(CZ) GBP304/12/G069 Institutional support: RVO:67985823 ; RVO:61388955 Keywords : delta - opioid receptor * monovalent ions * agonist and antagonist binding * [35S]GTPγS binding * membrane biophysics * Laurdan fluorescence Subject RIV: CE - Biochemistry Impact factor: 2.471, year: 2014

  4. How to Study Basement Membrane Stiffness as a Biophysical Trigger in Prostate Cancer and Other Age-related Pathologies or Metabolic Diseases.

    Science.gov (United States)

    Rodriguez-Teja, Mercedes; Breit, Claudia; Clarke, Mitchell; Talar, Kamil; Wang, Kai; Mohammad, Mohammad A; Pickwell, Sage; Etchandy, Guillermina; Stasiuk, Graeme J; Sturge, Justin

    2016-09-20

    Here we describe a protocol that can be used to study the biophysical microenvironment related to increased thickness and stiffness of the basement membrane (BM) during age-related pathologies and metabolic disorders (e.g. cancer, diabetes, microvascular disease, retinopathy, nephropathy and neuropathy). The premise of the model is non-enzymatic crosslinking of reconstituted BM (rBM) matrix by treatment with glycolaldehyde (GLA) to promote advanced glycation endproduct (AGE) generation via the Maillard reaction. Examples of laboratory techniques that can be used to confirm AGE generation, non-enzymatic crosslinking and increased stiffness in GLA treated rBM are outlined. These include preparation of native rBM (treated with phosphate-buffered saline, PBS) and stiff rBM (treated with GLA) for determination of: its AGE content by photometric analysis and immunofluorescent microscopy, its non-enzymatic crosslinking by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE) as well as confocal microscopy, and its increased stiffness using rheometry. The procedure described here can be used to increase the rigidity (elastic moduli, E) of rBM up to 3.2-fold, consistent with measurements made in healthy versus diseased human prostate tissue. To recreate the biophysical microenvironment associated with the aging and diseased prostate gland three prostate cell types were introduced on to native rBM and stiff rBM: RWPE-1, prostate epithelial cells (PECs) derived from a normal prostate gland; BPH-1, PECs derived from a prostate gland affected by benign prostatic hyperplasia (BPH); and PC3, metastatic cells derived from a secondary bone tumor originating from prostate cancer. Multiple parameters can be measured, including the size, shape and invasive characteristics of the 3D glandular acini formed by RWPE-1 and BPH-1 on native versus stiff rBM, and average cell length, migratory velocity and persistence of cell movement of 3D spheroids formed by PC3 cells under

  5. Structural biophysics

    International Nuclear Information System (INIS)

    Anon.

    1979-01-01

    Summaries of research projects conducted during 1978 and 1979 are presented. The structural biophysics group explores the high-resolution structure of biological macromolecules and cell organelles. Specific subject areas include: the basic characteristics of photosynthesis in plants; the chemical composition of individual fly ash particles at the site of their damaging action in tissues; direct analysis of frozen-hydrated biological samples by scanning electron microscopy; yeast genetics; the optical activity of DNA aggregates; measurement and characterization of lipoproteins; function of lipoproteins; and the effect of radiation and pollutants on mammalian cells

  6. Integrated Molecular and Cellular Biophysics

    CERN Document Server

    Raicu, Valerica

    2008-01-01

    This book integrates concepts and methods from physics, biology, biochemistry and physical chemistry into a standalone, unitary text of biophysics that aims to provide a quantitative description of structures and processes occurring in living matter. The book introduces graduate physics students and physicists interested in biophysics research to 'classical' as well as emerging areas of biophysics. The advanced undergraduate physics students and the life scientists are also invited to join in, by building on their knowledge of basic physics. Essential notions of biochemistry and biology are introduced, as necessary, throughout the book, while the reader's familiarity with basic knowledge of physics is assumed. Topics covered include interactions between biological molecules, physical chemistry of phospholipids association into bilayer membranes, DNA and protein structure and folding, passive and active electrical properties of the cell membrane, classical as well as fractal aspects of reaction kinetics and di...

  7. Biophysical radiosensitization

    International Nuclear Information System (INIS)

    Vladescu, C.; Apetroae, M.

    1983-01-01

    Experimental studies on normal and tumor-bearing rats revealed that chronic treatment with hydroquinone (5 mg/kg/day) inhibited catalase activity in liver, spleen, blood, and H 18R tumor. 3 H-hydroquinone (1.5 μCi/g body weight) showed tumor specificity, with maximum radioactivity in the tumor at 1 h after administration. The biological half-time of 3 H-hydroquinone in the tumor was 2 h, but there seems to exist a longer component, since 24 h after administration, some 30% of the maximum radioactivity could be detected in the tumor. Hydroquinone treatment produces a specific inhibition of catalase in the tumor and a higher degree of oxygenation at this level. These findings support the assumption that the mechanism of action of hydroquinone as an anticancer agent is achieved mainly via peroxide production. The oxygenation of the hypoxic tumoral tissue is done at non-toxic levels of hydroquinone, through a natural and specific biophysical pathway, recommanding hydroquinone for combined anticancer treatment (radiotherapy and chemotherapy). (orig.)

  8. Theoretical molecular biophysics

    CERN Document Server

    Scherer, Philipp O J

    2017-01-01

    This book gives an introduction to molecular biophysics. It starts from material properties at equilibrium related to polymers, dielectrics and membranes. Electronic spectra are developed for the understanding of elementary dynamic processes in photosynthesis including proton transfer and dynamics of molecular motors. Since the molecular structures of functional groups of bio-systems were resolved, it has become feasible to develop a theory based on the quantum theory and statistical physics with emphasis on the specifics of the high complexity of bio-systems. This introduction to molecular aspects of the field focuses on solvable models. Elementary biological processes provide as special challenge the presence of partial disorder in the structure which does not destroy the basic reproducibility of the processes. Apparently the elementary molecular processes are organized in a way to optimize the efficiency. Learning from nature by means exploring the relation between structure and function may even help to b...

  9. 2. biophysical work meeting

    International Nuclear Information System (INIS)

    1992-11-01

    The report comprises 18 papers held at the 2nd Biophysical Work Meeting, 11 - 13 September 1991 in Schlema, Germany. The history of biophysics in Germany particularly of radiation biophysics and radon research, measurements of the radiation effects of radon and the derivation of limits, radon balneotherapy and consequences of uranium ore mining are dealt with. (orig.) [de

  10. Biophysical shunt theory for neuropsychopathology: Part I.

    Science.gov (United States)

    Naisberg, Y; Avnon, M; Weizman, A

    1995-11-01

    We present a new model of the origin of schizophrenia based on biophysical ionic shunts in neuronal (electrical) pathways. Microstructural and molecular evidence is presented for the way in which changes in the neuronal membrane ionic channels may facilitate membrane property rearrangement, leading to a change in the density and composition of the ion channel charge which in turn causes a change in ionic flow orientation and distribution. We suggest that, under abnormal conditions, ionic flow shunts are created which redirect the biophysical collateral neuronal (electrical) pathways, resulting in psychiatric signs and symptoms. This model is complementary to the biological basis of schizophrenia.

  11. Biophysics of olfaction

    Energy Technology Data Exchange (ETDEWEB)

    Souza, Fabio Marques Simoes de [Cell and Developmental Biology, University of Colorado at Denver and Health Science Center, Campus Box 6511, PO Box 6511, 12801 East 17th Avenue, Aurora, CO 80045 (United States); Antunes, Gabriela [Psychobiology Sector and Department of Chemistry, Faculdade de Filosofia Ciencias e Letras de Ribeirao Preto, Universidade de Sao Paulo, Av. Bandeirantes, 3900, 14040-901, Ribeirao Preto, SP (Brazil)

    2007-03-15

    The majority of the biophysical models of olfaction have been focused on the electrical properties of the system, which is justified by the relative facility of recording the electrical activity of the olfactory cells. However, depending on the level of detail utilized, a biophysical model can explore molecular, cellular and network phenomena. This review presents the state of the art of the biophysical approach to understanding olfaction. The reader is introduced to the principal problems involving the study of olfaction and guided gradually to comprehend why it is important to develop biophysical models to investigate olfaction. A large number of representative biophysical efforts in olfaction, their main contributions, the trends for the next generations of biophysical models and the improvements that may be explored by future biophysicists of olfaction have been reviewed.

  12. Methods in Modern Biophysics

    CERN Document Server

    Nölting, Bengt

    2010-01-01

    Incorporating recent dramatic advances, this textbook presents a fresh and timely introduction to modern biophysical methods. An array of new, faster and higher-power biophysical methods now enables scientists to examine the mysteries of life at a molecular level. This innovative text surveys and explains the ten key biophysical methods, including those related to biophysical nanotechnology, scanning probe microscopy, X-ray crystallography, ion mobility spectrometry, mass spectrometry, proteomics, and protein folding and structure. Incorporating much information previously unavailable in tutorial form, Nölting employs worked examples and about 270 illustrations to fully detail the techniques and their underlying mechanisms. Methods in Modern Biophysics is written for advanced undergraduate and graduate students, postdocs, researchers, lecturers, and professors in biophysics, biochemistry and related fields. Special features in the 3rd edition: Introduces rapid partial protein ladder sequencing - an important...

  13. Methods in Modern Biophysics

    CERN Document Server

    Nölting, Bengt

    2006-01-01

    Incorporating recent dramatic advances, this textbook presents a fresh and timely introduction to modern biophysical methods. An array of new, faster and higher-power biophysical methods now enables scientists to examine the mysteries of life at a molecular level. This innovative text surveys and explains the ten key biophysical methods, including those related to biophysical nanotechnology, scanning probe microscopy, X-ray crystallography, ion mobility spectrometry, mass spectrometry, proteomics, and protein folding and structure. Incorporating much information previously unavailable in tutorial form, Nölting employs worked examples and 267 illustrations to fully detail the techniques and their underlying mechanisms. Methods in Modern Biophysics is written for advanced undergraduate and graduate students, postdocs, researchers, lecturers and professors in biophysics, biochemistry and related fields. Special features in the 2nd edition: • Illustrates the high-resolution methods for ultrashort-living protei...

  14. Biophysical characterization of GPCR oligomerization

    DEFF Research Database (Denmark)

    Mathiasen, Signe

    The biophysical characterization of the fundamental molecular mechanisms behind G-protein coupled receptors (GPCRs) oligomerization is proposed to be paramount for understanding the pharmacological consequence of receptor self-association. Here we developed an in vitro assay that allowed a quanti......The biophysical characterization of the fundamental molecular mechanisms behind G-protein coupled receptors (GPCRs) oligomerization is proposed to be paramount for understanding the pharmacological consequence of receptor self-association. Here we developed an in vitro assay that allowed...... a quantitative characterization of GPCR oligomerization. The assay provided the first quantification of the association energy of the β2 Adrenergic Receptor (β2AR), a prototypical GPCR. Furthermore we directly observed the time-dependent dimerization of β2AR and Cannabinoid receptor 1 at the single molecule...... level, and revealed the existence of several dimerization interfaces, each with specific kinetics. Finally we investigated how a property of the membrane solubilizing GPCRs affected oligomerization. We observed a dramatic decrease in oligomer stability with increasing geometrical membrane curvature. We...

  15. Advanced Techniques in Biophysics

    CERN Document Server

    Arrondo, José Luis R

    2006-01-01

    Technical advancements are basic elements in our life. In biophysical studies, new applications and improvements in well-established techniques are being implemented every day. This book deals with advancements produced not only from a technical point of view, but also from new approaches that are being taken in the study of biophysical samples, such as nanotechniques or single-cell measurements. This book constitutes a privileged observatory for reviewing novel applications of biophysical techniques that can help the reader enter an area where the technology is progressing quickly and where a comprehensive explanation is not always to be found.

  16. Forest Biophysical Parameters (SNF)

    Data.gov (United States)

    National Aeronautics and Space Administration — Biophysical parameters (DBH, NPP, biomass, bark area index, LAI, subcanopy LAI) by study site for Aspen and Spruce in the Superior National Forest, MN (SNF)

  17. Insights into the potential function and membrane organization of the TP0435 (Tp17) lipoprotein from Treponema pallidum derived from structural and biophysical analyses.

    Science.gov (United States)

    Brautigam, Chad A; Deka, Ranjit K; Liu, Wei Z; Norgard, Michael V

    2015-01-01

    The sexually transmitted disease syphilis is caused by the bacterial spirochete Treponema pallidum. This microorganism is genetically intractable, accounting for the large number of putative and undercharacterized members of the pathogen's proteome. In an effort to ascribe a function(s) to the TP0435 (Tp17) lipoprotein, we engineered a soluble variant of the protein (rTP0435) and determined its crystal structure at a resolution of 2.42 Å. The structure is characterized by an eight-stranded β-barrel protein with a shallow "basin" at one end of the barrel and an α-helix stacked on the opposite end. Furthermore, there is a disulfide-linked dimer of the protein in the asymmetric unit of the crystals. Solution hydrodynamic experiments established that purified rTP0435 is monomeric, but specifically forms the disulfide-stabilized dimer observed in the crystal structure. The data herein, when considered with previous work on TP0435, imply plausible roles for the protein in either ligand binding, treponemal membrane architecture, and/or pathogenesis. © 2014 The Protein Society.

  18. Single Particle Orientation and Rotational Tracking (SPORT) in biophysical studies

    Science.gov (United States)

    Gu, Yan; Ha, Ji Won; Augspurger, Ashley E.; Chen, Kuangcai; Zhu, Shaobin; Fang, Ning

    2013-10-01

    The single particle orientation and rotational tracking (SPORT) techniques have seen rapid development in the past 5 years. Recent technical advances have greatly expanded the applicability of SPORT in biophysical studies. In this feature article, we survey the current development of SPORT and discuss its potential applications in biophysics, including cellular membrane processes and intracellular transport.The single particle orientation and rotational tracking (SPORT) techniques have seen rapid development in the past 5 years. Recent technical advances have greatly expanded the applicability of SPORT in biophysical studies. In this feature article, we survey the current development of SPORT and discuss its potential applications in biophysics, including cellular membrane processes and intracellular transport. Electronic supplementary information (ESI) available: Three supplementary movies and an experimental section. See DOI: 10.1039/c3nr02254d

  19. Biophysics of molecular gastronomy.

    Science.gov (United States)

    Brenner, Michael P; Sörensen, Pia M

    2015-03-26

    Chefs and scientists exploring biophysical processes have given rise to molecular gastronomy. In this Commentary, we describe how a scientific understanding of recipes and techniques facilitates the development of new textures and expands the flavor palette. The new dishes that result engage our senses in unexpected ways. PAPERCLIP. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Recent progress in Biophysics

    International Nuclear Information System (INIS)

    Bemski, G.

    1980-03-01

    Recent progress in biophysics is reviewed, and three examples of the use of physical techniques and ideas in biological research are given. The first one deals with the oxygen transporting protein-hemoglobin, the second one with photosynthesis, and the third one with image formation, using nuclear magnetic resonance. (Author) [pt

  1. Structure and biophysics

    CERN Document Server

    Puglisi, Joseph D

    2007-01-01

    This volume is a collection of articles from the proceedings of the ISSBMR 7th Course: Structure and Biophysics - New Technologies for Current Challenges in Biology and Beyond. This NATO Advanced Institute (ASI) was held in Erice at the Ettore Majorana Foundation and Centre for Scientific Culture on 22 June through 3 July 2005. The ASI brought together a diverse group of experts in the fields of Structural Biology, Biophysics and Physics. Prominent lecturers, from seven different countries, and students from around the world participated in the NATO ASI organized by Professors Joseph Puglisi (Stanford University, USA) and Alexander Arseniev (Moscow, RU). Advances in nuclear magnetic resonance spectroscopy (NMR) and x-ray crystallography have allowed the three-dimensional structures of many biological macromolecules and their complexes, including the ribosome and RNA polymerase to be solved. Fundamental principles of NMR spectroscopy and dynamics, x-ray crystallography, computation and experimental dynamics we...

  2. Biophysics an introduction

    CERN Document Server

    Cotteril, Rodney

    2002-01-01

    Biophysics: An Introduction, is a concise balanced introduction to this subject. Written in an accessible and readable style, the book takes a fresh, modern approach with the author successfully combining key concepts and theory with relevant applications and examples drawn from the field as a whole. Beginning with a brief introduction to the origins of biophysics, the book takes the reader through successive levels of complexity, from atoms to molecules, structures, systems and ultimately to the behaviour of organisms. The book also includes extensive coverage of biopolymers, biomembranes, biological energy, and nervous systems. The text not only explores basic ideas, but also discusses recent developments, such as protein folding, DNA/RNA conformations, molecular motors, optical tweezers and the biological origins of consciousness and intelligence.

  3. Theoretical Molecular Biophysics

    CERN Document Server

    Scherer, Philipp

    2010-01-01

    "Theoretical Molecular Biophysics" is an advanced study book for students, shortly before or after completing undergraduate studies, in physics, chemistry or biology. It provides the tools for an understanding of elementary processes in biology, such as photosynthesis on a molecular level. A basic knowledge in mechanics, electrostatics, quantum theory and statistical physics is desirable. The reader will be exposed to basic concepts in modern biophysics such as entropic forces, phase separation, potentials of mean force, proton and electron transfer, heterogeneous reactions coherent and incoherent energy transfer as well as molecular motors. Basic concepts such as phase transitions of biopolymers, electrostatics, protonation equilibria, ion transport, radiationless transitions as well as energy- and electron transfer are discussed within the frame of simple models.

  4. Model cell membranes

    DEFF Research Database (Denmark)

    Günther-Pomorski, Thomas; Nylander, Tommy; Cardenas Gomez, Marite

    2014-01-01

    The high complexity of biological membranes has motivated the development and application of a wide range of model membrane systems to study biochemical and biophysical aspects of membranes in situ under well defined conditions. The aim is to provide fundamental understanding of processes control...

  5. Thermal Manikins & Clothing Biophysics Laboratories

    Data.gov (United States)

    Federal Laboratory Consortium — Five biophysical evaluation chambers containing fully sensored, articulated, moveable copper manikins, and other metallic models of feet and hands are available for...

  6. Biophysical pathology in cancer transformation

    Czech Academy of Sciences Publication Activity Database

    Pokorný, Jiří; Pokorný, Jan

    S1, Nov (2013), s. 1-9 ISSN 2324-9110 R&D Projects: GA ČR(CZ) GAP102/11/0649 Institutional support: RVO:68378271 ; RVO:67985882 Keywords : cancer biophysics * Warburg effect * reverse Warburg effect * biological electrodynamics * coherent states Subject RIV: BO - Biophysics

  7. Biophysics of DNA

    CERN Document Server

    Vologodskii, Alexander

    2015-01-01

    Surveying the last sixty years of research, this book describes the physical properties of DNA in the context of its biological functioning. It is designed to enable both students and researchers of molecular biology, biochemistry and physics to better understand the biophysics of DNA, addressing key questions and facilitating further research. The chapters integrate theoretical and experimental approaches, emphasising throughout the importance of a quantitative knowledge of physical properties in building and analysing models of DNA functioning. For example, the book shows how the relationship between DNA mechanical properties and the sequence specificity of DNA-protein binding can be analyzed quantitatively by using our current knowledge of the physical and structural properties of DNA. Theoretical models and experimental methods in the field are critically considered to enable the reader to engage effectively with the current scientific literature on the physical properties of DNA.

  8. Biophysics of radiation action

    International Nuclear Information System (INIS)

    Dertinger, H.

    1984-01-01

    Understanding the cellular response to ionizing radiation is not only necessary to meet the requirements of radioprotection, but also for medical application of radiation in cancer treatment. In terms of radiobiology, cancer therapy means the selective inactivation of malignant cells without affecting the normal healthy tissue. However, for several physical and biological reasons, this ideal situation is normally not attained. The elaboration of biophysical parameters that could be used to improve the selective sterilization of tumor cells has become one of the main activities of cellular radiobiology during the last two decades. Progress in this field has been facilitated by the development of tissue culture techniques allowing to grow and analyze cells in a synthetic nutrient medium. This chapter describes the physical and biological factors which determine cellular radiosensitivity and which are important to know for better understanding the cellular radiation action, in particular with reference to cancer treatment

  9. Biophysics and cancer

    CERN Document Server

    Nicolini, Claudio

    1986-01-01

    Since the early times of the Greek philosophers Leucippus and Democritus, and later of the Roman philosopher Lucretius, a simple, fundamental idea emerged that brought the life sciences into the realm of the physical sciences. Atoms, after various interactions, were assumed to acquire stable configurations that corresponded either to the living or to the inanimate world. This simple and unitary theory, which has evolved in successive steps to our present time, remarkably maintained its validity despite several centuries of alternative vicissitudes, and is the foundation of modern biophysics. Some of the recent developments of this ancient idea are the discovery of the direct relationship between spatial structures and chemical activity of such molecules as methane and benzene, and the later discovery of the three-dimensional structure of double-helical DNA, and of its relationship with biological activity. The relationship between the structure of various macromolecules and the function of living cells was on...

  10. Biophysical models in hadrontherapy

    Science.gov (United States)

    Scholz, M.; Elsaesser, T.

    One major rationale for the application of ion beams in tumor therapy is their increased relative biological effectiveness RBE in the Bragg peak region For dose prescription the increased effectiveness has to be taken into account in treatment planning Hence the complex dependencies of RBE on the dose level biological endpoint position in the field etc require biophysical models which have to fulfill two important criteria simplicity and quantitative precision Simplicity means that the number of free parameters should be kept at a minimum Due to the lack of precise quantitative data at least at present this requirement is incompatible with approaches aiming at the molecular modeling of the whole chain of production processing and repair of biological damages Quantitative precision is required since steep gradients in the dose response curves are observed for most tumor and normal tissues thus even small uncertainties in the estimation of the biologically effective dose can transform into large uncertainties in the clinical outcome The paper will give a general introduction into the field followed by a brief description of a specific model the so called Local Effect Model LEM This model has been successfully applied within treatment planning in the GSI pilot project for carbon ion tumor therapy over almost 10 years now The model is based on the knowledge of charged particle track structure in combination with the response of the biological objects to conventional photon radiation The model will be critically discussed with respect to other

  11. Biophysics of protein evolution and evolutionary protein biophysics

    Science.gov (United States)

    Sikosek, Tobias; Chan, Hue Sun

    2014-01-01

    The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence–structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by ‘hidden’ conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution. PMID:25165599

  12. The physical basis of biochemistry the foundations of molecular biophysics

    CERN Document Server

    Bergethon, Peter R

    1998-01-01

    The objective of this book is to provide a unifying approach to the study of biophysical chemistry for the advanced undergraduate who has had a year of physics, organic chem­ istry, calculus, and biology. This book began as a revised edition of Biophysical Chemistry: Molecules to Membranes, which Elizabeth Simons and I coauthored. That short volume was written in an attempt to provide a concise text for a one-semester course in biophysical chemistry at the graduate level. The experience of teaching biophysical chemistry to bi­ ologically oriented students over the last decade has made it clear that the subject requires a more fundamental text that unifies the many threads of modem science: physics, chem­ istry, biology, mathematics, and statistics. This book represents that effort. This volume is not a treatment of modem biophysical chemistry with its rich history and many contro­ versies, although a book on that topic is also needed. The Physical Basis of Biochemistry is an introduction to the philosophy...

  13. Molecular Interactions at Membranes

    DEFF Research Database (Denmark)

    Jagalski, Vivien

    Biological membranes are essential and complex structures in every living cell consisting of a fluid lipid bilayer sheet and membrane proteins. Its significance makes biological membranes not only interesting for medical research, but also has made it a target for toxins in the course of evolution....... Today, we know more than ever before about the properties of biological membranes. Advanced biophysical techniques and sophisticated membrane models allow us to answer specific questions about the structure of the components within membranes and their interactions. However, many detailed structural...... mechanisms of membrane compounds, including compounds associated with membranes, are still unknown due to the challenges that arise when probing the hydrophobic nature of the membrane's interior. For integral membrane proteins that span through the entire membrane, the amphiphilic environment is essential...

  14. Biophysical changes induced by xenon on phospholipid bilayers.

    Science.gov (United States)

    Booker, Ryan D; Sum, Amadeu K

    2013-05-01

    Structural and dynamic changes in cell membrane properties induced by xenon, a volatile anesthetic molecule, may affect the function of membrane-mediated proteins, providing a hypothesis for the mechanism of general anesthetic action. Here, we use molecular dynamics simulation and differential scanning calorimetry to examine the biophysical and thermodynamic effects of xenon on model lipid membranes. Our results indicate that xenon atoms preferentially localize in the hydrophobic core of the lipid bilayer, inducing substantial increases in the area per lipid and bilayer thickness. Xenon depresses the membrane gel-liquid crystalline phase transition temperature, increasing membrane fluidity and lipid head group spacing, while inducing net local ordering effects in a small region of the lipid carbon tails and modulating the bilayer lateral pressure profile. Our results are consistent with a role for nonspecific, lipid bilayer-mediated mechanisms in producing xenon's general anesthetic action. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. Radiation dosimetry and radiation biophysics

    International Nuclear Information System (INIS)

    Anon.

    1981-01-01

    Radiation dosimetry and radiation biophysics are two closely integrated programs whose joint purpose is to explore the connections between the primary physical events produced by radiation and their biological consequences in cellular systems. The radiation dosimetry program includes the theoretical description of primary events and their connection with the observable biological effects. This program also is concerned with the design and measurement of physical parameters used in theory or to support biological experiments. The radiation biophysics program tests and uses the theoretical developments for experimental design, and provides information for further theoretical development through experiments on cellular systems

  16. Radiation dosimetry and radiation biophysics

    International Nuclear Information System (INIS)

    Anon.

    1979-01-01

    Radiation dosimetry and radiation biophysics are two closely integrated programs whose joint purpose is to explore the connections between the primary physical events produced by radiation and their biological consequences in cellular systems. The radiation dosimetry program includes the theoretical description of primary events and their connection with the observable biological effects. This program also is concerned with design and measurement of those physical parameters used in the theory or to support biological experiments. The radiation biophysics program tests and makes use of the theoretical developments for experimental design. Also, this program provides information for further theoretical development through experiments on cellular systems

  17. The biophysics of neuronal growth

    International Nuclear Information System (INIS)

    Franze, Kristian; Guck, Jochen

    2010-01-01

    For a long time, neuroscience has focused on biochemical, molecular biological and electrophysiological aspects of neuronal physiology and pathology. However, there is a growing body of evidence indicating the importance of physical stimuli for neuronal growth and development. In this review we briefly summarize the historical background of neurobiophysics and give an overview over the current understanding of neuronal growth from a physics perspective. We show how biophysics has so far contributed to a better understanding of neuronal growth and discuss current inconsistencies. Finally, we speculate how biophysics may contribute to the successful treatment of lesions to the central nervous system, which have been considered incurable until very recently.

  18. Ninth International Workshop on Plant Membrane Biology

    Energy Technology Data Exchange (ETDEWEB)

    1993-12-31

    This report is a compilation of abstracts from papers which were discussed at a workshop on plant membrane biology. Topics include: plasma membrane ATP-ases; plant-environment interactions, membrane receptors; signal transduction; ion channel physiology; biophysics and molecular biology; vaculor H+ pumps; sugar carriers; membrane transport; and cellular structure and function.

  19. Biophysical applications of satellite remote sensing

    CERN Document Server

    Hanes, Jonathan

    2014-01-01

    Including an introduction and historical overview of the field, this comprehensive synthesis of the major biophysical applications of satellite remote sensing includes in-depth discussion of satellite-sourced biophysical metrics such as leaf area index.

  20. Fundamental Concepts in Biophysics Volume 1

    CERN Document Server

    Jue, Thomas

    2009-01-01

    HANDBOOK OF MODERN BIOPHYSICS Series Editor Thomas Jue, PhD Handbook of Modern Biophysics brings current biophysics topics into focus, so that biology, medical, engineering, mathematics, and physical-science students or researchers can learn fundamental concepts and the application of new techniques in addressing biomedical challenges. Chapters explicate the conceptual framework of the physics formalism and illustrate the biomedical applications. With the addition of problem sets, guides to further study, and references, the interested reader can continue to explore independently the ideas presented. Volume I: Fundamental Concepts in Biophysics Editor Thomas Jue, PhD In Fundamental Concepts in Biophysics, prominent professors have established a foundation for the study of biophysics related to the following topics: Mathematical Methods in Biophysics Quantum Mechanics Basic to Biophysical Methods Computational Modeling of Receptor–Ligand Binding and Cellular Signaling Processes Fluorescence Spectroscopy Elec...

  1. Refresher Course on Advances in Biophysics

    Indian Academy of Sciences (India)

    Administrator

    Biophysics today uses concepts and methods from physics and chemistry to elucidate the workings of biological processes at molecular, cellular, and organismal level. This course will introduce teachers of biophysics in postgraduate courses to some of the recent advances in biophysical theory and techniques. The aim is ...

  2. Biophysical Profiling of Tumor Cell Lines

    Directory of Open Access Journals (Sweden)

    Frederick Coffman

    2011-01-01

    Full Text Available Despite significant differences in genetic profiles, cancer cells share common phenotypic properties, including membrane-associated changes that facilitate invasion and metastasis. The Corning Epic® optical biosensor was used to monitor dynamic mass rearrangements within and proximal to the cell membrane in tumor cell lines derived from cancers of the colon, bone, cervix, lung and breast. Data was collected in real time and required no exogenously added signaling moiety (signal-free technology. Cell lines displayed unique profiles over the time-courses: the time-courses all displayed initial signal increases to maximal values, but the rate of increase to those maxima and the value of those maxima were distinct for each cell line. The rate of decline following the maxima also differed among cell lines. There were correlations between the signal maxima and the observed metastatic behavior of the cells in xenograft experiments; for most cell types the cells that were more highly metastatic in mice had lower time-course maxima values, however the reverse was seen in breast cancer cells. The unique profiles of these cell lines and the correlation of at least one profile characteristic with metastatic behavior demonstrate the potential utility of biophysical tumor cell profiling in the study of cancer biology.

  3. Space Biophysics: Accomplishments, Trends, Challenges

    Science.gov (United States)

    Smith, Jeffrey D.

    2015-01-01

    Physics and biology are inextricably linked. All the chemical and biological processes of life are dutifully bound to follow the rules and laws of physics. In space, these physical laws seem to turn on their head and biological systems, from microbes to humans, adapt and evolve in myriad ways to cope with the changed physical influences of the space environment. Gravity is the most prominent change in space that influences biology. In microgravity, the physical processes of sedimentation, density-driven convective flow, influence of surface tension and fluid pressure profoundly influence biology at the molecular and cellular level as well as at the whole-body level. Gravity sensing mechanisms are altered, structural and functional components of biology (such as bone and muscle) are reduced and changes in the way fluids and gasses behave also drive the way microbial systems and biofilms grow as well as the way plants and animals adapt. The radiation environment also effects life in space. Solar particle events and high energy cosmic radiation can cause serious damage to DNA and other biomolecules. The results can cause mutation, cellular damage or death, leading to health consequences of acute radiation damage or long-term health consequences such as increased cancer risk. Space Biophysics is the study and utilization of physical changes in space that cause changes in biological systems. The unique physical environment in space has been used successfully to grow high-quality protein crystals and 3D tissue cultures that could not be grown in the presence of unidirectional gravitational acceleration here on Earth. All biological processes that change in space have their root in a biophysical alteration due to microgravity and/or the radiation environment of space. In order to fully-understand the risks to human health in space and to fully-understand how humans, plants, animals and microbes can safely and effectively travel and eventually live for long periods beyond

  4. 19th International School of Biophysics "Ettore Majorana"

    CERN Document Server

    Blank, M; Bioelectrochemistry III : Charge Separation across Biomembranes

    1988-01-01

    This book contains aseries of review papers related to the lectures given at the Third Course on Bioelectrochemistry held at Erice in November 1988, in the framework of the International School of Biophysics. The topics covered by this course, "Charge Separation Across Biomembranes, " deal with the electrochemical aspects of some basic phenomena in biological systems, such as transport of ions, ATP synthesis, formation and maintenance of ionic and protonic gradients. In the first part of the course some preliminary lectures introduce the students to the most basic phenomena and technical aspects of membrane bioelectrochemistry. The remaining part of the course is devoted to the description of a selected group of membrane-enzyme systems, capable of promoting, or exploiting, the processes of separation of electrically charged entities (electrons or ions) across the membrane barrier. These systems are systematically discussed both from a structural and functional point of view. The effort of the many dis...

  5. Engineered biomaterial and biophysical stimulation as combinatorial strategies to address prosthetic infection by pathogenic bacteria.

    Science.gov (United States)

    Boda, Sunil Kumar; Basu, Bikramjit

    2017-10-01

    A plethora of antimicrobial strategies are being developed to address prosthetic infection. The currently available methods for implant infection treatment include the use of antibiotics and revision surgery. Among the bacterial strains, Staphylococcus species pose significant challenges particularly, with regard to hospital acquired infections. In order to combat such life threatening infectious diseases, researchers have developed implantable biomaterials incorporating nanoparticles, antimicrobial reinforcements, surface coatings, slippery/non-adhesive and contact killing surfaces. This review discusses a few of the biomaterial and biophysical antimicrobial strategies, which are in the developmental stage and actively being pursued by several research groups. The clinical efficacy of biophysical stimulation methods such as ultrasound, electric and magnetic field treatments against prosthetic infection depends critically on the stimulation protocol and parameters of the treatment modality. A common thread among the three biophysical stimulation methods is the mechanism of bactericidal action, which is centered on biophysical rupture of bacterial membranes, the generation of reactive oxygen species (ROS) and bacterial membrane depolarization evoked by the interference of essential ion-transport. Although the extent of antimicrobial effect, normally achieved through biophysical stimulation protocol is insufficient to warrant therapeutic application, a combination of antibiotic/ROS inducing agents and biophysical stimulation methods can elicit a clinically relevant reduction in viable bacterial numbers. In this review, we present a detailed account of both the biomaterial and biophysical approaches for achieving maximum bacterial inactivation. Summarizing, the biophysical stimulation methods in a combinatorial manner with material based strategies can be a more potent solution to control bacterial infections. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B

  6. Quantum Nanobiology and Biophysical Chemistry

    DEFF Research Database (Denmark)

    2013-01-01

    An introduction was provided in the first issue by way of an Editorial to this special two issue volume of Current Physical Chemistry – “Quantum Nanobiology and Biophysical Chemistry” [1]. The Guest Editors would like to thank all the authors and referees who have contributed to this second issue...... protypical photoactive proteins. The two contributions mentioned in the previous editorial where Jalkanen et al. provide a theoretical analysis of a model histidine bearing peptide, including integrated structure, solvation, and vibrational absorption and vibrational circular dichroism treatments...

  7. Research Institute for Medical Biophysics

    International Nuclear Information System (INIS)

    Wynchank, S.

    1989-01-01

    The effects of ionising and non-ionising radiation on rodent tumours and normal tissue were studied in terms of cellular repair and the relevant biochemical and biophysical changes following radiation. Rodent tumours investigated in vivo were the CaNT adenocarcinoma and a chemically induced transplantable rhabdomyosarcoma. Radiations used were 100KVp of X-Rays, neutron beams, various magnetic fields, and microwave radiation of 2450MHz. The biochemical parameters measured were, inter alia, levels of adenosine-5'-triphoshate (ATP) and the specific activity of hexokinase (HK). Metabolic changes in ATP levels and the activity of HK were observed in tumour and normal tissues following ionising and non-ionising radiation in normoxia and hypoxia. The observation that the effect of radiation and chemotherapeutic treatment of some tumours may be size dependent can possibly now be explained by the variation of ATP content with tumour size. The enhanced tumour HK specific activity implies increased metabolism, possibly a consequence of cellular requirements to maintain homeostasis during repair processes. Other research projects of the Research Institute for Medical Biophysics involved, inter alia, gastroesophageal scintigraphies to evaluate the results of new forms of therapy. 1 ill

  8. Biophysical aspects of photodynamic therapy.

    Science.gov (United States)

    Juzeniene, Asta; Nielsen, Kristian Pagh; Moan, Johan

    2006-01-01

    Over the last three decades photodynamic therapy (PDT) has been developed to a useful clinical tool, a viable alternative in the treatment of cancer and other diseases. Several disciplines have contributed to this development: chemistry in the development of new photosensitizing agents, biology in the elucidation of cellular processes involved in PDT, pharmacology and physiology in identifying the mechanisms of distribution of photosensitizers in an organism, and, last but not least, physics in the development of better light sources, dosimetric concepts and construction of imaging devices, optical sensors and spectroscopic methods for determining sensitizer concentrations in different tissues. Physics and biophysics have also helped to focus on the role of pH for sensitizer accumulation, dose rate effects, oxygen depletion, temperature, and optical penetration of light of different wavelengths into various types of tissue. These are all important parameters for optimally effective PDT. The present review will give a brief, physically based, overview of PDT and then discuss some of the main biophysical aspects of this therapeutic modality.

  9. The Mechanics and Biophysics of Hearing

    CERN Document Server

    Geisler, C; Matthews, John; Ruggero, Mario; Steele, Charles

    1990-01-01

    Proceedings of a workshop on the physics and biophysics of hearing that brought together experimenters and modelers working on all aspects of audition. Topics covered include: cochlear mechanical measurements, cochlear models, mechanicals and biophysics of hair cells, efferent control, and ultrastructure.

  10. Nanoscale biophysics of the cell

    CERN Document Server

    Ashrafuzzaman, Mohammad

    2018-01-01

    Macroscopic cellular structures and functions are generally investigated using biological and biochemical approaches. But these methods are no longer adequate when one needs to penetrate deep into the small-scale structures and understand their functions. The cell is found to hold various physical structures, molecular machines, and processes that require physical and mathematical approaches to understand and indeed manipulate them. Disorders in general cellular compartments, perturbations in single molecular structures, drug distribution therein, and target specific drug-binding, etc. are mostly physical phenomena. This book will show how biophysics has revolutionized our way of addressing the science and technology of nanoscale structures of cells, and also describes the potential for manipulating the events that occur in them.

  11. Novicidin interactions with phospholipid membranes

    DEFF Research Database (Denmark)

    Balakrishnan, Vijay Shankar

    Antimicrobial peptides target bacterial cell membranes and are considered as potential antibiotics. Their interactions with cell membranes are studied using different approaches. This thesis comprises of the biophysical investigations on the antimicrobial peptide Novicidin, interacting...... with liposomes. The lipid-induced changes in the peptide due to membrane binding, and the peptide-induced changes in the membrane properties were investigated using various spectroscopic and calorimetric methods, and the structural and thermodynamic aspects of peptide-lipid interactions are discussed. This helps...... in understanding not only the antimicrobial nature of Novicidin, but also sheds light on the membrane-peptide interactions....

  12. Voltage-Gated Sodium Channels: Biophysics, Pharmacology, and Related Channelopathies

    Science.gov (United States)

    Savio-Galimberti, Eleonora; Gollob, Michael H.; Darbar, Dawood

    2012-01-01

    Voltage-gated sodium channels (VGSC) are multi-molecular protein complexes expressed in both excitable and non-excitable cells. They are primarily formed by a pore-forming multi-spanning integral membrane glycoprotein (α-subunit) that can be associated with one or more regulatory β-subunits. The latter are single-span integral membrane proteins that modulate the sodium current (INa) and can also function as cell adhesion molecules. In vitro some of the cell-adhesive functions of the β-subunits may play important physiological roles independently of the α-subunits. Other endogenous regulatory proteins named “channel partners” or “channel interacting proteins” (ChiPs) like caveolin-3 and calmodulin/calmodulin kinase II (CaMKII) can also interact and modulate the expression and/or function of VGSC. In addition to their physiological roles in cell excitability and cell adhesion, VGSC are the site of action of toxins (like tetrodotoxin and saxitoxin), and pharmacologic agents (like antiarrhythmic drugs, local anesthetics, antiepileptic drugs, and newly developed analgesics). Mutations in genes that encode α- and/or β-subunits as well as the ChiPs can affect the structure and biophysical properties of VGSC, leading to the development of diseases termed sodium “channelopathies”.  This review will outline the structure, function, and biophysical properties of VGSC as well as their pharmacology and associated channelopathies and highlight some of the recent advances in this field. PMID:22798951

  13. Voltage-gated sodium channels: biophysics, pharmacology, and related channelopathies

    Directory of Open Access Journals (Sweden)

    Eleonora eSavio Galimberti

    2012-07-01

    Full Text Available Voltage-gated sodium channels (VGSC are multi-molecular protein complexes expressed in both excitable and non-excitable cells. They are primarily formed by a pore-forming multi-spanning integral membrane glycoprotein (α-subunit that can be associated with one or more regulatory β-subunits. The latter are single-span integral membrane proteins that modulate the sodium current (INa and can also function as cell-adhesion molecules (CAMs. In-vitro some of the cell-adhesive functions of the β-subunits may play important physiological roles independently of the α-subunits. Other endogenous regulatory proteins named channel partners or channel interacting proteins (ChiPs like caveolin-3 and calmodulin/calmodulin kinase II (CaMKII can also interact and modulate the expression and/or function of VGSC. In addition to their physiological roles in cell excitability and cell adhesion, VGSC are the site of action of toxins (like tetrodotoxin and saxitoxin, and pharmacologic agents (like antiarrhythmic drugs, local anesthetics, antiepileptic drugs, and newly developed analgesics. Mutations in genes that encode α- and/or β-subunits as well as the ChiPs can affect the structure and biophysical properties of VGSC, leading to the development of diseases termed sodium channelopathies. This review will outline the structure, function and biophysical properties of VGSC as well as their pharmacology and associated channelopathies and highlight some of the recent advances in this field

  14. Biophysical characteristics of cells cultured on cholesteryl ester liquid crystals.

    Science.gov (United States)

    Soon, Chin Fhong; Omar, Wan Ibtisam Wan; Berends, Rebecca F; Nayan, Nafarizal; Basri, Hatijah; Tee, Kian Sek; Youseffi, Mansour; Blagden, Nick; Denyer, Morgan Clive Thomas

    2014-01-01

    This study aimed at examining the biophysical characteristics of human derived keratinocytes (HaCaT) cultured on cholesteryl ester liquid crystals (CELC). CELC was previously shown to improve sensitivity in sensing cell contractions. Characteristics of the cell integrin expressions and presence of extracellular matrix (ECM) proteins on the liquid crystals were interrogated using various immunocytochemical techniques. The investigation was followed by characterization of the chemical properties of the liquid crystals (LC) after immersion in cell culture media using Fourier transform infrared spectroscopy (FTIR). The surface morphology of cells adhered to the LC was studied using atomic force microscopy (AFM). Consistent with the expressions of the integrins α2, α3 and β1, extracellular matrix proteins (laminin, collagen type IV and fibronectin) were found secreted by the HaCaT onto CELC and these proteins were also secreted by cells cultured on the glass substrates. FTIR analysis of the LC revealed the existence of spectrum assigned to cholesterol and ester moieties that are essential compounds for the metabolizing activities of keratinocytes. The immunostainings indicated that cell adhesion on the LC is mediated by self-secreted ECM proteins. As revealed by the AFM imaging, the constraint in cell membrane spread on the LC leads to the increase in cell surface roughness and thickness of cell membrane. The biophysical expressions of cells on biocompatible CELC suggested that CELC could be a new class of biological relevant material. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. Historical and Critical Review on Biophysical Economics

    Science.gov (United States)

    Adigüzel, Yekbun

    2016-07-01

    Biophysical economics is initiated with the long history of the relation of economics with ecological basis and biophysical perspectives of the physiocrats. It inherently has social, economic, biological, environmental, natural, physical, and scientific grounds. Biological entities in economy like the resources, consumers, populations, and parts of production systems, etc. could all be dealt by biophysical economics. Considering this wide scope, current work is a “biophysical economics at a glance” rather than a comprehensive review of the full range of topics that may just be adequately covered in a book-length work. However, the sense of its wide range of applications is aimed to be provided to the reader in this work. Here, modern approaches and biophysical growth theory are presented after the long history and an overview of the concepts in biophysical economics. Examples of the recent studies are provided at the end with discussions. This review is also related to the work by Cleveland, “Biophysical Economics: From Physiocracy to Ecological Economics and Industrial Ecology” [C. J. Cleveland, in Advances in Bioeconomics and Sustainability: Essay in Honor of Nicholas Gerogescu-Roegen, eds. J. Gowdy and K. Mayumi (Edward Elgar Publishing, Cheltenham, England, 1999), pp. 125-154.]. Relevant parts include critics and comments on the presented concepts in a parallelized fashion with the Cleveland’s work.

  16. An introduction to environmental biophysics

    CERN Document Server

    Campbell, Gaylon S

    1977-01-01

    The study of environmental biophysics probably began earlier in man's history than that of any other science. The study of organism-environment interaction provided a key to survival and progress. Systematic study of the science and recording of experimental results goes back many hundreds of years. Ben­ jamin Franklin, the early American statesman, inventor, printer, and scientist studied conduction, evaporation, and radiation. One of his observations is as follows: My desk on which I now write, and the lock of my desk, are both exposed to the same temperature of the air, and have therefore the same degree of heat or cold; yet if I lay my hand successively on the wood and on the metal, the latter feels much the coldest, not that it is really so, but being a better conductor, it more readily than the wood takes away and draws into itself the fire that was in my skin. 1 Franklin probably was not the first to discover this principle, and certainly was not the last. Modem researchers rediscover this principle f...

  17. Applications of synchrotron radiation in Biophysics

    International Nuclear Information System (INIS)

    Bemski, G.

    1983-01-01

    A short introduction to the generation of the synchrotron radiation is made. Following, the applications of such a radiation in biophysics with emphasis to the study of the hemoglobin molecule are presented. (L.C.) [pt

  18. Symposium on Biophysics and Physiology of Biological Transport

    CERN Document Server

    Capraro, V; Porter, K; Robertson, J

    1967-01-01

    The study of cell membranes began to attract increasing interest before the turn of the present century with the observations of 0 verton. Since that time many investigators have become interested in the broad problem of structure and function of the membrane and today we find ourselVes at a stage in which several branches of research, particularly physical chemistry, biochemistry, biophysics, physiology and pharmacology have come together, leading to the possibility of obtaining a better perspective of the overall problems. The purpose of this Symposium was to assemble in an orderly sequence representations of the knowledge of membranes achieved to date in the areas of the various disciplines. It was thought that to bring together many points of view on a problem should allow the conferees to see better what had been accomplished, what has been overlooked and what needs further development. It is to be hoped that efforts of this type have and will fulfill the desired purpose. This volume contains the majorit...

  19. Biophysics of malarial parasite exit from infected erythrocytes.

    Science.gov (United States)

    Chandramohanadas, Rajesh; Park, YongKeun; Lui, Lena; Li, Ang; Quinn, David; Liew, Kingsley; Diez-Silva, Monica; Sung, Yongjin; Dao, Ming; Lim, Chwee Teck; Preiser, Peter Rainer; Suresh, Subra

    2011-01-01

    Upon infection and development within human erythrocytes, P. falciparum induces alterations to the infected RBC morphology and bio-mechanical properties to eventually rupture the host cells through parasitic and host derived proteases of cysteine and serine families. We used previously reported broad-spectrum inhibitors (E64d, EGTA-AM and chymostatin) to inhibit these proteases and impede rupture to analyze mechanical signatures associated with parasite escape. Treatment of late-stage iRBCs with E64d and EGTA-AM prevented rupture, resulted in no major RBC cytoskeletal reconfiguration but altered schizont morphology followed by dramatic re-distribution of three-dimensional refractive index (3D-RI) within the iRBC. These phenotypes demonstrated several-fold increased iRBC membrane flickering. In contrast, chymostatin treatment showed no 3D-RI changes and caused elevated fluctuations solely within the parasitophorous vacuole. We show that E64d and EGTA-AM supported PV breakdown and the resulting elevated fluctuations followed non-Gaussian pattern that resulted from direct merozoite impingement against the iRBC membrane. Optical trapping experiments highlighted reduced deformability of the iRBC membranes upon rupture-arrest, more specifically in the treatments that facilitated PV breakdown. Taken together, our experiments provide novel mechanistic interpretations on the role of parasitophorous vacuole in maintaining the spherical schizont morphology, the impact of PV breakdown on iRBC membrane fluctuations leading to eventual parasite escape and the evolution of membrane stiffness properties of host cells in which merozoites were irreversibly trapped, recourse to protease inhibitors. These findings provide a comprehensive, previously unavailable, body of information on the combined effects of biochemical and biophysical factors on parasite egress from iRBCs.

  20. Biophysical Regulation of Vascular Differentiation and Assembly

    CERN Document Server

    Gerecht, Sharon

    2011-01-01

    The ability to grow stem cells in the laboratory and to guide their maturation to functional cells allows us to study the underlying mechanisms that govern vasculature differentiation and assembly in health and disease. Accumulating evidence suggests that early stages of vascular growth are exquisitely tuned by biophysical cues from the microenvironment, yet the scientific understanding of such cellular environments is still in its infancy. Comprehending these processes sufficiently to manipulate them would pave the way to controlling blood vessel growth in therapeutic applications. This book assembles the works and views of experts from various disciplines to provide a unique perspective on how different aspects of its microenvironment regulate the differentiation and assembly of the vasculature. In particular, it describes recent efforts to exploit modern engineering techniques to study and manipulate various biophysical cues. Biophysical Regulation of Vascular Differentiation and Assembly provides an inter...

  1. Biophysical Modeling of Respiratory Organ Motion

    Science.gov (United States)

    Werner, René

    Methods to estimate respiratory organ motion can be divided into two groups: biophysical modeling and image registration. In image registration, motion fields are directly extracted from 4D ({D}+{t}) image sequences, often without concerning knowledge about anatomy and physiology in detail. In contrast, biophysical approaches aim at identification of anatomical and physiological aspects of breathing dynamics that are to be modeled. In the context of radiation therapy, biophysical modeling of respiratory organ motion commonly refers to the framework of continuum mechanics and elasticity theory, respectively. Underlying ideas and corresponding boundary value problems of those approaches are described in this chapter, along with a brief comparison to image registration-based motion field estimation.

  2. Global energy modeling - A biophysical approach

    Energy Technology Data Exchange (ETDEWEB)

    Dale, Michael

    2010-09-15

    This paper contrasts the standard economic approach to energy modelling with energy models using a biophysical approach. Neither of these approaches includes changing energy-returns-on-investment (EROI) due to declining resource quality or the capital intensive nature of renewable energy sources. Both of these factors will become increasingly important in the future. An extension to the biophysical approach is outlined which encompasses a dynamic EROI function that explicitly incorporates technological learning. The model is used to explore several scenarios of long-term future energy supply especially concerning the global transition to renewable energy sources in the quest for a sustainable energy system.

  3. Parameter estimation in neuronal stochastic differential equation models from intracellular recordings of membrane potentials in single neurons

    DEFF Research Database (Denmark)

    Ditlevsen, Susanne; Samson, Adeline

    2016-01-01

    Dynamics of the membrane potential in a single neuron can be studied by estimating biophysical parameters from intracellular recordings. Diffusion processes, given as continuous solutions to stochastic differential equations, are widely applied as models for the neuronal membrane potential evolut...

  4. Membrane order in the plasma membrane and endocytic recycling compartment.

    Science.gov (United States)

    Iaea, David B; Maxfield, Frederick R

    2017-01-01

    The cholesterol content of membranes plays an important role in organizing membranes for signal transduction and protein trafficking as well as in modulating the biophysical properties of membranes. While the properties of model or isolated membranes have been extensively studied, there has been little evaluation of internal membranes in living cells. Here, we use a Nile Red based probe, NR12S, and ratiometric live cell imaging, to analyze the membrane order of the plasma membrane and endocytic recycling compartment. We find that after a brief incubation to allow endocytosis, NR12S is distributed between the plasma membrane and the endocytic recycling compartment. The NR12S reports that the endocytic recycling compartment is more highly ordered than the plasma membrane. We also find that the plasma membrane and the endocytic recycling compartment are differentially affected by altering cellular cholesterol levels. The membrane order of the plasma membrane, but not the endocytic recycling compartment, is altered significantly when cellular cholesterol content is increased or decreased by 20%. These results demonstrate that changes in cellular cholesterol differentially alter membrane order within different organelles.

  5. Biophysics of Hair Cell Sensory Systems

    NARCIS (Netherlands)

    Duifhuis, Hendrikus; Horst, Johannes; van Dijk, Pim; van Netten, Sietse

    1993-01-01

    The last decade revealed to auditory researchers that hair cells can not only detect and process mechanical energy, but are also able to produce it. Thanks to the active hair cell, ears can produce otoacoustic emissions. This book gives the newest insights into the biophysics and physiology of

  6. Epigenetic modulation of the biophysical properties of drug-resistant cell lipids to restore drug transport and endocytic functions.

    Science.gov (United States)

    Vijayaraghavalu, Sivakumar; Peetla, Chiranjeevi; Lu, Shan; Labhasetwar, Vinod

    2012-09-04

    In our recent studies exploring the biophysical characteristics of resistant cell lipids, and the role they play in drug transport, we demonstrated the difference of drug-resistant breast cancer cells from drug-sensitive cells in lipid composition and biophysical properties, suggesting that cancer cells acquire a drug-resistant phenotype through the alteration of lipid synthesis to inhibit intracellular drug transport to protect from cytotoxic effect. In cancer cells, epigenetic changes (e.g., DNA hypermethylation) are essential to maintain this drug-resistant phenotype. Thus, altered lipid synthesis may be linked to epigenetic mechanisms of drug resistance. We hypothesize that reversing DNA hypermethylation in resistant cells with an epigenetic drug could alter lipid synthesis, changing the cell membrane's biophysical properties to facilitate drug delivery to overcome drug resistance. Herein we show that treating drug-resistant breast cancer cells (MCF-7/ADR) with the epigenetic drug 5-aza-2'-deoxycytidine (decitabine) significantly alters cell lipid composition and biophysical properties, causing the resistant cells to acquire biophysical characteristics similar to those of sensitive cell (MCF-7) lipids. Following decitabine treatment, resistant cells demonstrated increased sphingomyelinase activity, resulting in a decreased sphingomyelin level that influenced lipid domain structures, increased membrane fluidity, and reduced P-glycoprotein expression. Changes in the biophysical characteristics of resistant cell lipids facilitated doxorubicin transport and restored endocytic function for drug delivery with a lipid-encapsulated form of doxorubicin, enhancing the drug efficacy. In conclusion, we have established a new mechanism for efficacy of an epigenetic drug, mediated through changes in lipid composition and biophysical properties, in reversing cancer drug resistance.

  7. Single File Dynamics Advances with a Focus on Biophysical Relevance

    Science.gov (United States)

    Flomenbom, Ophir

    2014-08-01

    In this review (appearing in the Special Issue on single file dynamics in biophysics and related extensions), three recently treated variants in file dynamics are presented: files with density that is not fixed, files with heterogeneous particles, and files with slow particles. The results in these files include: • In files with a density law that is not fixed, but decays as a power law with an exponent a the distance from the origin, the particle in the origin mean square displacement (MSD) scales like MSD t[1+a]/2, with a Gaussian probability density function (PDF). This extends the scaling, MSD t1/2, seen in a constant density file. • When, in addition, the particles' diffusion coefficients are distributed like a power law with an exponent γ (around the origin), the MSD follows MSD t[1-γ]/[2/(1+a) - γ], with a Gaussian PDF. • In anomalous files that are renewal, namely, when all particles attempt a jump together, yet, with jump times taken from a PDF that decays as a power law with an exponent -1 - ɛ, ψ(t) t-1-ɛ, the MSD scales like the MSD of the corresponding normal file, in the power ɛ. • In anomalous files of independent particles, the MSD is very slow and scales like MSD log2(t). Even more exciting, the particles form clusters, defining a dynamical phase transition: depending on the anomaly power ɛ, the percentage of particles in clusters ξ follows ξ = √ {1-ǎrepsilon3}, yet when ɛ > 1, fluidity rather than clusters is seen. We talk about utilizing these results while focusing on biophysical processes and applications: dynamics in channels, membranes, biosensors, etc. Special Issue Comments: In this article, results about recently suggested variants in single file dynamics appear: heterogeneous files and slow files, yet also, the relevance with biophysical processes. It is related to the Special Issue articles about expansions in files,61 files with force,62 and the zig zag occurrences in files.63

  8. Teaching wave phenomena via biophysical applications

    Science.gov (United States)

    Reich, Daniel; Robbins, Mark; Leheny, Robert; Wonnell, Steven

    2014-03-01

    Over the past several years we have developed a two-semester second-year physics course sequence for students in the biosciences, tailored in part to the needs of undergraduate biophysics majors. One semester, ``Biological Physics,'' is based on the book of that name by P. Nelson. This talk will focus largely on the other semester, ``Wave Phenomena with Biophysical Applications,'' where we provide a novel introduction to the physics of waves, primarily through the study of experimental probes used in the biosciences that depend on the interaction of electromagnetic radiation with matter. Topic covered include: Fourier analysis, sound and hearing, diffraction - culminating in an analysis of x-ray fiber diffraction and its use in the determination of the structure of DNA - geometrical and physical optics, the physics of modern light microscopy, NMR and MRI. Laboratory exercises tailored to this course will also be described.

  9. Biophysical Evaluation of SonoSteam®:

    DEFF Research Database (Denmark)

    Andersen, Ann Zahle; Duelund, Lars; Brewer, Jonathan R.

    /response relationship between SonoSteam treatment time and changes in collagen I, and a depth dependency in bacterial reduction, which points toward CFU counts overestimating total bacterial reduction. In conclusion the biophysical methods provide a less biased, reproducible and highly detailed system description......In this study we employ a biophysical and molecular approach for the investigation of qualitative and quantitative changes in both food surface and bacteria upon surface decontamination by SonoSteam®. SonoSteam® is a recently developed method of food surface decontamination, which employs steam...... and ultrasound for effective heat transfer and short treatment times, resulting in significant reduction in surface bacteria. An efficient decontamination method should be cheap and fast, while eliminating harmful microorganism without decreasing the quality of the food. However, all known methods represent...

  10. Biophysics and the Challenges of Emerging Threats

    CERN Document Server

    Puglisi, Joseph D

    2009-01-01

    This volume is a collection of articles from the proceedings of the International School of Structural Biology and Magnetic Resonance 8th Course: Biophysics and the Challenges of Emerging Threats. This NATO Advance Study Institute (ASI) was held in Erice at the Ettore Majorana Foundation and Centre for Scientific Culture on 19 through 30 June 2007. The ASI brought together a diverse group of experts who bridged the fields of virology and biology, biophysics, chemistry and physics. Prominent lecturers and students from around the world representant a total of 24 countries participated in the NATO ASI organized by Professors Joseph Puglisi (Stanford University, USA) and Alexander Arseniev (Moscow, RU). The central hypothesis underlying this ASI was that interdisciplinary research, merging principles of physics, chemistry and biology, can drive new discovery in detecting and fighting bioterrorism agents, lead to cleaner environments, and help propel development in NATO partner countries. The ASI merged the relat...

  11. Handbook of Single-Molecule Biophysics

    CERN Document Server

    Hinterdorfer, Peter

    2009-01-01

    The last decade has seen the development of a number of novel biophysical methods that allow the manipulation and study of individual biomolecules. The ability to monitor biological processes at this fundamental level of sensitivity has given rise to an improved understanding of the underlying molecular mechanisms. Through the removal of ensemble averaging, distributions and fluctuations of molecular properties can be characterized, transient intermediates identified, and catalytic mechanisms elucidated. By applying forces on biomolecules while monitoring their activity, important information can be obtained on how proteins couple function to structure. The Handbook of Single-Molecule Biophysics provides an introduction to these techniques and presents an extensive discussion of the new biological insights obtained from them. Coverage includes: Experimental techniques to monitor and manipulate individual biomolecules The use of single-molecule techniques in super-resolution and functional imaging Single-molec...

  12. A biophysical analysis of latitudinal tree line

    Science.gov (United States)

    Goetz, S. J.; Loranty, M. M.; Berner, L.; Jin, Y.; Randerson, J. T.

    2011-12-01

    Northern latitudinal tree line represents the interface between boreal forests and tundra ecosystems, and is the ecophysiological limit of tree recruitment and persistence. The transition between tundra and forest is typically gradual, occurring over tens to hundreds of kilometers. This gradient represents a substantial change in the biophysical properties of the earth surface, one that is particularly important in ecosystems that are snow covered for much of the year. Tree line is, however, commonly delineated by the point of the northern most tree, with no gradient between forested and non-forested ecosystems. As a consequence crisp delineations of tree line incorporated into models introduce error in surface radiation budgets due to inaccurate albedo representations. Errors in modeled carbon and water fluxes are likely as well. Here we use satellite observations to quantify several key biophysical properties across latitudinal tree line for a series of sites throughout the pan-boreal region We find decreases in NDVI and increases in albedo across the transition from boreal forest to tundra, as expected. However, in the absence of topographical barriers we find that these transitions can occur over upwards of 100 km, and that biophysical properties characteristic of tundra ecosystems can occur as far as 100 km south of tree line. This suggests that land surface models likely overestimate surface radiation budgets and carbon fluxes in the boreal biome. We discuss our results in the context of land surface models, noting specific examples from archived model runs.

  13. Enhancing Irreversible Electroporation by Manipulating Cellular Biophysics with a Molecular Adjuvant.

    Science.gov (United States)

    Ivey, Jill W; Latouche, Eduardo L; Richards, Megan L; Lesser, Glenn J; Debinski, Waldemar; Davalos, Rafael V; Verbridge, Scott S

    2017-07-25

    Pulsed electric fields applied to cells have been used as an invaluable research tool to enhance delivery of genes or other intracellular cargo, as well as for tumor treatment via electrochemotherapy or tissue ablation. These processes involve the buildup of charge across the cell membrane, with subsequent alteration of transmembrane potential that is a function of cell biophysics and geometry. For traditional electroporation parameters, larger cells experience a greater degree of membrane potential alteration. However, we have recently demonstrated that the nuclear/cytoplasm ratio (NCR), rather than cell size, is a key predictor of response for cells treated with high-frequency irreversible electroporation (IRE). In this study, we leverage a targeted molecular therapy, ephrinA1, known to markedly collapse the cytoplasm of cells expressing the EphA2 receptor, to investigate how biophysical cellular changes resulting from NCR manipulation affect the response to IRE at varying frequencies. We present evidence that the increase in the NCR mitigates the cell death response to conventional electroporation pulsed-electric fields (∼100 μs), consistent with the previously noted size dependence. However, this same molecular treatment enhanced the cell death response to high-frequency electric fields (∼1 μs). This finding demonstrates the importance of considering cellular biophysics and frequency-dependent effects in developing electroporation protocols, and our approach provides, to our knowledge, a novel and direct experimental methodology to quantify the relationship between cell morphology, pulse frequency, and electroporation response. Finally, this novel, to our knowledge, combinatorial approach may provide a paradigm to enhance in vivo tumor ablation through a molecular manipulation of cellular morphology before IRE application. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  14. ECClipids17: adapting atomistic lipid models to correct cation-membrane interactions

    Czech Academy of Sciences Publication Activity Database

    Melcr, Josef; Ollila, Samuli; Baxová, Katarína; Jungwirth, Pavel; Martinez-Seara, Hector

    2017-01-01

    Roč. 46, Suppl 1 (2017), S224 ISSN 0175-7571. [IUPAB congress /19./ and EBSA congress /11./. 16.07.2017-20.07.2017, Edinburgh] Institutional support: RVO:61388963 Keywords : ECC * membrane interactions Subject RIV: BO - Biophysics

  15. Terahertz dielectric relaxation of biological water confined in model membranes made of lyotropic phospholipids

    NARCIS (Netherlands)

    Paparo, D.; Tielrooij, K.J.; Bakker, H.J.; Bonn, M.

    2009-01-01

    Understanding water-membrane interactions is a fundamental issue in biophysics since these interactions are at the basis of many key molecular processes occurring in membranes. The hydrogen-bond network of water molecules is highly dynamic and its dynamical structure influences membrane fluidity and

  16. Radiobiology, biochemistry and radiation biophysics at CYLAB

    International Nuclear Information System (INIS)

    Ftacnikova, S.

    1998-01-01

    The Cyclotron Laboratory (CYLAB) should fill the gap in the field of nuclear medicine, radiotherapy, basic research, metrology of ionizing radiation, education and implications of accelerator technology existing today in Slovak Republic. The main planned activities of this facility are in the fields of nuclear medicine (production of radioisotopes for Positron Emission Tomography - PET and for oncology) and radiotherapy (neutron capture therapy, fast neutron therapy and proton therapy). The radiobiological and biophysical research will be closely connected with medical applications, particularly with radiotherapy. Problems to be addressed include the determination of the values of Relative Biological Effectiveness (RBE) for different types of ionizing radiation involved in the therapy, microdosimetric measurements and calculations, which are indispensable in the calculation of the absorbed dose (lineal and specific energy spectra) at the cellular and macromolecular level. Radiation biophysics and medical physics help in creating therapeutic plans for radiotherapy (NCT and fast neutron therapy). In nuclear medicine, in diagnostic and therapeutical procedures it is necessary to assess the biodistribution of radiopharmaceuticals and to calculate doses in target and critical organs and to determine whole body burden - effective equivalent dose for newly developed radiopharmaceuticals

  17. Modeling disordered protein interactions from biophysical principles.

    Directory of Open Access Journals (Sweden)

    Lenna X Peterson

    2017-04-01

    Full Text Available Disordered protein-protein interactions (PPIs, those involving a folded protein and an intrinsically disordered protein (IDP, are prevalent in the cell, including important signaling and regulatory pathways. IDPs do not adopt a single dominant structure in isolation but often become ordered upon binding. To aid understanding of the molecular mechanisms of disordered PPIs, it is crucial to obtain the tertiary structure of the PPIs. However, experimental methods have difficulty in solving disordered PPIs and existing protein-protein and protein-peptide docking methods are not able to model them. Here we present a novel computational method, IDP-LZerD, which models the conformation of a disordered PPI by considering the biophysical binding mechanism of an IDP to a structured protein, whereby a local segment of the IDP initiates the interaction and subsequently the remaining IDP regions explore and coalesce around the initial binding site. On a dataset of 22 disordered PPIs with IDPs up to 69 amino acids, successful predictions were made for 21 bound and 18 unbound receptors. The successful modeling provides additional support for biophysical principles. Moreover, the new technique significantly expands the capability of protein structure modeling and provides crucial insights into the molecular mechanisms of disordered PPIs.

  18. A mathematical approach to protein biophysics

    CERN Document Server

    Scott, L Ridgway

    2017-01-01

    This book explores quantitative aspects of protein biophysics and attempts to delineate certain rules of molecular behavior that make atomic scale objects behave in a digital way.  This book will help readers to understand how certain biological systems involving proteins function as digital information systems despite the fact that underlying processes are analog in nature. The in-depth explanation of proteins from a quantitative point of view and the variety of level of exercises (including physical experiments) at the end of each chapter will appeal to graduate and senior undergraduate students in mathematics, computer science, mechanical engineering, and physics, wanting to learn about the biophysics of proteins.  L. Ridgway Scott has been Professor of Computer Science and of Mathematics at the University of Chicago since 1998, and the Louis Block Professor since 2001.  He obtained a B.S. degree (Magna Cum Laude) from Tulane University in 1969 and a PhD degree in Mathematics from the Massachusetts Ins...

  19. Cellular Biophysics During Freezing of Rat and Mouse Sperm Predicts Post-thaw Motility1

    Science.gov (United States)

    Hagiwara, Mie; Choi, Jeung Hwan; Devireddy, Ramachandra V.; Roberts, Kenneth P.; Wolkers, Willem F.; Makhlouf, Antoine; Bischof, John C.

    2009-01-01

    Though cryopreservation of mouse sperm yields good survival and motility after thawing, cryopreservation of rat sperm remains a challenge. This study was designed to evaluate the biophysics (membrane permeability) of rat in comparison to mouse to better understand the cooling rate response that contributes to cryopreservation success or failure in these two sperm types. In order to extract subzero membrane hydraulic permeability in the presence of ice, a differential scanning calorimeter (DSC) method was used. By analyzing rat and mouse sperm frozen at 5°C/min and 20°C/min, heat release signatures characteristic of each sperm type were obtained and correlated to cellular dehydration. The dehydration response was then fit to a model of cellular water transport (dehydration) by adjusting cell-specific biophysical (membrane hydraulic permeability) parameters Lpg and ELp. A “combined fit” (to 5°C/min and 20°C/min data) for rat sperm in Biggers-Whitten-Whittingham media yielded Lpg = 0.007 μm min−1 atm−1 and ELp = 17.8 kcal/mol, and in egg yolk cryopreservation media yielded Lpg = 0.005 μm min−1 atm−1 and ELp = 14.3 kcal/mol. These parameters, especially the activation energy, were found to be lower than previously published parameters for mouse sperm. In addition, the biophysical responses in mouse and rat sperm were shown to depend on the constituents of the cryopreservation media, in particular egg yolk and glycerol. Using these parameters, optimal cooling rates for cryopreservation were predicted for each sperm based on a criteria of 5%–15% normalized cell water at −30°C during freezing in cryopreservation media. These predicted rates range from 53°C/min to 70°C/min and from 28°C/min to 36°C/min in rat and mouse, respectively. These predictions were validated by comparison to experimentally determined cryopreservation outcomes, in this case based on motility. Maximum motility was obtained with freezing rates between 50°C/min and 80

  20. Cellular biophysics during freezing of rat and mouse sperm predicts post-thaw motility.

    Science.gov (United States)

    Hagiwara, Mie; Choi, Jeung Hwan; Devireddy, Ramachandra V; Roberts, Kenneth P; Wolkers, Willem F; Makhlouf, Antoine; Bischof, John C

    2009-10-01

    Though cryopreservation of mouse sperm yields good survival and motility after thawing, cryopreservation of rat sperm remains a challenge. This study was designed to evaluate the biophysics (membrane permeability) of rat in comparison to mouse to better understand the cooling rate response that contributes to cryopreservation success or failure in these two sperm types. In order to extract subzero membrane hydraulic permeability in the presence of ice, a differential scanning calorimeter (DSC) method was used. By analyzing rat and mouse sperm frozen at 5 degrees C/min and 20 degrees C/min, heat release signatures characteristic of each sperm type were obtained and correlated to cellular dehydration. The dehydration response was then fit to a model of cellular water transport (dehydration) by adjusting cell-specific biophysical (membrane hydraulic permeability) parameters L(pg) and E(Lp). A "combined fit" (to 5 degrees C/min and 20 degrees C/min data) for rat sperm in Biggers-Whitten-Whittingham media yielded L(pg) = 0.007 microm min(-1) atm(-1) and E(Lp) = 17.8 kcal/mol, and in egg yolk cryopreservation media yielded L(pg) = 0.005 microm min(-1) atm(-1) and E(Lp) = 14.3 kcal/mol. These parameters, especially the activation energy, were found to be lower than previously published parameters for mouse sperm. In addition, the biophysical responses in mouse and rat sperm were shown to depend on the constituents of the cryopreservation media, in particular egg yolk and glycerol. Using these parameters, optimal cooling rates for cryopreservation were predicted for each sperm based on a criteria of 5%-15% normalized cell water at -30 degrees C during freezing in cryopreservation media. These predicted rates range from 53 degrees C/min to 70 degrees C/min and from 28 degrees C/min to 36 degrees C/min in rat and mouse, respectively. These predictions were validated by comparison to experimentally determined cryopreservation outcomes, in this case based on motility. Maximum

  1. Importance of the hexagonal lipid phase in biological membrane organisation

    Directory of Open Access Journals (Sweden)

    Juliette eJouhet

    2013-12-01

    Full Text Available Abstract:Domains are present in every natural membrane. They are characterised by a distinctive protein and/or lipid composition. Their size is highly variable from the nano- to the micrometer scale. The domains confer specific properties to the membrane leading to original structure and function. The determinants leading to domain organisation are therefore important but remain obscure. This review presents how the ability of lipids to organize into hexagonal II or lamellar phases can promote particular local structures within membranes. Since biological membranes are composed of a mixture of lipids, each with distinctive biophysical properties, lateral and transversal sorting of lipids can promote creation of domains inside the membrane through local modulation of the lipid phase. Lipid biophysical properties have been characterized for long based on in vitro analyses using non-natural lipid molecules; their re-examinations using natural lipids might open interesting perspectives on membrane architecture occurring in vivo in various cellular and physiological contexts.

  2. A biophysical approach to the optimisation of dendritic-tumour cell electrofusion

    International Nuclear Information System (INIS)

    Sukhorukov, Vladimir L.; Reuss, Randolph; Endter, Joerg M.; Fehrmann, Steffen; Katsen-Globa, Alisa; Gessner, Petra; Steinbach, Andrea; Mueller, Kilian J.; Karpas, Abraham; Zimmermann, Ulrich; Zimmermann, Heiko

    2006-01-01

    Electrofusion of tumour and dendritic cells (DCs) is a promising approach for production of DC-based anti-tumour vaccines. Although human DCs are well characterised immunologically, little is known about their biophysical properties, including dielectric and osmotic parameters, both of which are essential for the development of efficient electrofusion protocols. In the present study, human DCs from the peripheral blood along with a tumour cell line used as a model fusion partner were examined by means of time-resolved cell volumetry and electrorotation. Based on the biophysical cell data, the electrofusion protocol could be rapidly optimised with respect to the sugar composition of the fusion medium, duration of hypotonic treatment, frequency range for stable cell alignment, and field strengths of breakdown pulses triggering membrane fusion. The hypotonic electrofusion consistently gave a tumour-DC hybrid rate of up to 19%, as determined by counting dually labelled fluorescent hybrids in a microscope. This fusion rate is nearly twice as high as that usually reported in the literature for isotonic media. The experimental findings and biophysical approach presented here are generally useful for the development of efficient electrofusion protocols, especially for rare and valuable human cells

  3. Resolving the biophysics of axon transmembrane polarization in a single closed-form description

    Energy Technology Data Exchange (ETDEWEB)

    Melendy, Robert F., E-mail: rfmelendy@liberty.edu [School of Engineering and Computational Sciences, Liberty University, Lynchburg, Virginia 24515 (United States)

    2015-12-28

    When a depolarizing event occurs across a cell membrane there is a remarkable change in its electrical properties. A complete depolarization event produces a considerably rapid increase in voltage that propagates longitudinally along the axon and is accompanied by changes in axial conductance. A dynamically changing magnetic field is associated with the passage of the action potential down the axon. Over 75 years of research has gone into the quantification of this phenomenon. To date, no unified model exist that resolves transmembrane polarization in a closed-form description. Here, a simple but formative description of propagated signaling phenomena in the membrane of an axon is presented in closed-form. The focus is on using both biophysics and mathematical methods for elucidating the fundamental mechanisms governing transmembrane polarization. The results presented demonstrate how to resolve electromagnetic and thermodynamic factors that govern transmembrane potential. Computational results are supported by well-established quantitative descriptions of propagated signaling phenomena in the membrane of an axon. The findings demonstrate how intracellular conductance, the thermodynamics of magnetization, and current modulation function together in generating an action potential in a unified closed-form description. The work presented in this paper provides compelling evidence that three basic factors contribute to the propagated signaling in the membrane of an axon. It is anticipated this work will compel those in biophysics, physical biology, and in the computational neurosciences to probe deeper into the classical and quantum features of membrane magnetization and signaling. It is hoped that subsequent investigations of this sort will be advanced by the computational features of this model without having to resort to numerical methods of analysis.

  4. The trans-membrane potential of biological membranes in computer simulation

    Czech Academy of Sciences Publication Activity Database

    Melcr, Josef; Timr, Štěpán; Jungwirth, Pavel

    2015-01-01

    Roč. 44, Suppl 1 (2015), S170 ISSN 0175-7571. [EBSA European Biophysics Congress /10./. 18.07.2015-22.07.2015, Dresden] Institutional support: RVO:61388963 Keywords : molecular dynamics * trans-membrane potential Subject RIV: CF - Physical ; Theoretical Chemistry

  5. Single-molecule experiments in biophysics: Exploring the thermal ...

    Indian Academy of Sciences (India)

    cules contributes to our understanding of the nonequilibrium thermal behavior of small systems. Keywords. Biophysics; single-molecule experiments; fluctuation theorems. PACS Nos 05.70.Ln; 82.37.Rs; 87.10.+e; 87.15.Ya. 1. Biomolecules, molecular demons and statistical physics. Biophysics is a relatively young discipline ...

  6. Evaluating the suitability of coupled biophysical models for fishery management

    NARCIS (Netherlands)

    Hinrichsen, H.H.; Dickey-Collas, M.; Huret, M.; Peck, M.A.

    2011-01-01

    The potential role of coupled biophysical models in enhancing the conservation, management, and recovery of fish stocks is assessed, with emphasis on anchovy, cod, herring, and sprat in European waters. The assessment indicates that coupled biophysical models are currently capable of simulating

  7. Microwave Tissue Ablation: Biophysics, Technology and Applications

    Science.gov (United States)

    2010-01-01

    Microwave ablation is an emerging treatment option for many cancers, cardiac arrhythmias and other medical conditions. During treatment, microwaves are applied directly to tissues to produce rapid temperature elevations sufficient to produce immediate coagulative necrosis. The engineering design criteria for each application differ, with individual consideration for factors such as desired ablation zone size, treatment duration, and procedural invasiveness. Recent technological developments in applicator cooling, power control and system optimization for specific applications promise to increase the utilization of microwave ablation in the future. This article will review the basic biophysics of microwave tissue heating, provide an overview of the design and operation of current equipment, and outline areas for future research for microwave ablation. PMID:21175404

  8. Biophysics of NASA radiation quality factors.

    Science.gov (United States)

    Cucinotta, Francis A

    2015-09-01

    NASA has implemented new radiation quality factors (QFs) for projecting cancer risks from space radiation exposures to astronauts. The NASA QFs are based on particle track structure concepts with parameters derived from available radiobiology data, and NASA introduces distinct QFs for solid cancer and leukaemia risk estimates. The NASA model was reviewed by the US National Research Council and approved for use by NASA for risk assessment for International Space Station missions and trade studies of future exploration missions to Mars and other destinations. A key feature of the NASA QFs is to represent the uncertainty in the QF assessments and evaluate the importance of the QF uncertainty to overall uncertainties in cancer risk projections. In this article, the biophysical basis for the probability distribution functions representing QF uncertainties was reviewed, and approaches needed to reduce uncertainties were discussed. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  9. Bioelectrochemistry II membrane phenomena

    CERN Document Server

    Blank, M

    1987-01-01

    This book contains the lectures of the second course devoted to bioelectro­ chemistry, held within the framework of the International School of Biophysics. In this course another very large field of bioelectrochemistry, i. e. the field of Membrane Phenomena, was considered, which itself consists of several different, but yet related subfields. Here again, it can be easily stated that it is impossible to give a complete and detailed picture of all membrane phenomena of biological interest in a short course of about one and half week. Therefore the same philosophy, as the one of the first course, was followed, to select a series of lectures at postgraduate level, giving a synthesis of several membrane phenomena chosen among the most'important ones. These lectures should show the large variety of membrane-regulated events occurring in living bodies, and serve as sound interdisciplinary basis to start a special­ ized study of biological phenomena, for which the investigation using the dual approach, physico-che...

  10. Progress in surface and membrane science

    CERN Document Server

    Danielli, J F; Cadenhead, D A

    1973-01-01

    Progress in Surface and Membrane Science, Volume 6 covers the developments in the study of surface and membrane science. The book discusses the progress in surface and membrane science; the solid state chemistry of the silver halide surface; and the experimental and theoretical aspects of the double layer at the mercury-solution interface. The text also describes contact-angle hysteresis; ion binding and ion transport produced by neutral lipid-soluble molecules; and the biophysical interactions of blood proteins with polymeric and artificial surfaces. Physical chemists, biophysicists, and phys

  11. Biophysical Properties and Antiviral Activities of Measles Fusion Protein Derived Peptide Conjugated with 25-Hydroxycholesterol.

    Science.gov (United States)

    Gomes, Bárbara; Santos, Nuno C; Porotto, Matteo

    2017-10-31

    Measles virus (MV) infection is re-emerging, despite the availability of an effective vaccine. The mechanism of MV entry into a target cell relies on coordinated action between the MV hemagglutinin (H) receptor binding protein and the fusion envelope glycoprotein (F) which mediates fusion between the viral and cell membranes. Peptides derived from the C -terminal heptad repeat (HRC) of F can interfere with this process, blocking MV infection. As previously described, biophysical properties of HRC-derived peptides modulate their antiviral potency. In this work, we characterized a MV peptide fusion inhibitor conjugated to 25-hydroxycholesterol (25HC), a cholesterol derivative with intrinsic antiviral activity, and evaluated its interaction with membrane model systems and human blood cells. The peptide (MV.

  12. Quality Saving Mechanisms of Mitochondria during Aging in a Fully Time-Dependent Computational Biophysical Model.

    Science.gov (United States)

    Mellem, Daniel; Fischer, Frank; Jaspers, Sören; Wenck, Horst; Rübhausen, Michael

    2016-01-01

    Mitochondria are essential for the energy production of eukaryotic cells. During aging mitochondria run through various processes which change their quality in terms of activity, health and metabolic supply. In recent years, many of these processes such as fission and fusion of mitochondria, mitophagy, mitochondrial biogenesis and energy consumption have been subject of research. Based on numerous experimental insights, it was possible to qualify mitochondrial behaviour in computational simulations. Here, we present a new biophysical model based on the approach of Figge et al. in 2012. We introduce exponential decay and growth laws for each mitochondrial process to derive its time-dependent probability during the aging of cells. All mitochondrial processes of the original model are mathematically and biophysically redefined and additional processes are implemented: Mitochondrial fission and fusion is separated into a metabolic outer-membrane part and a protein-related inner-membrane part, a quality-dependent threshold for mitophagy and mitochondrial biogenesis is introduced and processes for activity-dependent internal oxidative stress as well as mitochondrial repair mechanisms are newly included. Our findings reveal a decrease of mitochondrial quality and a fragmentation of the mitochondrial network during aging. Additionally, the model discloses a quality increasing mechanism due to the interplay of the mitophagy and biogenesis cycle and the fission and fusion cycle of mitochondria. It is revealed that decreased mitochondrial repair can be a quality saving process in aged cells. Furthermore, the model finds strategies to sustain the quality of the mitochondrial network in cells with high production rates of reactive oxygen species due to large energy demands. Hence, the model adds new insights to biophysical mechanisms of mitochondrial aging and provides novel understandings of the interdependency of mitochondrial processes.

  13. Quality Saving Mechanisms of Mitochondria during Aging in a Fully Time-Dependent Computational Biophysical Model.

    Directory of Open Access Journals (Sweden)

    Daniel Mellem

    Full Text Available Mitochondria are essential for the energy production of eukaryotic cells. During aging mitochondria run through various processes which change their quality in terms of activity, health and metabolic supply. In recent years, many of these processes such as fission and fusion of mitochondria, mitophagy, mitochondrial biogenesis and energy consumption have been subject of research. Based on numerous experimental insights, it was possible to qualify mitochondrial behaviour in computational simulations. Here, we present a new biophysical model based on the approach of Figge et al. in 2012. We introduce exponential decay and growth laws for each mitochondrial process to derive its time-dependent probability during the aging of cells. All mitochondrial processes of the original model are mathematically and biophysically redefined and additional processes are implemented: Mitochondrial fission and fusion is separated into a metabolic outer-membrane part and a protein-related inner-membrane part, a quality-dependent threshold for mitophagy and mitochondrial biogenesis is introduced and processes for activity-dependent internal oxidative stress as well as mitochondrial repair mechanisms are newly included. Our findings reveal a decrease of mitochondrial quality and a fragmentation of the mitochondrial network during aging. Additionally, the model discloses a quality increasing mechanism due to the interplay of the mitophagy and biogenesis cycle and the fission and fusion cycle of mitochondria. It is revealed that decreased mitochondrial repair can be a quality saving process in aged cells. Furthermore, the model finds strategies to sustain the quality of the mitochondrial network in cells with high production rates of reactive oxygen species due to large energy demands. Hence, the model adds new insights to biophysical mechanisms of mitochondrial aging and provides novel understandings of the interdependency of mitochondrial processes.

  14. Membrane dynamics

    DEFF Research Database (Denmark)

    Bendix, Pól Martin

    2015-01-01

    Current topics include membrane-protein interactions with regard to membrane deformation or curvature sensing by BAR domains. Also, we study the dynamics of membrane tubes of both cells and simple model membrane tubes. Finally, we study membrane phase behavior which has important implications...

  15. Rhizosphere biophysics and root water uptake

    Science.gov (United States)

    Carminati, Andrea; Zarebanadkouki, Mohsen; Ahmed, Mutez A.; Passioura, John

    2016-04-01

    The flow of water into the roots and the (putative) presence of a large resistance at the root-soil interface have attracted the attention of plant and soil scientists for decades. Such resistance has been attributed to a partial contact between roots and soil, large gradients in soil matric potential around the roots, or accumulation of solutes at the root surface creating a negative osmotic potential. Our hypothesis is that roots are capable of altering the biophysical properties of the soil around the roots, the rhizosphere, facilitating root water uptake in dry soils. In particular, we expect that root hairs and mucilage optimally connect the roots to the soil maintaining the hydraulic continuity across the rhizosphere. Using a pressure chamber apparatus we measured the relation between transpiration rate and the water potential difference between soil and leaf xylem during drying cycles in barley mutants with and without root hairs. The samples were grown in well structured soils. At low soil moistures and high transpiration rates, large drops in water potential developed around the roots. These drops in water potential recovered very slowly, even after transpiration was severely decreased. The drops in water potential were much bigger in barley mutants without root hairs. These mutants failed to sustain high transpiration rates in dry conditions. To explain the nature of such drops in water potential across the rhizosphere we performed high resolution neutron tomography of the rhizosphere of the barleys with and without root hairs growing in the same soil described above. The tomograms suggested that the hydraulic contact between the soil structures was the highest resistance for the water flow in dry conditions. The tomograms also indicate that root hairs and mucilage improved the hydraulic contact between roots and soil structures. At high transpiration rates and low water contents, roots extracted water from the rhizosphere, while the bulk soil, due its

  16. Anionic lipids and the maintenance of membrane electrostatics in eukaryotes.

    Science.gov (United States)

    Platre, Matthieu Pierre; Jaillais, Yvon

    2017-02-01

    A wide range of signaling processes occurs at the cell surface through the reversible association of proteins from the cytosol to the plasma membrane. Some low abundant lipids are enriched at the membrane of specific compartments and thereby contribute to the identity of cell organelles by acting as biochemical landmarks. Lipids also influence membrane biophysical properties, which emerge as an important feature in specifying cellular territories. Such parameters are crucial for signal transduction and include lipid packing, membrane curvature and electrostatics. In particular, membrane electrostatics specifies the identity of the plasma membrane inner leaflet. Membrane surface charges are carried by anionic phospholipids, however the exact nature of the lipid(s) that powers the plasma membrane electrostatic field varies among eukaryotes and has been hotly debated during the last decade. Herein, we discuss the role of anionic lipids in setting up plasma membrane electrostatics and we compare similarities and differences that were found in different eukaryotic cells.

  17. Biophysical insights into cancer transformation and treatment

    Czech Academy of Sciences Publication Activity Database

    Pokorný, Jiří; Foletti, A.; Kobilková, J.; Jandová, Anna; Vrba, J.; Vrba, J. jr.; Nedbalová, M.; Čoček, A.; Danani, A.; Tuszynski, J. A.

    2013-01-01

    Roč. 2013, č. 195028 (2013) ISSN 1537-744X R&D Projects: GA ČR(CZ) GAP102/11/0649 Institutional support: RVO:67985882 Keywords : fatty acid * mitochondrial membrane * cancer cell Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 1.219, year: 2013

  18. Biophysical and biomathematical adventures in radiobiology

    Energy Technology Data Exchange (ETDEWEB)

    Scott, B.R.

    1991-01-01

    Highlights of my biophysical and biomathematical adventures in radiobiology is presented. Early adventures involved developing state-vector models'' for specific harmful effects (cell killing, life shortening) of exposure to radiation. More recent adventures led to developing hazard-function models'' for predicting biological effects (e.g., cell killing, mutations, tumor induction) of combined exposure to different toxicants. Hazard-function models were also developed for predicting harm to man from exposure to large radiation doses. Major conclusions derived from the modeling adventures are as follows: (1) synergistic effects of different genotoxic agents should not occur at low doses; (2) for exposure of the lung or bone marrow to large doses of photon radiation, low rates of exposure should be better tolerated than high rates; and (3) for some types of radiation (e.g., alpha particles and fission neutrons), moderate doses delivered at a low rate may be more harmful than the same dose given at a high rate. 53 refs., 7 figs.

  19. Contribution to researches in biophysics and biology

    International Nuclear Information System (INIS)

    Luccioni, Catherine

    2000-01-01

    In this accreditation to supervise research, the author indicates its curriculum and scientific works which mainly dealt with the different agents used in chemotherapy. Scientific works addressed anti-carcinogenic pharmacology, applied biophysics, and researches in oncology and radiobiology. Current research projects deal with mechanisms of cellular transformation and the implication of the anti-oxidising metabolism and of nucleotide metabolism in cell radio-sensitivity. Teaching and research supervising activities are also indicated. Several articles are proposed in appendix: Average quality factor and dose equivalent meter based on microdosimetry techniques; Activity of thymidylate synthetase, thymidine kinase and galactokinase in primary and xenografted human colorectal cancers in relation to their chromosomal patterns; Nucleotide metabolism in human gliomas, relation to the chromosomal profile; Pyrimidine nucleotide metabolism in human colon carcinomas: comparison of normal tissues, primary tumors and xenografts; Modifications of the antioxidant metabolism during proliferation and differentiation of colon tumours cell lines; Modulation of the antioxidant enzymes, p21 and p53 expression during proliferation and differentiation of human melanoma cell lines; Purine metabolism in 2 human melanoma cell lines, relation with proliferation and differentiation; Radiation-induced changes in nucleotide metabolism of 2 colon cancer cell lines with different radio-sensitivities

  20. Review of FEWS NET Biophysical Monitoring Requirements

    Science.gov (United States)

    Ross, K. W.; Brown, Molly E.; Verdin, J.; Underwood, L. W.

    2009-01-01

    The Famine Early Warning System Network (FEWS NET) provides monitoring and early warning support to decision makers responsible for responding to famine and food insecurity. FEWS NET transforms satellite remote sensing data into rainfall and vegetation information that can be used by these decision makers. The National Aeronautics and Space Administration has recently funded activities to enhance remote sensing inputs to FEWS NET. To elicit Earth observation requirements, a professional review questionnaire was disseminated to FEWS NET expert end-users: it focused upon operational requirements to determine additional useful remote sensing data and; subsequently, beneficial FEWS NET biophysical supplementary inputs. The review was completed by over 40 experts from around the world, enabling a robust set of professional perspectives to be gathered and analyzed rapidly. Reviewers were asked to evaluate the relative importance of environmental variables and spatio-temporal requirements for Earth science data products, in particular for rainfall and vegetation products. The results showed that spatio-temporal resolution requirements are complex and need to vary according to place, time, and hazard: that high resolution remote sensing products continue to be in demand, and that rainfall and vegetation products were valued as data that provide actionable food security information.

  1. Biophysical and biomathematical adventures in radiobiology

    International Nuclear Information System (INIS)

    Scott, B.R.

    1991-01-01

    Highlights of my biophysical and biomathematical adventures in radiobiology is presented. Early adventures involved developing ''state-vector models'' for specific harmful effects (cell killing, life shortening) of exposure to radiation. More recent adventures led to developing ''hazard-function models'' for predicting biological effects (e.g., cell killing, mutations, tumor induction) of combined exposure to different toxicants. Hazard-function models were also developed for predicting harm to man from exposure to large radiation doses. Major conclusions derived from the modeling adventures are as follows: (1) synergistic effects of different genotoxic agents should not occur at low doses; (2) for exposure of the lung or bone marrow to large doses of photon radiation, low rates of exposure should be better tolerated than high rates; and (3) for some types of radiation (e.g., alpha particles and fission neutrons), moderate doses delivered at a low rate may be more harmful than the same dose given at a high rate. 53 refs., 7 figs

  2. Neutrons and model membranes

    Science.gov (United States)

    Fragneto, G.

    2012-11-01

    Current research in membrane protein biophysics highlights the emerging role of lipids in shaping membrane protein function. Cells and organisms have developed sophisticated mechanisms for controlling the lipid composition and many diseases are related to the failure of these mechanisms. One of the recent advances in the field is the discovery of the existence of coexisting micro-domains within a single membrane, important for regulating some signaling pathways. Many important properties of these domains remain poorly characterized. The characterization and analysis of bio-interfaces represent a challenge. Performing measurements on these few nanometer thick, soft, visco-elastic and dynamic systems is close to the limits of the available tools and methods. Neutron scattering techniques including small angle scattering, diffraction, reflectometry as well as inelastic methods are rapidly developing for these studies and are attracting an increasing number of biologists and biophysicists at large facilities. This manuscript will review some recent progress in the field and provide perspectives for future developments. It aims at highlighting neutron reflectometry as a versatile method to tackle questions dealing with the understanding and function of biomembranes and their components. The other important scattering methods are only briefly introduced.

  3. Developing spatial biophysical accounting for multiple ecosystem services

    NARCIS (Netherlands)

    Remme, R.P.; Schroter, M.; Hein, L.G.

    2014-01-01

    Ecosystem accounting is receiving increasing interest as a way to systematically monitor the conditions of ecosystems and the ecosystem services they provide. A critical element of ecosystem accounting is understanding spatially explicit flows of ecosystem services. We developed spatial biophysical

  4. Biophysical approach to low back pain: a pilot report

    Czech Academy of Sciences Publication Activity Database

    Foletti, A.; Pokorný, Jiří

    2015-01-01

    Roč. 34, č. 2 (2015), s. 156-159 ISSN 1536-8378 Institutional support: RVO:67985882 Keywords : Bioelectromagnetic medicine * Biophysical therapy * Coherence domains Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 1.208, year: 2015

  5. Genotype-induced changes in biophysical properties of frontal cortex lipid raft from APP/PS1 transgenic mice

    Directory of Open Access Journals (Sweden)

    Mario L Diaz

    2012-11-01

    Full Text Available Alterations in the lipid composition of lipid rafts have been demonstrated both in human brain and transgenic mouse models, and it has been postulated that aberrant lipid composition in lipid rafts is partly responsible for neuronal degeneration. In order to assess the impact of lipid changes on lipid raft functional properties, we have aimed at determining relevant physicochemical modifications in lipid rafts purified from frontal cortex of wild type (WT and APP/PS1 double transgenic mice. By means of steady-state fluorescence anisotropy analyses using two lipid soluble fluorescent probes, TMA-DPH (1-[(4-trimethyl-aminophenyl]-6-phenyl-1,3,5-hexatriene and DPH (1,6-diphenyl-1,3,5-hexatriene, we demonstrate that cortical lipid rafts from WT and APP/PS1 animals exhibit different biophysical behaviours, depending on genotype but also on age. Thus, aged APP/PS1 animals exhibited slightly more liquid-ordered lipid rafts than WT counterparts. Membrane microviscosity napp analyses demonstrate that WT lipid rafts are more fluid than APP/PS1 animals of similar age, both at the aqueous interface and hydrophobic core of the membrane. napp in APP/PS1 animals was higher for DPH than for TMA-DPH under similar experimental conditions, indicating that the internal core of the membrane is more viscous than the raft membrane at the aqueous interface. The most dramatic changes in biophysical properties of lipid rafts were observed when membrane cholesterol was depleted with methyl-beta-cyclodextrin. Overall, our results indicate that APP/PS1 genotype strongly affects physicochemical properties of lipid raft. Such alterations appear not to be homogeneous across the raft membrane axis, but rather are more prominent at the membrane plane. These changes correlate with aberrant proportions of sphingomyelin, cholesterol and saturated fatty acids, as well as polyunsaturated fatty acids, measured in lipid rafts from frontal cortex in this familial model of

  6. Biophysics of Human Hair Structural, Nanomechanical, and Nanotribological Studies

    CERN Document Server

    Bhushan, Bharat

    2010-01-01

    This book presents the biophysics of hair. It deals with the structure of hair, its mechanical properties, the nanomechanical characterization, tensile deformation, tribological characterization, the thickness distribution and binding interactions on hair surface. Another important topic of the book is the health of hair, human hair and skin, hair care, cleaning and conditioning treatments and damaging processes. It is the first book on the biophysical properties of hair.

  7. Antenatal Surveillance in Twin Pregnancies Using the Biophysical Profile.

    Science.gov (United States)

    Booker, Whitney; Fox, Nathan S; Gupta, Simi; Carroll, Rachel; Saltzman, Daniel H; Klauser, Chad K; Rebarber, Andrei

    2015-11-01

    Objectives-The nonstress test is currently the most widely used modality for antenatal surveillance in twin pregnancies, with a quoted false-positive rate of 11%-12%. Our objective was to report our experience with the sonographic portion of the biophysical profile in twin pregnancies as the primary screening modality.Methods-Women with twin pregnancies delivered by a single maternal-fetal medicine practice from 2005 to 2013 were included. We excluded monoamniotic twins. Twin pregnancies began weekly sonography for the biophysical profile starting at 32 to 33 weeks, or earlier if indicated. The nonstress test was performed if the sonographic biophysical profile score was less than 8 of 8. We reviewed biophysical profile scores and outcomes for all patients who delivered at 33 weeks or later to assess the false-positive rate for the biophysical profile, as well as the incidence of intrauterine fetal death (IUFD) after initiation of antenatal surveillance.Results-A total of 539 twin pregnancies were included. The incidence of IUFD per patient was 2 per 539 (0.4%; 95% confidence interval [CI], 0.1%-1.3%), and the incidence of IUFD per fetus was 2 per 1078 (0.19%; 95% CI, 0.05%-0.7%). The overall positive screen rate was 24 per 539 (4.45%; 95% CI, 3.0%-6.5%). The false-positive screen rate, defined as an abnormal biophysical profile that did not diagnose an IUFD or lead to delivery, was 10 per 539 (1.9%; 95% CI, 1.0%-3.4%).Conclusions-In twin pregnancies the use of the sonographic biophysical profile for routine antenatal surveillance has a low false-positive rate, with a very low incidence of IUFD. The sonographic biophysical profile should be considered as a primary mode for antenatal surveillance in twin pregnancies, with a reflex nonstress test for an abnormal score. © 2015 by the American Institute of Ultrasound in Medicine.

  8. Broad spectrum antiviral activity for paramyxoviruses is modulated by biophysical properties of fusion inhibitory peptides.

    Science.gov (United States)

    Mathieu, Cyrille; Augusto, Marcelo T; Niewiesk, Stefan; Horvat, Branka; Palermo, Laura M; Sanna, Giuseppina; Madeddu, Silvia; Huey, Devra; Castanho, Miguel A R B; Porotto, Matteo; Santos, Nuno C; Moscona, Anne

    2017-03-08

    Human paramyxoviruses include global causes of lower respiratory disease like the parainfluenza viruses, as well as agents of lethal encephalitis like Nipah virus. Infection is initiated by viral glycoprotein-mediated fusion between viral and host cell membranes. Paramyxovirus viral fusion proteins (F) insert into the target cell membrane, and form a transient intermediate that pulls the viral and cell membranes together as two heptad-repeat regions refold to form a six-helix bundle structure that can be specifically targeted by fusion-inhibitory peptides. Antiviral potency can be improved by sequence modification and lipid conjugation, and by adding linkers between the protein and lipid components. We exploit the uniquely broad spectrum antiviral activity of a parainfluenza F-derived peptide sequence that inhibits both parainfluenza and Nipah viruses, to investigate the influence of peptide orientation and intervening linker length on the peptides' interaction with transitional states of F, solubility, membrane insertion kinetics, and protease sensitivity. We assessed the impact of these features on biodistribution and antiviral efficacy in vitro and in vivo. The engineering approach based on biophysical parameters resulted in a peptide that is a highly effective inhibitor of both paramyxoviruses and a set of criteria to be used for engineering broad spectrum antivirals for emerging paramyxoviruses.

  9. Assessing sustainable biophysical human-nature connectedness at regional scales

    Science.gov (United States)

    Dorninger, Christian; Abson, David J.; Fischer, Joern; von Wehrden, Henrik

    2017-05-01

    Humans are biophysically connected to the biosphere through the flows of materials and energy appropriated from ecosystems. While this connection is fundamental for human well-being, many modern societies have—for better or worse—disconnected themselves from the natural productivity of their immediate regional environment. In this paper, we conceptualize the biophysical human-nature connectedness of land use systems at regional scales. We distinguish two mechanisms by which primordial connectedness of people to regional ecosystems has been circumvented via the use of external inputs. First, ‘biospheric disconnection’ refers to people drawing on non-renewable minerals from outside the biosphere (e.g. fossils, metals and other minerals). Second, ‘spatial disconnection’ arises from the imports and exports of biomass products and imported mineral resources used to extract and process ecological goods. Both mechanisms allow for greater regional resource use than would be possible otherwise, but both pose challenges for sustainability, for example, through waste generation, depletion of non-renewable resources and environmental burden shifting to distant regions. In contrast, biophysically reconnected land use systems may provide renewed opportunities for inhabitants to develop an awareness of their impacts and fundamental reliance on ecosystems. To better understand the causes, consequences, and possible remedies related to biophysical disconnectedness, new quantitative methods to assess the extent of regional biophysical human-nature connectedness are needed. To this end, we propose a new methodological framework that can be applied to assess biophysical human-nature connectedness in any region of the world.

  10. Deciphering the BAR code of membrane modulators.

    Science.gov (United States)

    Salzer, Ulrich; Kostan, Julius; Djinović-Carugo, Kristina

    2017-07-01

    The BAR domain is the eponymous domain of the "BAR-domain protein superfamily", a large and diverse set of mostly multi-domain proteins that play eminent roles at the membrane cytoskeleton interface. BAR domain homodimers are the functional units that peripherally associate with lipid membranes and are involved in membrane sculpting activities. Differences in their intrinsic curvatures and lipid-binding properties account for a large variety in membrane modulating properties. Membrane activities of BAR domains are further modified and regulated by intramolecular or inter-subunit domains, by intermolecular protein interactions, and by posttranslational modifications. Rather than providing detailed cell biological information on single members of this superfamily, this review focuses on biochemical, biophysical, and structural aspects and on recent findings that paradigmatically promote our understanding of processes driven and modulated by BAR domains.

  11. Anisotropic Membrane Curvature Sensing by Amphipathic Peptides.

    Science.gov (United States)

    Gómez-Llobregat, Jordi; Elías-Wolff, Federico; Lindén, Martin

    2016-01-05

    Many proteins and peptides have an intrinsic capacity to sense and induce membrane curvature, and play crucial roles for organizing and remodeling cell membranes. However, the molecular driving forces behind these processes are not well understood. Here, we describe an approach to study curvature sensing by simulating the interactions of single molecules with a buckled lipid bilayer. We analyze three amphipathic antimicrobial peptides, a class of membrane-associated molecules that specifically target and destabilize bacterial membranes, and find qualitatively different sensing characteristics that would be difficult to resolve with other methods. Our findings provide evidence for direction-dependent curvature sensing mechanisms in amphipathic peptides and challenge existing theories of hydrophobic insertion. The buckling approach is generally applicable to a wide range of curvature-sensing molecules, and our results provide strong motivation to develop new experimental methods to track position and orientation of membrane proteins. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  12. Layer-by-layer cell membrane assembly

    Science.gov (United States)

    Matosevic, Sandro; Paegel, Brian M.

    2013-11-01

    Eukaryotic subcellular membrane systems, such as the nuclear envelope or endoplasmic reticulum, present a rich array of architecturally and compositionally complex supramolecular targets that are as yet inaccessible. Here we describe layer-by-layer phospholipid membrane assembly on microfluidic droplets, a route to structures with defined compositional asymmetry and lamellarity. Starting with phospholipid-stabilized water-in-oil droplets trapped in a static droplet array, lipid monolayer deposition proceeds as oil/water-phase boundaries pass over the droplets. Unilamellar vesicles assembled layer-by-layer support functional insertion both of purified and of in situ expressed membrane proteins. Synthesis and chemical probing of asymmetric unilamellar and double-bilayer vesicles demonstrate the programmability of both membrane lamellarity and lipid-leaflet composition during assembly. The immobilized vesicle arrays are a pragmatic experimental platform for biophysical studies of membranes and their associated proteins, particularly complexes that assemble and function in multilamellar contexts in vivo.

  13. [Biophysical principles of collagen cross-linking].

    Science.gov (United States)

    Spörl, E; Raiskup-Wolf, F; Pillunat, L E

    2008-02-01

    The reduced mechanical stability of the cornea in keratoconus or in keratectasia after Lasik may be increased by photooxidative cross-linking of corneal collagen. The biophysical principles are compiled for the safe and effective application of this new treatment method. The setting of the therapy parameters should be elucidated from the absorption behaviour of the cornea. The safety of the method for the endothelium cells and the lens will be discussed. The induced cross-links are shown to be the result of changes in the physico-chemical properties of the cornea. To reach a high absorption of the irradiation energy in the cornea, riboflavin of a concentration of 0.1% and UV light of a wavelength of 370 nm, corresponding to the relative maximum of absorption of riboflavin, were used. An irradiance of 3 mW/cm(2) and an irradiation time of 30 min lead to an increase of the mechanical stiffness. The endothelium cells will be protected due to the high absorption within the cornea, that means the damaging threshold of the endothelium cells will not be reached in a 400 microm thick stroma. As evidence for cross-links we can consider the increase of the biomechanical stiffness, the increased resistance against enzymatic degradation, a higher shrinkage temperature, a lower swelling rate and an increased diameter of collagen fibres. The therapy parameters were tested experimentally and have been proven clinically in the corneal collagen cross-linking. These parameters should be respected to reach a safe cross-linking effect without damage of the adjacent tissues.

  14. Membrane fusion

    DEFF Research Database (Denmark)

    Bendix, Pól Martin

    2015-01-01

    At Stanford University, Boxer lab, I worked on membrane fusion of small unilamellar lipid vesicles to flat membranes tethered to glass surfaces. This geometry closely resembles biological systems in which liposomes fuse to plasma membranes. The fusion mechanism was studied using DNA zippering...... between complementary strands linked to the two apposing membranes closely mimicking the zippering mechanism of SNARE fusion complexes....

  15. Biobased Membrane

    NARCIS (Netherlands)

    Koenders, E.A.B.; Zlopasa, J.; Picken, S.J.

    2015-01-01

    The present invention is in the field of a composition for forming a bio-compatible membrane applicable to building material, such as concrete, cement, etc., to a meth od of applying said composition for forming a bio-compatible membrane, a biocompatible membrane, use of said membrane for various

  16. An allosteric gating model recapitulates the biophysical properties of IK,L expressed in mouse vestibular type I hair cells.

    Science.gov (United States)

    Spaiardi, Paolo; Tavazzani, Elisa; Manca, Marco; Milesi, Veronica; Russo, Giancarlo; Prigioni, Ivo; Marcotti, Walter; Magistretti, Jacopo; Masetto, Sergio

    2017-11-01

    Vestibular type I and type II hair cells and their afferent fibres send information to the brain regarding the position and movement of the head. The characteristic feature of type I hair cells is the expression of a low-voltage-activated outward rectifying K + current, I K,L , whose biophysical properties and molecular identity are still largely unknown. In vitro, the afferent nerve calyx surrounding type I hair cells causes unstable intercellular K + concentrations, altering the biophysical properties of I K,L . We found that in the absence of the calyx, I K,L in type I hair cells exhibited unique biophysical activation properties, which were faithfully reproduced by an allosteric channel gating scheme. These results form the basis for a molecular and pharmacological identification of I K,L . Type I and type II hair cells are the sensory receptors of the mammalian vestibular epithelia. Type I hair cells are characterized by their basolateral membrane being enveloped in a single large afferent nerve terminal, named the calyx, and by the expression of a low-voltage-activated outward rectifying K + current, I K,L . The biophysical properties and molecular profile of I K,L are still largely unknown. By using the patch-clamp whole-cell technique, we examined the voltage- and time-dependent properties of I K,L in type I hair cells of the mouse semicircular canal. We found that the biophysical properties of I K,L were affected by an unstable K + equilibrium potential (V eq K + ). Both the outward and inward K + currents shifted V eq K + consistent with K + accumulation or depletion, respectively, in the extracellular space, which we attributed to a residual calyx attached to the basolateral membrane of the hair cells. We therefore optimized the hair cell dissociation protocol in order to isolate mature type I hair cells without their calyx. In these cells, the uncontaminated I K,L showed a half-activation at -79.6 mV and a steep voltage dependence (2.8 mV). I K,L also

  17. Mechanosensitivity of cell membranes. Ion channels, lipid matrix and cytoskeleton.

    Science.gov (United States)

    Petrov, A G; Usherwood, P N

    1994-01-01

    Physical and biophysical mechanisms of mechano-sensitivity of cell membranes are reviewed. The possible roles of the lipid matrix and of the cytoskeleton in membrane mechanoreception are discussed. Techniques for generation of static strains and dynamic curvatures of membrane patches are considered. A unified model for stress-activated and stress-inactivated ion channels under static strains is described. A review of work on stress-sensitive pores in lipid-peptide model membranes is presented. The possible role of flexoelectricity in mechano-electric transduction, e.g. in auditory receptors is discussed. Studies of flexoelectricity in model lipid membranes, lipid-peptide membranes and natural membranes containing ion channels are reviewed. Finally, possible applications in molecular electronics of mechanosensors employing some of the recognized principles of mechano-electric transduction in natural membranes are discussed.

  18. Nonequilibrium Thermodynamics of Ion Flux through Membrane Channels

    Directory of Open Access Journals (Sweden)

    Chi-Pan Hsieh

    2017-01-01

    Full Text Available Ion flux through membrane channels is passively driven by the electrochemical potential differences across the cell membrane. Nonequilibrium thermodynamics has been successful in explaining transport mechanisms, including the ion transport phenomenon. However, physiologists may not be familiar with biophysical concepts based on the view of entropy production. In this paper, I have reviewed the physical meanings and connections between nonequilibrium thermodynamics and the expressions commonly used in describing ion fluxes in membrane physiology. The fluctuation theorem can be applied to interpret the flux ratio in the small molecular systems. The multi-ion single-file feature of the ion channel facilitates the utilization of the natural tendency of electrochemical driving force to couple specific biophysical processes and biochemical reactions on the membrane.

  19. Translocation of cell penetrating peptides and calcium-induced membrane fusion share same mechanism

    Czech Academy of Sciences Publication Activity Database

    Magarkar, Aniket; Allolio, Christoph; Jurkiewicz, Piotr; Baxová, Katarína; Šachl, Radek; Horinek, D.; Heinz, V.; Rachel, R.; Ziegler, C.; Jungwirth, Pavel

    2017-01-01

    Roč. 46, Suppl 1 (2017), S386 ISSN 0175-7571. [IUPAB congress /19./ and EBSA congress /11./. 16.07.2017-20.07.2017, Edinburgh] Institutional support: RVO:61388963 ; RVO:61388955 Keywords : membrane interactions * membrane fusion * cell penetration Subject RIV: BO - Biophysics

  20. Role of the Transmembrane Potential in the Membrane Proton Leak

    Czech Academy of Sciences Publication Activity Database

    Ruprecht, A.; Sokolenko, E. A.; Beck, V.; Ninnemann, O.; Jabůrek, Martin; Trimbuch, T.; Klishin, S. S.; Ježek, Petr; Skulachev, V. P.; Pohl, E. E.

    2010-01-01

    Roč. 98, č. 8 (2010), s. 1503-1511 ISSN 0006-3495 R&D Projects: GA MŠk ME09018; GA ČR(CZ) GA303/07/0105 Institutional research plan: CEZ:AV0Z50110509 Keywords : proton leak * membrane potential * uncoupling proteins Subject RIV: BO - Biophysics Impact factor: 4.218, year: 2010

  1. Effects of seaweed sterols fucosterol and desmosterol on lipid membranes

    DEFF Research Database (Denmark)

    Mouritsen, Ole G.; Bagatolli, Luis A.; Duelund, Lars

    2017-01-01

    in animals, ergosterol in fungi and yeast, phytosterols in higher plants, and e.g., fucosterol and desmosterol in algae. The question arises as to which specific properties do sterols impart to membranes and to which extent do these properties differ among the different sterols. Using a range of biophysical...

  2. Charge Inversion in semi-permeable membranes

    Science.gov (United States)

    Das, Siddhartha; Sinha, Shayandev; Jing, Haoyuan

    Role of semi-permeable membranes like lipid bilayer is ubiquitous in a myriad of physiological and pathological phenomena. Typically, lipid membranes are impermeable to ions and solutes; however, protein channels embedded in the membrane allow the passage of selective, small ions across the membrane enabling the membrane to adopt a semi-permeable nature. This semi-permeability, in turn, leads to electrostatic potential jump across the membrane, leading to effects such as regulation of intracellular calcium, extracellular-vesicle-membrane interactions, etc. In this study, we theoretically demonstrate that this semi-permeable nature may trigger the most remarkable charge inversion (CI) phenomenon in the cytosol-side of the negatively-charged lipid bilayer membrane that are selectively permeable to only positive ions of a given salt. This CI is manifested as the changing of the sign of the electrostatic potential from negative to positive from the membrane-cytosol interface to deep within the cytosol. We study the impact of the parameters such as the concentration of this salt with selectively permeable ions as well as the concentration of an external salt in the development of this CI phenomenon. We anticipate such CI will profoundly influence the interaction of membrane and intra-cellular moieties (e.g., exosome or multi-cellular vesicles) having implications for a host of biophysical processes.

  3. Effect of Plasma Membrane Semipermeability in Making the Membrane Electric Double Layer Capacitances Significant.

    Science.gov (United States)

    Sinha, Shayandev; Sachar, Harnoor Singh; Das, Siddhartha

    2018-01-30

    Electric double layers (or EDLs) formed at the membrane-electrolyte interface (MEI) and membrane-cytosol interface (MCI) of a charged lipid bilayer plasma membrane develop finitely large capacitances. However, these EDL capacitances are often much larger than the intrinsic capacitance of the membrane, and all of these capacitances are in series. Consequently, the effect of these EDL capacitances in dictating the overall membrane-EDL effective capacitance C eff becomes negligible. In this paper, we challenge this conventional notion pertaining to the membrane-EDL capacitances. We demonstrate that, on the basis of the system parameters, the EDL capacitance for both the permeable and semipermeable membranes can be small enough to influence C eff . For the semipermeable membranes, however, this lowering of the EDL capacitance can be much larger, ensuring a reduction of C eff by more than 20-25%. Furthermore, for the semipermeable membranes, the reduction in C eff is witnessed over a much larger range of system parameters. We attribute such an occurrence to the highly nonintuitive electrostatic potential distribution associated with the recently discovered phenomena of charge-inversion-like electrostatics and the attainment of a positive zeta potential at the MCI for charged semipermeable membranes. We anticipate that our findings will impact the quantification and the identification of a large number of biophysical phenomena that are probed by measuring the plasma membrane capacitance.

  4. Ultra-high-density 3D DNA arrays within nanoporous biocompatible membranes for single-molecule-level detection and purification of circulating nucleic acids

    Czech Academy of Sciences Publication Activity Database

    Aramesh, M.; Shimoni, O.; Fox, K.; Karle, T.J.; Lohrmann, A.; Ostrikov, K.; Prawer, S.; Červenka, Jiří

    2015-01-01

    Roč. 7, č. 14 (2015), s. 5998-6006 ISSN 2040-3364 Institutional support: RVO:68378271 Keywords : Fourier-transform spectroscopy * alumina membranes * oligonucleotide hybridization Subject RIV: BO - Biophysics Impact factor: 7.760, year: 2015

  5. Membranous nephropathy

    Science.gov (United States)

    ... check for hepatitis B, hepatitis C, and syphilis Complement levels Cryoglobulin test Treatment The goal of treatment ... not as helpful for people with membranous nephropathy. Medicines used treat membranous nephropathy include: Angiotensin-converting enzyme ( ...

  6. Microfluidic devices for investigation of biomimetic membranes for sensor and separation applications

    DEFF Research Database (Denmark)

    Pszon-Bartosz, Kamila Justyna

    The term biomimetic membrane denotes membrane that mimics biological cell membrane. Artificially made membranes are powerful tools for the fundamental biophysical studies of membrane proteins. Moreover, they may be used in biomedicine, serving as biosensors in high-throughput screening of potential...... drug candidates and in separation technologies, where an exciting example is water purification device based on biomimetic membranes containing aquaporins (highly water selective proteins). However, there are many challenges that must be overcome in order to build biomimetic membrane-based devices...... for industrial applications. Among them are the inherent fragility of lipid membranes, the challenge of up-scaling the effective membrane area and the quantification of the protein delivery to the lipid membrane which may determined the biomimetic membrane application. This PhD thesis addresses the above...

  7. Novel physical chemistry approaches in biophysical researches with advanced application of lasers: Detection and manipulation.

    Science.gov (United States)

    Iwata, Koichi; Terazima, Masahide; Masuhara, Hiroshi

    2018-02-01

    Novel methodologies utilizing pulsed or intense CW irradiation obtained from lasers have a major impact on biological sciences. In this article, recent development in biophysical researches fully utilizing the laser irradiation is described for three topics, time-resolved fluorescence spectroscopy, time-resolved thermodynamics, and manipulation of the biological assemblies by intense laser irradiation. First, experimental techniques for time-resolved fluorescence spectroscopy are concisely explained in Section 2. As an example of the recent application of time-resolved fluorescence spectroscopy to biological systems, evaluation of the viscosity of lipid bilayer membranes is described. The results of the spectroscopic experiments strongly suggest the presence of heterogeneous membrane structure with two different viscosity values in liposomes formed by a single phospholipid. Section 3 covers the time-resolved thermodynamics. Thermodynamical properties are important to characterize biomolecules. However, measurement of these quantities for short-lived intermediate species has been impossible by traditional thermodynamical techniques. Recently, development of a spectroscopic method based on the transient grating method enables us to measure these quantities and also to elucidate reaction kinetics which cannot be detected by other spectroscopic methods. The principle of the measurements and applications to some protein reactions are reviewed. Manipulation and fabrication of supramolecues, amino acids, proteins, and living cells by intense laser irradiation are described in Section 4. Unconventional assembly, crystallization and growth, amyloid fibril formation, and living cell manipulation are achieved by CW laser trapping and femtosecond laser-induced cavitation bubbling. Their spatio-temporal controllability is opening a new avenue in the relevant molecular and bioscience research fields. This article is part of a Special Issue entitled "Biophysical Exploration of

  8. Biophysical parameters modification could overcome essential hearing gaps.

    Science.gov (United States)

    Kern, A; Heid, C; Steeb, W-H; Stoop, N; Stoop, R

    2008-08-29

    A majority of hearing defects are due to malfunction of the outer hair cells (OHCs), those cells within the mammalian hearing sensor (the cochlea) that provide an active amplification of the incoming signal. Malformation of the hearing sensor, ototoxic drugs, acoustical trauma, infections, or the effect of aging affect often a whole frequency interval, which leads to a substantial loss of speech intelligibility. Using an energy-based biophysical model of the passive cochlea, we obtain an explicit description of the dependence of the tonotopic map on the biophysical parameters of the cochlea. Our findings indicate the possibility that by suitable local modifications of the biophysical parameters by microsurgery, even very salient gaps of the tonotopic map could be bridged.

  9. Biophysical parameters modification could overcome essential hearing gaps.

    Directory of Open Access Journals (Sweden)

    A Kern

    Full Text Available A majority of hearing defects are due to malfunction of the outer hair cells (OHCs, those cells within the mammalian hearing sensor (the cochlea that provide an active amplification of the incoming signal. Malformation of the hearing sensor, ototoxic drugs, acoustical trauma, infections, or the effect of aging affect often a whole frequency interval, which leads to a substantial loss of speech intelligibility. Using an energy-based biophysical model of the passive cochlea, we obtain an explicit description of the dependence of the tonotopic map on the biophysical parameters of the cochlea. Our findings indicate the possibility that by suitable local modifications of the biophysical parameters by microsurgery, even very salient gaps of the tonotopic map could be bridged.

  10. Evaluating landscape health: Integrating societal goals and biophysical process

    Science.gov (United States)

    Rapport, D.J.; Gaudet, C.; Karr, J.R.; Baron, Jill S.; Bohlen, C.; Jackson, W.; Jones, B.; Naiman, R.J.; Norton, B.; Pollock, M. M.

    1998-01-01

    Evaluating landscape change requires the integration of the social and natural sciences. The social sciences contribute to articulating societal values that govern landscape change, while the natural sciences contribute to understanding the biophysical processes that are influenced by human activity and result in ecological change. Building upon Aldo Leopold's criteria for landscape health, the roles of societal values and biophysical processes in shaping the landscape are explored. A framework is developed for indicators of landscape health and integrity. Indicators of integrity are useful in measuring biological condition relative to the condition in landscapes largely unaffected by human activity, while indicators of health are useful in evaluating changes in highly modified landscapes. Integrating societal goals and biophysical processes requires identification of ecological services to be sustained within a given landscape. It also requires the proper choice of temporal and spatial scales. Societal values are based upon inter-generational concerns at regional scales (e.g. soil and ground water quality). Assessing the health and integrity of the environment at the landscape scale over a period of decades best integrates societal values with underlying biophysical processes. These principles are illustrated in two contrasting case studies: (1) the South Platte River study demonstrates the role of complex biophysical processes acting at a distance; and (2) the Kissimmee River study illustrates the critical importance of social, cultural and economic concerns in the design of remedial action plans. In both studies, however, interactions between the social and the biophysical governed the landscape outcomes. The legacy of evolution and the legacy of culture requires integration for the purpose of effectively coping with environmental change.

  11. Biophysical stimulation of bone fracture repair, regeneration and remodelling

    Directory of Open Access Journals (Sweden)

    Chao E. Y.S.

    2003-12-01

    Full Text Available Biophysical stimulation to enhance bone fracture repair and bone regenerate maturation to restore its structural strength must rely on both the biological and biomechanical principle according to the local tissue environment and the type of mechanical stress to be born by the skeletal joint system. This paper reviews the possible interactions between biophysical stimuli and cellular responses in healing bone fractures and proceeds to speculate the prospects and limitations of different experimental models in evaluating and optimising such non-invasive interventions. It is important to realize that bone fracture repair has several pathways with various combinations of bone formation mechanisms, but there may only be one bone remodeling principle regulated by the hypothesis proposed by Wolff. There are different mechanical and biophysical stimuli that could provide effective augmentation of fracture healing and bone regenerate maturation. The key requirements of establishing these positive interactions are to define the precise cellular response to the stimulation signal in an in vitro environment and to use well-established animal models to quantify and optimise the therapeutic regimen in a time-dependent manner. This can only be achieved through research collaboration among different disciplines using scientific methodologies. In addition, the specific forms of biophysical stimulation and its dose effect and application timing must be carefully determined and validated. Technological advances in achieving focalized stimulus delivery with adjustable signal type and intensity, in the ability to monitor healing callus mechanical property non-invasively, and in the establishment of a robust knowledgebase to develop effective and reliable treatment protocols are the essential pre-requisites to make biophysical stimulation acceptable in the main arena of health care. Finally, it is important to bear in mind that successful fracture repair or bone

  12. Reorganization of plasma membrane lipid domains during conidial germination.

    Science.gov (United States)

    Santos, Filipa C; Fernandes, Andreia S; Antunes, Catarina A C; Moreira, Filipe P; Videira, Arnaldo; Marinho, H Susana; de Almeida, Rodrigo F M

    2017-02-01

    Neurospora crassa, a filamentous fungus, in the unicellular conidial stage has ideal features to study sphingolipid (SL)-enriched domains, which are implicated in fundamental cellular processes ranging from antifungal resistance to apoptosis. Several changes in lipid metabolism and in the membrane composition of N. crassa occur during spore germination. However, the biophysical impact of those changes is unknown. Thus, a biophysical study of N. crassa plasma membrane, particularly SL-enriched domains, and their dynamics along conidial germination is prompted. Two N. crassa strains, wild-type (WT) and slime, which is devoid of cell wall, were studied. Conidial growth of N. crassa WT from a dormancy state to an exponential phase was accompanied by membrane reorganization, namely an increase of membrane fluidity, occurring faster in a supplemented medium than in Vogel's minimal medium. Gel-like domains, likely enriched in SLs, were found in both N. crassa strains, but were particularly compact, rigid and abundant in the case of slime cells, even more than in budding yeast Saccharomyces cerevisiae. In N. crassa, our results suggest that the melting of SL-enriched domains occurs near growth temperature (30°C) for WT, but at higher temperatures for slime. Regarding biophysical properties strongly affected by ergosterol, the plasma membrane of slime conidia lays in between those of N. crassa WT and S. cerevisiae cells. The differences in biophysical properties found in this work, and the relationships established between membrane lipid composition and dynamics, give new insights about the plasma membrane organization and structure of N. crassa strains during conidial growth. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Preface: Special Topic on Single-Molecule Biophysics.

    Science.gov (United States)

    Makarov, Dmitrii E; Schuler, Benjamin

    2018-03-28

    Single-molecule measurements are now almost routinely used to study biological systems and processes. The scope of this special topic emphasizes the physics side of single-molecule observations, with the goal of highlighting new developments in physical techniques as well as conceptual insights that single-molecule measurements bring to biophysics. This issue also comprises recent advances in theoretical physical models of single-molecule phenomena, interpretation of single-molecule signals, and fundamental areas of statistical mechanics that are related to single-molecule observations. A particular goal is to illustrate the increasing synergy between theory, simulation, and experiment in single-molecule biophysics.

  14. [Biophysical methods in assessment of the skin microcirculation system].

    Science.gov (United States)

    Dynnik, O B; Mostovoĭ, S E; Berezovskiĭ, V A

    2008-01-01

    In this work has been analyzed the potential of biophysics methods in estimations of the microcirculatory system. Capillaroresistometry, Computer capillaroscopy and Laser Doppler Flowmetry can to detect of the endothelial dysfunction in the patients with chronic hepatic diseases. This instrumentals biophysics methods may be used in clinical investigations for screening early pathological conditions with dysfunction of the microcirculatory system. The methods Laser Doppler Flowmetry is important for investigations the patients with others diseases and for dynamical monitoring by quality of the treatment. The purpose of these methods an objective estimation of disorders in the microcirculatory system.

  15. Cell biology, biophysics, and mechanobiology: From the basics to Clinics.

    Science.gov (United States)

    Zeng, Y

    2017-04-29

    Cell biology, biomechanics and biophysics are the key subjects that guide our understanding in diverse areas of tissue growth, development, remodeling and homeostasis. Novel discoveries such as molecular mechanism, and mechanobiological mechanism in cell biology, biomechanics and biophysics play essential roles in our understanding of the pathogenesis of various human diseases, as well as in designing the treatment of these diseases. In addition, studies in these areas will also facilitate early diagnostics of human diseases, such as cardiovascular diseases and cancer. In this special issue, we collected 10 original research articles and 1 review...

  16. Institute of Biochemistry and Biophysics. Research Report 1996-1997

    International Nuclear Information System (INIS)

    1998-01-01

    Scientific interests of the Institute of Biochemistry and Biophysics of the Polish Academy of Sciences have evolved from classical biochemistry, biophysics and physiological chemistry to up-to-date molecular biology. Research interests are focussed on replication, mutagenesis and repair of DNA; regulation of gene expression at various levels; biosynthesis and post-translational modifications of proteins; gene sequencing and functional analysis of open reading frames; structure, function and regulation of enzymes; conformation of proteins and peptides; modelling of structures and prediction of functions of proteins; mechanisms of electron transfer in polypeptides

  17. Evaluation of biophysical skin parameters and assessment of hair growth in patients with acne treated with isotretinoin.

    Science.gov (United States)

    Kmieć, Małgorzata L; Pajor, Anna; Broniarczyk-Dyła, Grażyna

    2013-12-01

    Treatment of the severe forms of acne vulgaris remains a challenge. Isotretinoin is a drug often used in these cases. Retinoids affect the mechanisms that play a role in the pathogenesis of acne, reduce the production of sebum and sizes of the sebaceous glands. However, isotretinoin appears to have undesirable side effects in the skin, mucous membranes and hair. THE AIM OF THIS STUDY WAS TO ASSESS THE EFFECT OF ACNE VULGARIS TREATMENT WITH ISOTRETINOIN ON BIOPHYSICAL SKIN PARAMETERS: skin sebum and stratum corneum hydration levels, transepidermal water loss values, pH, erythema and hair growth parameters: total number, density and proportion of anagen hair. THE STUDY INCLUDED THIRTY PATIENTS WITH ACNE TYPES: papulopustular, conglobata and phlegmonosa. Patients were treated with isotretinoin at a dose of 0.5-1.0 mg/kg/day for a period of 4-7 months. The measurements of skin biophysical parameters were performed before and after the treatment using Sebumeter SM815, Corneometer CM825, Tewameter TM300, MX Mexameter MX18 and Skin-pH-Meter PH908. Hair growth parameters were evaluated with FotoFinder Dermoscope using the TrichoScan Professional V3.0.8.76 software. The results of biophysical skin parameter measurements after the treatment showed a reduction in the severity of seborrhea. However, the skin was dry, which confirmed a lowered degree of stratum corneum hydration and an increase in transepidermal water loss values. Moreover, severity of erythema, an increase in pH value, and variations in selected hair growth parameters: decrease in total count, density and proportion of anagen hair were demonstrated. The reduction in the skin sebum levels was observed after the treatment. There was dryness of the skin, which was confirmed by biophysical skin parameter measurements. Changes in the hair growth parameters showed telogen effluvium hair loss.

  18. A historical forest management conundrum: do social and biophysical mix?

    Science.gov (United States)

    Heidi. Bigler-Cole

    2005-01-01

    Forest managers face an array of prickly, seemingly intractable environmental problems. They have traditionally turned to the biophysical sciences to help gauge potential management effects, weigh alternatives, and set priorities. Over the past several decades, forest managers have watched management plans disintegrate in the face of grassroots-level protests, quarrels...

  19. A theoretical description of elastic pillar substrates in biophysical experiments

    NARCIS (Netherlands)

    Mohrdieck, Camilla; Wanner, Alexander; Roos, Wouter; Roth, Alexander; Sackmann, Erich; Spatz, Joachim P.; Arzt, Eduard

    2005-01-01

    Arrays of elastic pillars are used in biophysical experiments as sensors for traction forces. The evaluation of the forces can be complicated if they are coupled to the pillar displacements over large distances. This is the case if many of the pillars are interconnected by elastic linkages as, for

  20. Southwest Ecological Restoration Institutes (SWERI) Biophysical Monitoring Workshop Report

    Science.gov (United States)

    Joseph Seidenberg; Judy Springer; Tessa Nicolet; Mike Battaglia; Christina Vothja

    2009-01-01

    On October 15-16, 2009, the Southwest Ecological Restoration Institutes (SWERI) hosted a workshop in which the participants would 1) build a common understanding of the types of monitoring that are occurring in forested ecosystems of the Southwest; 2) analyze and agree on an efficient, yet robust set of biophysical variables that can be used by land mangers and...

  1. Prostaglandin phospholipid conjugates with unusual biophysical and cytotoxic properties

    DEFF Research Database (Denmark)

    Pedersen, Palle Jacob; Adolph, Sidsel K.; Andresen, Thomas Lars

    2010-01-01

    The synthesis of two secretory phospholipase A(2) IIA sensitive 15-deoxy-Delta(12,14)-prostaglandin J(2) phospholipid conjugates is described and their biophysical and biological properties are reported. The conjugates spontaneously form particles in the liposome size region upon dispersion in an...

  2. Seminal Fluid Analysis And Biophysical Profile: Findings And ...

    African Journals Online (AJOL)

    Seminal Fluid Analysis And Biophysical Profile: Findings And Relevance In Infertile Males In Ilorin, Nigeria. EK Oghagbon, AAG Jimoh, SA Adebisi. Abstract. To determine if there was a bearing of body mass index (BMI) on male infertility, a cross-sectional study of males of infertile couples, attending our infertility clinic was ...

  3. Biophysical constraints on leaf expansion in a tall conifer.

    Science.gov (United States)

    Fredrick C. Meinzer; Barbara J. Bond; Jennifer A. Karanian

    2008-01-01

    The physiological mechanisms responsible for reduced extension growth as trees increase in height remain elusive. We evaluated biophysical constraints on leaf expansion in old-growth Douglas-fir (Psuedotsuga menziesii (Mirb.) Franco) trees. Needle elongation rates, plastic and elastic extensibility, bulk leaf water, (L...

  4. Beyond NDVI: Extraction of biophysical variables from remote sensing imagery

    NARCIS (Netherlands)

    Clevers, J.G.P.W.

    2014-01-01

    This chapter provides an overview of methods used for the extraction of biophysical vegetation variables from remote sensing imagery. It starts with the description of the main spectral regions in the optical window of the electromagnetic spectrum based on typical spectral signatures of land

  5. Going beyond the biophysical when mapping national forests

    Science.gov (United States)

    Geoff Koch; Lee Cerveny

    2018-01-01

    Resource managers have long mapped biophysical forest data. Often lacking, however, is relevant social science data for understanding the variety of human needs a given landscape fulfills.For nearly a decade, Lee Cerveny has been exploring how to provide this data on public lands around the Pacific Northwest. Cerveny is a research...

  6. Kinetics and Thermodynamics of Membrane Protein Folding

    Directory of Open Access Journals (Sweden)

    Ernesto A. Roman

    2014-03-01

    Full Text Available Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins. In comparison, advances in the membrane protein folding field lag far behind. Although membrane proteins constitute about a third of the proteins encoded in known genomes, stability studies on membrane proteins have been impaired due to experimental limitations. Furthermore, no systematic experimental strategies are available for folding these biomolecules in vitro. Common denaturing agents such as chaotropes usually do not work on helical membrane proteins, and ionic detergents have been successful denaturants only in few cases. Refolding a membrane protein seems to be a craftsman work, which is relatively straightforward for transmembrane β-barrel proteins but challenging for α-helical membrane proteins. Additional complexities emerge in multidomain membrane proteins, data interpretation being one of the most critical. In this review, we will describe some recent efforts in understanding the folding mechanism of membrane proteins that have been reversibly refolded allowing both thermodynamic and kinetic analysis. This information will be discussed in the context of current paradigms in the protein folding field.

  7. Surface-enhanced Raman scattering: a new optical probe in molecular biophysics and biomedicine

    DEFF Research Database (Denmark)

    Kneipp, J.; Wittig, B.; Bohr, Henrik

    2010-01-01

    Sensitive and detailed molecular structural information plays an increasing role in molecular biophysics and molecular medicine. Therefore, vibrational spectroscopic techniques, such as Raman scattering, which provide high structural information content are of growing interest in biophysical...

  8. Small-Angle X-ray Scattering Screening Complements Conventional Biophysical Analysis

    DEFF Research Database (Denmark)

    Tian, Xinsheng; Langkilde, Annette Eva; Thorolfsson, Matthias

    2014-01-01

    introduce small-angle X-ray scattering (SAXS) to characterize antibody solution behavior, which strongly complements conventional biophysical analysis. First, we apply a variety of conventional biophysical techniques for the evaluation of structural, conformational, and colloidal stability and report...

  9. Polish Academy of Sciences Institute of Biochemistry and Biophysics research report 1994-1995

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-12-31

    Scientific interests of Institute of Biochemistry and Biophysics Polish Academy of Sciences are focused on DNA replication and repair, gene expression, gene sequencing and molecular biophysics. The work reviews research projects of the Institute in 1994-1995.

  10. Polish Academy of Sciences Institute of Biochemistry and Biophysics research report 1994-1995

    International Nuclear Information System (INIS)

    1996-01-01

    Scientific interests of Institute of Biochemistry and Biophysics Polish Academy of Sciences are focused on DNA replication and repair, gene expression, gene sequencing and molecular biophysics. The work reviews research projects of the Institute in 1994-1995

  11. Mapping technological and biophysical capacities of watersheds to regulate floods

    Science.gov (United States)

    Mogollón, Beatriz; Villamagna, Amy M.; Frimpong, Emmanuel A.; Angermeier, Paul

    2016-01-01

    Flood regulation is a widely valued and studied service provided by watersheds. Flood regulation benefits people directly by decreasing the socio-economic costs of flooding and indirectly by its positive impacts on cultural (e.g., fishing) and provisioning (e.g., water supply) ecosystem services. Like other regulating ecosystem services (e.g., pollination, water purification), flood regulation is often enhanced or replaced by technology, but the relative efficacy of natural versus technological features in controlling floods has scarcely been examined. In an effort to assess flood regulation capacity for selected urban watersheds in the southeastern United States, we: (1) used long-term flood records to assess relative influence of technological and biophysical indicators on flood magnitude and duration, (2) compared the widely used runoff curve number (RCN) approach for assessing the biophysical capacity to regulate floods to an alternative approach that acknowledges land cover and soil properties separately, and (3) mapped technological and biophysical flood regulation capacities based on indicator importance-values derived for flood magnitude and duration. We found that watersheds with high biophysical (via the alternative approach) and technological capacities lengthened the duration and lowered the peak of floods. We found the RCN approach yielded results opposite that expected, possibly because it confounds soil and land cover processes, particularly in urban landscapes, while our alternative approach coherently separates these processes. Mapping biophysical (via the alternative approach) and technological capacities revealed great differences among watersheds. Our study improves on previous mapping of flood regulation by (1) incorporating technological capacity, (2) providing high spatial resolution (i.e., 10-m pixel) maps of watershed capacities, and (3) deriving importance-values for selected landscape indicators. By accounting for technology that enhances

  12. Characterising antimicrobial protein-membrane complexes

    International Nuclear Information System (INIS)

    Xun, Gloria; Dingley, Andrew; Tremouilhac, Pierre

    2009-01-01

    Full text: Antimicrobial proteins (AMPs) are host defence molecules that protect organisms from microbial infection. A number of hypotheses for AMP activity have been proposed which involve protein membrane interactions. However, there is a paucity of information describing AMP-membrane complexes in detail. The aim of this project is to characterise the interactions of amoebapore-A (APA-1) with membrane models using primarily solution-state NMR spectroscopy. APA-1 is an AMP which is regulated by a pH-dependent dimerisation event. Based on the atomic resolution solution structure of monomeric APA-1, it is proposed that this dimerisation is a prerequisite for ring-like hexameric pore formation. Due to the cytotoxicity of APA-1, we have developed a cell-free system to produce this protein. To facilitate our studies, we have adapted the cell-free system to isotope label APA-1. 13 C /15 N -enriched APA-1 sample was achieved and we have begun characterising APA-1 dimerisation and membrane interactions using NMR spectroscopy and other biochemical/biophysical methods. Neutron reflectometry is a surface-sensitive technique and therefore represents an ideal technique to probe how APA-1 interacts with membranes at the molecular level under different physiological conditions. Using Platypus, the pH-induced APA-1-membrane interactions should be detectable as an increase of the amount of protein adsorbed at the membrane surface and changes in the membrane properties. Specifically, detailed information of the structure and dimensions of the protein-membrane complex, the position and amount of the protein in the membrane, and the perturbation of the membrane phospholipids on protein incorporation can be extracted from the neutron reflectometry measurement. Such information will enable critical assessment of current proposed mechanisms of AMP activity in bacterial membranes and complement our NMR studies

  13. Receptor-targeted lentiviral vectors are exceptionally sensitive toward the biophysical properties of the displayed single-chain Fv.

    Science.gov (United States)

    Friedel, Thorsten; Hanisch, Lydia J; Muth, Anke; Honegger, Annemarie; Abken, Hinrich; Plückthun, Andreas; Buchholz, Christian J; Schneider, Irene C

    2015-04-01

    An increasing number of applications require the expression of single-chain variable fragments (scFv) fusion proteins in mammalian cells at the cell surface membrane. Here we assessed the CD30-specific scFv HRS3, which is used in immunotherapy, for its ability to retarget lentiviral vectors (LVs) to CD30 and to mediate selective gene transfer into CD30-positive cells. Fused to the C-terminus of the type-II transmembrane protein hemagglutinin (H) of measles virus and expressed in LV packaging cells, gene transfer mediated by the released LV particles was inefficient. A series of point mutations in the scFv framework regions addressing its biophysical properties, which substantially improved production and increased the melting temperature without impairing its kinetic binding behavior to CD30, also improved the performance of LV particles. Gene transfer into CD30-positive cells increased ∼100-fold due to improved transport of the H-scFv protein to the plasma membrane. Concomitantly, LV particle aggregation and syncytia formation in packaging cells were substantially reduced. The data suggest that syncytia formation can be triggered by trans-cellular dimerization of H-scFv proteins displayed on adjacent cells. Taken together, we show that the biophysical properties of the targeting ligand have a decisive role for the gene transfer efficiency of receptor-targeted LVs. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  14. Investigation of quercetin-induced HepG2 cell apoptosis-associated cellular biophysical alterations by atomic force microscopy.

    Science.gov (United States)

    Pi, Jiang; Li, Baole; Tu, Lvying; Zhu, Haiyan; Jin, Hua; Yang, Fen; Bai, Haihua; Cai, Huaihong; Cai, Jiye

    2016-01-01

    Quercetin, a wildly distributed bioflavonoid, has been proved to possess excellent antitumor activity on hepatocellular carcinoma (HCC). In the present study, the biophysical properties of HepG2 cells were qualitatively and quantitatively determined using high resolution atomic force microscopy (AFM) to understand the anticancer effects of quercetin on HCC cells at nanoscale. The results showed that quercetin could induce severe apoptosis in HepG2 cells through arrest of cell cycle and disruption of mitochondria membrane potential. Additionally, the nuclei and F-actin structures of HepG2 cells were destroyed by quercetin treatment as well. AFM morphological data showed some typical apoptotic characterization of HepG2 cells with increased particle size and roughness in the ultrastructure of cell surface upon quercetin treatment. As an important biophysical property of cells, the membrane stiffness of HepG2 cells was further quantified by AFM force measurements, which indicated that HepG2 cells became much stiffer after quercetin treatment. These results collectively suggest that quercetin can be served as a potential therapeutic agent for HCC, which not only extends our understanding of the anticancer effects of quercetin against HCC cells into nanoscale, but also highlights the applications of AFM for the investigation of anticancer drugs. © Wiley Periodicals, Inc.

  15. Alcohols enhance the rate of acetic acid diffusion inS. cerevisiae: biophysical mechanisms and implications for acetic acid tolerance.

    Science.gov (United States)

    Lindahl, Lina; Genheden, Samuel; Faria-Oliveira, Fábio; Allard, Stefan; Eriksson, Leif A; Olsson, Lisbeth; Bettiga, Maurizio

    2017-12-01

    Microbial cell factories with the ability to maintain high productivity in the presence of weak organic acids, such as acetic acid, are required in many industrial processes. For example, fermentation media derived from lignocellulosic biomass are rich in acetic acid and other weak acids. The rate of diffusional entry of acetic acid is one parameter determining the ability of microorganisms to tolerance the acid. The present study demonstrates that the rate of acetic acid diffusion in S. cerevisiae is strongly affected by the alcohols ethanol and n-butanol. Ethanol of 40 g/L and n-butanol of 8 g/L both caused a 65% increase in the rate of acetic acid diffusion, and higher alcohol concentrations caused even greater increases. Molecular dynamics simulations of membrane dynamics in the presence of alcohols demonstrated that the partitioning of alcohols to the head group region of the lipid bilayer causes a considerable increase in the membrane area, together with reduced membrane thickness and lipid order. These changes in physiochemical membrane properties lead to an increased number of water molecules in the membrane interior, providing biophysical mechanisms for the alcohol-induced increase in acetic acid diffusion rate. n-butanol affected S. cerevisiae and the cell membrane properties at lower concentrations than ethanol, due to greater and deeper partitioning in the membrane. This study demonstrates that the rate of acetic acid diffusion can be strongly affected by compounds that partition into the cell membrane, and highlights the need for considering interaction effects between compounds in the design of microbial processes.

  16. Alcohols enhance the rate of acetic acid diffusion in S. cerevisiae: biophysical mechanisms and implications for acetic acid tolerance

    Science.gov (United States)

    Lindahl, Lina; Genheden, Samuel; Faria-Oliveira, Fábio; Allard, Stefan; Eriksson, Leif A.; Olsson, Lisbeth; Bettiga, Maurizio

    2017-01-01

    Microbial cell factories with the ability to maintain high productivity in the presence of weak organic acids, such as acetic acid, are required in many industrial processes. For example, fermentation media derived from lignocellulosic biomass are rich in acetic acid and other weak acids. The rate of diffusional entry of acetic acid is one parameter determining the ability of microorganisms to tolerance the acid. The present study demonstrates that the rate of acetic acid diffusion in S. cerevisiae is strongly affected by the alcohols ethanol and n-butanol. Ethanol of 40 g/L and n-butanol of 8 g/L both caused a 65% increase in the rate of acetic acid diffusion, and higher alcohol concentrations caused even greater increases. Molecular dynamics simulations of membrane dynamics in the presence of alcohols demonstrated that the partitioning of alcohols to the head group region of the lipid bilayer causes a considerable increase in the membrane area, together with reduced membrane thickness and lipid order. These changes in physiochemical membrane properties lead to an increased number of water molecules in the membrane interior, providing biophysical mechanisms for the alcohol-induced increase in acetic acid diffusion rate. n-butanol affected S. cerevisiae and the cell membrane properties at lower concentrations than ethanol, due to greater and deeper partitioning in the membrane. This study demonstrates that the rate of acetic acid diffusion can be strongly affected by compounds that partition into the cell membrane, and highlights the need for considering interaction effects between compounds in the design of microbial processes. PMID:29354649

  17. The ER membrane protein complex is a transmembrane domain insertase

    Science.gov (United States)

    Guna, Alina; Volkmar, Norbert; Christianson, John C.; Hegde, Ramanujan S.

    2018-01-01

    Insertion of proteins into membranes is an essential cellular process. The extensive biophysical and topological diversity of membrane proteins necessitates multiple insertion pathways that remain incompletely defined. Here, we found that known membrane insertion pathways fail to effectively engage tail-anchored membrane proteins with moderately hydrophobic transmembrane domains. These proteins are instead shielded in the cytosol by calmodulin. Dynamic release from calmodulin allowed sampling of the endoplasmic reticulum (ER), where the conserved ER membrane protein complex (EMC) was shown to be essential for efficient insertion in vitro and in cells. Purified EMC in synthetic liposomes catalyzed insertion of its substrates in a reconstituted system. Thus, EMC is a transmembrane domain insertase, a function that may explain its widely pleiotropic membrane-associated phenotypes across organisms. PMID:29242231

  18. Biophysical properties and computational modeling of calcium spikes in serotonergic neurons of the dorsal raphe nucleus.

    Science.gov (United States)

    Tuckwell, Henry C

    2013-06-01

    Serotonergic neurons of the dorsal raphe nuclei, with their extensive innervation of nearly the whole brain have important modulatory effects on many cognitive and physiological processes. They play important roles in clinical depression and other psychiatric disorders. In order to quantify the effects of serotonergic transmission on target cells it is desirable to construct computational models and to this end these it is necessary to have details of the biophysical and spike properties of the serotonergic neurons. Here several basic properties are reviewed with data from several studies since the 1960s to the present. The quantities included are input resistance, resting membrane potential, membrane time constant, firing rate, spike duration, spike and afterhyperpolarization (AHP) amplitude, spike threshold, cell capacitance, soma and somadendritic areas. The action potentials of these cells are normally triggered by a combination of sodium and calcium currents which may result in autonomous pacemaker activity. We here analyse the mechanisms of high-threshold calcium spikes which have been demonstrated in these cells the presence of TTX (tetrodotoxin). The parameters for calcium dynamics required to give calcium spikes are quite different from those for regular spiking which suggests the involvement of restricted parts of the soma-dendritic surface as has been found, for example, in hippocampal neurons. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  19. Bioelectrical Signals and Ion Channels in the Modeling of Multicellular Patterns and Cancer Biophysics

    Science.gov (United States)

    Cervera, Javier; Alcaraz, Antonio; Mafe, Salvador

    2016-02-01

    Bioelectrical signals and ion channels are central to spatial patterns in cell ensembles, a problem of fundamental interest in positional information and cancer processes. We propose a model for electrically connected cells based on simple biological concepts: i) the membrane potential of a single cell characterizes its electrical state; ii) the long-range electrical coupling of the multicellular ensemble is realized by a network of gap junction channels between neighboring cells; and iii) the spatial distribution of an external biochemical agent can modify the conductances of the ion channels in a cell membrane and the multicellular electrical state. We focus on electrical effects in small multicellular ensembles, ignoring slow diffusional processes. The spatio-temporal patterns obtained for the local map of cell electric potentials illustrate the normalization of regions with abnormal cell electrical states. The effects of intercellular coupling and blocking of specific channels on the electrical patterns are described. These patterns can regulate the electrically-induced redistribution of charged nanoparticles over small regions of a model tissue. The inclusion of bioelectrical signals provides new insights for the modeling of cancer biophysics because collective multicellular states show electrical coupling mechanisms that are not readily deduced from biochemical descriptions at the individual cell level.

  20. Biophysical mechanisms of phospholipase A2 activation and their use in liposome-based drug delivery

    DEFF Research Database (Denmark)

    Jørgensen, Kaj; Davidsen, Jesper; Mouritsen, Ole G.

    2002-01-01

    Secretory phospholipase A(2) (PLA(2)) is a ubiquitous water-soluble enzyme found in venom, pancreatic, and cancerous fluid. It is also known to play a role in membrane remodeling processes as well as in cellular signaling cascades. PLA(2) is interfacially active and functions mainly on organized ...... into these mechanisms has been used to propose a novel principle for liposomal drug targeting, release, and absorption triggered by secretory PLA(2).(C) 2002 Federation of European Biochemical Societies. Published by Elsevier Science B.V. All rights reserved.......Secretory phospholipase A(2) (PLA(2)) is a ubiquitous water-soluble enzyme found in venom, pancreatic, and cancerous fluid. It is also known to play a role in membrane remodeling processes as well as in cellular signaling cascades. PLA(2) is interfacially active and functions mainly on organized...... reviewed. Results obtained from a variety of experimental and theoretical studies of PLA(2) activity on lipid-bilayer substrates are then presented which provide insight into the biophysical mechanisms of PLA(2) activation on lipid bilayers and liposomes of different composition. The insight...

  1. Biophysical analysis of the interaction of granulysin-derived peptides with enterobacterial endotoxins.

    Science.gov (United States)

    Chen, Xi; Howe, Jörg; Andrä, Jörg; Rössle, Manfred; Richter, Walter; da Silva, Ana Paula Galvão; Krensky, Alan M; Clayberger, Carol; Brandenburg, Klaus

    2007-10-01

    To combat infections by Gram-negative bacteria, it is not only necessary to kill the bacteria but also to neutralize pathogenicity factors such as endotoxin (lipopolysaccharide, LPS). The development of antimicrobial peptides based on mammalian endotoxin-binding proteins is a promising tool in the fight against bacterial infections, and septic shock syndrome. Here, synthetic peptides derived from granulysin (Gra-pep) were investigated in microbiological and biophysical assays to understand their interaction with LPS. We analyzed the influence of the binding of Gra-pep on (1) the acyl chain melting of the hydrophobic moiety of LPS, lipid A, by Fourier-transform spectroscopy, (2) the aggregate structure of LPS by small-angle X-ray scattering and cryo-transmission electron microscopy, and 3) the enthalpy change by isothermal titration calorimetry. In addition, the influence of Gra-pep on the incorporation of LPS and LPS-LBP (lipopolysaccharide-binding protein) complexes into negatively charged liposomes was monitored. Our findings demonstrate a characteristic change in the aggregate structure of LPS into multilamellar stacks in the presence of Gra-pep, but little or no change of acyl chain fluidity. Neutralization of LPS by Gra-pep is not due to a scavenging effect in solution, but rather proceeds after incorporation into target membranes, suggesting a requisite membrane-bound step.

  2. Synthesis of specifically deuterated ceramide [AP]-C18 and its biophysical characterization using neutron diffraction.

    Science.gov (United States)

    Sonnenberger, Stefan; Eichner, Adina; Hauß, Thomas; Schroeter, Annett; Neubert, Reinhard H H; Dobner, Bodo

    2017-04-01

    The very heterogeneous group of ceramides is known to be mandatory for proper barrier functions of the outermost layer of mammalian skin, referred to as stratum corneum (SC). The synthesis of a specifically deuterated ceramide [AP]-C18 variant is described. The synthesized ceramide contains the racemic forms of the α hydroxy fatty acid. For the biophysical implementation, the received diastereomeric ceramide was applied in a neutron diffraction experiment. Therefore, a SC lipid model membrane was prepared containing the described ceramide (CER), cholesterol (CHOL), stearic acid (SA), and cholesterol sulfate (ChS) in a ratio of 55/25/15/5wt%. Thus, we were able to localize the deuterated molecule part within the bilayers. In the process, a short-periodicity phase (SPP) was observed with a unit cell scale of about 44Å. For the first time, we were able to confirm former ideas concerning the arrangement of the CER within this quaternary lipid model membrane. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Membrane paradigm

    International Nuclear Information System (INIS)

    Price, R.H.; Thorne, K.S.

    1986-01-01

    The membrane paradigm is a modified frozen star approach to modeling black holes, with particles and fields assuming a complex, static, boundary-layer type structure (membrane) near the event horizon. The membrane has no effects on the present or future evolution of particles and fields above itself. The mathematical representation is a combination of a formalism containing terms for the shear and bulk viscosity, surface pressure, momentum, temperature, entropy, etc., of the horizon and the 3+1 formalism. The latter model considers a family of three-dimensional spacelike hypersurfaces in one-dimensional time. The membrane model considers a magnetic field threading the hole and undergoing torque from the hole rotation. The field is cleaned by the horizon and distributed over the horizon so that ohmic dissipation is minimized. The membrane paradigm is invalid inside the horizon, but is useful for theoretically probing the properties of slowly evolving black holes

  4. Membrane processes

    Science.gov (United States)

    Staszak, Katarzyna

    2017-11-01

    The membrane processes have played important role in the industrial separation process. These technologies can be found in all industrial areas such as food, beverages, metallurgy, pulp and paper, textile, pharmaceutical, automotive, biotechnology and chemical industry, as well as in water treatment for domestic and industrial application. Although these processes are known since twentieth century, there are still many studies that focus on the testing of new membranes' materials and determining of conditions for optimal selectivity, i. e. the optimum transmembrane pressure (TMP) or permeate flux to minimize fouling. Moreover the researchers proposed some calculation methods to predict the membrane processes properties. In this article, the laboratory scale experiments of membrane separation techniques, as well their validation by calculation methods are presented. Because membrane is the "heart" of the process, experimental and computational methods for its characterization are also described.

  5. Adaptive transition rates in excitable membranes

    Directory of Open Access Journals (Sweden)

    Shimon Marom

    2009-02-01

    Full Text Available Adaptation of activity in excitable membranes occurs over a wide range of timescales. Standard computational approaches handle this wide temporal range in terms of multiple states and related reaction rates emanating from the complexity of ionic channels. The study described here takes a different (perhaps complementary approach, by interpreting ion channel kinetics in terms of population dynamics. I show that adaptation in excitable membranes is reducible to a simple Logistic-like equation in which the essential non-linearity is replaced by a feedback loop between the history of activation and an adaptive transition rate that is sensitive to a single dimension of the space of inactive states. This physiologically measurable dimension contributes to the stability of the system and serves as a powerful modulator of input-output relations that depends on the patterns of prior activity; an intrinsic scale free mechanism for cellular adaptation that emerges from the microscopic biophysical properties of ion channels of excitable membranes.

  6. Dissipative dynamics of fluid lipid membranes enriched in cholesterol.

    Science.gov (United States)

    Arriaga, Laura R; Rodríguez-García, Ruddi; Moleiro, Lara H; Prévost, Sylvain; López-Montero, Iván; Hellweg, Thomas; Monroy, Francisco

    2017-09-01

    Cholesterol is an intriguing component of fluid lipid membranes: It makes them stiffer but also more fluid. Despite the enormous biological significance of this complex dynamical behavior, which blends aspects of membrane elasticity with viscous friction, their mechanical bases remain however poorly understood. Here, we show that the incorporation of physiologically relevant contents of cholesterol in model fluid membranes produces a fourfold increase in the membrane bending modulus. However, the increase in the compression rigidity that we measure is only twofold; this indicates that cholesterol increases coupling between the two membrane leaflets. In addition, we show that although cholesterol makes each membrane leaflet more fluid, it increases the friction between the membrane leaflets. This dissipative dynamics causes opposite but advantageous effects over different membrane motions: It allows the membrane to rearrange quickly in the lateral dimension, and to simultaneously dissipate out-of-plane stresses through friction between the two membrane leaflets. Moreover, our results provide a clear correlation between coupling and friction of membrane leaflets. Furthermore, we show that these rigid membranes are optimal to resist slow deformations with minimum energy dissipation; their optimized stability might be exploited to design soft technological microsystems with an encoded mechanics, vesicles or capsules for instance, useful beyond classical applications as model biophysical systems. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Membrane solid-state NMR in Canada: A historical perspective.

    Science.gov (United States)

    Auger, Michèle

    2017-11-01

    This manuscript presents an overview of more than 40years of membrane solid-state nuclear magnetic resonance (NMR) research in Canada. This technique is a method of choice for the study of the structure and dynamics of lipid bilayers; bilayer interactions with a variety of molecules such as membrane peptides, membrane proteins and drugs; and to investigate membrane peptide and protein structure, dynamics, and topology. Canada has a long tradition in this field of research, starting with pioneering work on natural and model membranes in the 1970s in a context of emergence of biophysics in the country. The 1980s and 1990s saw an emphasis on studying lipid structures and dynamics, and peptide-lipid and protein-lipid interactions. The study of bicelles began in the 1990s, and in the 2000s there was a rise in the study of membrane protein structures. Novel perspectives include using dynamic nuclear polarization (DNP) for membrane studies and using NMR in live cells. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Membrane Shape Instability Induced by Protein Crowding.

    Science.gov (United States)

    Chen, Zhiming; Atefi, Ehsan; Baumgart, Tobias

    2016-11-01

    Peripheral proteins can bend membranes through several different mechanisms, including scaffolding, wedging, oligomerization, and crowding. The crowding effect in particular has received considerable attention recently, in part because it is a colligative mechanism-implying that it could, in principle, be explored by any peripheral protein. Here we sought to clarify to what extent this mechanism is exploited by endocytic accessory proteins. We quantitatively investigate membrane curvature generation by means of a GUV shape stability assay. We found that the amount of crowding required to induce membrane curvature is correlated with membrane tension. Importantly, we also revealed that at the same membrane tension, the crowding mechanism requires far higher protein coverage to induce curvature changes compared to those observed for the endophilin BAR domain, serving here as an example of an endocytic accessory protein. Our results are important for the design of membrane-targeted biosensors as well as the understanding of mechanisms of biological membrane shaping. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  9. Biophysical dosimetry using electron paramagnetic resonance in human tooth

    International Nuclear Information System (INIS)

    Khan, R.F.H.; Boreham, D.R.; Rink, W.J.

    2002-01-01

    Accidental dosimetry utilizing radiation induced paramagnetic species in biophysical tissues like teeth is a technique; that can measure the amount of radiation exposure to an individual. The major problem in implementing this technique at low doses is the presence of native organic signal, and various other artifacts produced as a result of sample processing. After a series of experimental trials, we developed an optimum set of rules, which uses high temperature ultrasonic treatment of enamel in KOH, multiple sample rotation during in-cavity measurement of natural and calibrated added irradiations, and dose construction using a backward extrapolation method. By using this we report the successful dose reconstruction in a few of our laboratory samples in 100 mGy range (76.29 ± 30.14) mGy with reasonably low uncertainty. Keywords: biophysical dosimetry, human tooth enamel, low dose measurements, accidental dosimetry (author)

  10. Biophysical Evaluation of Food Decontamination Effects on Tissue and Bacteria

    DEFF Research Database (Denmark)

    Andersen, Ann Zahle; Duelund, Lars; Brewer, Jonathan

    2011-01-01

    that there are no contradictions between data obtained by either approach. However, the biophysical methods draw a much more nuanced picture of the effects and efficiency of the investigated decontamination method, revealing, e.g., an exponential dose/response relationship between SonoSteam® treatment time and changes in collagen...... consumer responses or meeting legislative contamination limits. However, in the often very costly, optimization process of a new method, more quantitative and unbiased results are invaluable. In this study, we employed a biophysical approach for the investigation of qualitative and quantitative changes...... in both food surface and bacteria upon surface decontamination by SonoSteam®. SonoSteam® is a recently developed method of food surface decontamination, which employs steam and ultrasound for effective heat transfer and short treatment times, resulting in significant reduction in surface bacteria. We...

  11. Biophysical approach to low back pain: a pilot report.

    Science.gov (United States)

    Foletti, Alberto; Pokorný, Jiry

    2015-01-01

    Since biophysical treatment has been reported to be effective in the general management of pain, we decided to assess the specific effect and treatment duration of this therapeutic strategy in low back pain. We were interested in verifying the possibility that a single clinical procedure could reduce pain and improve patients' quality of life within a period of three months. An Electromagnetic Information Transfer Through Aqueous System was employed to record endogenous therapeutic signals from each individual using an electromagnetic recording device (Med Select 729). A highly significant reduction in the Roland Morris low back pain and disability questionnaire score was observed after 3 months following a single biophysical intervention (11.83 ± 6 at baseline versus 2.3 ± 3.25 at 3 months, p < 0.0001). This preliminary report provides further evidence of the theoretical implications and clinical applications of Quantum Electro Dynamic concepts in biology and medicine.

  12. The biophysics of renal sympathetic denervation using radiofrequency energy.

    Science.gov (United States)

    Patel, Hitesh C; Dhillon, Paramdeep S; Mahfoud, Felix; Lindsay, Alistair C; Hayward, Carl; Ernst, Sabine; Lyon, Alexander R; Rosen, Stuart D; di Mario, Carlo

    2014-05-01

    Renal sympathetic denervation is currently performed in the treatment of resistant hypertension by interventionists who otherwise do not typically use radiofrequency (RF) energy ablation in their clinical practice. Adequate RF lesion formation is dependent upon good electrode-tissue contact, power delivery, electrode-tissue interface temperature, target-tissue impedance and the size of the catheter's active electrode. There is significant interplay between these variables and hence an appreciation of the biophysical determinants of RF lesion formation is required to provide effective and safe clinical care to our patients. In this review article, we summarize the biophysics of RF ablation and explain why and how complications of renal sympathetic denervation may occur and discuss methods to minimise them.

  13. Biophysical Evaluation of Food Decontamination Effects on Tissue and Bacteria

    DEFF Research Database (Denmark)

    Andersen, Ann Zahle; Duelund, Lars; Brewer, Jonathan R.

    2011-01-01

    employ differential scanning calorimetry, second harmonics generation imaging microscopy, two-photon fluorescence microscopy, and green fluorescence protein-expressing bacteria and compare our results with those obtained by traditional methods of food quality and safety evaluations. Our results show...... consumer responses or meeting legislative contamination limits. However, in the often very costly, optimization process of a new method, more quantitative and unbiased results are invaluable. In this study, we employed a biophysical approach for the investigation of qualitative and quantitative changes...... that there are no contradictions between data obtained by either approach. However, the biophysical methods draw a much more nuanced picture of the effects and efficiency of the investigated decontamination method, revealing, e.g., an exponential dose/response relationship between SonoSteam® treatment time and changes in collagen...

  14. Evolution and Biophysics of the Escherichia coli lac Operon

    Science.gov (United States)

    Ray, J. Christian; Igoshin, Oleg; Quan, Selwyn; Monds, Russell; Cooper, Tim; Balázsi, Gábor

    2011-03-01

    To understand, predict, and control the evolution of living organisms, we consider biophysical effects and molecular network architectures. The lactose utilization system of E. coli is among the most well-studied molecular networks in biology, making it an ideal candidate for such studies. Simulations show how the genetic architecture of the wild-type operon attenuates large metabolic intermediate fluctuations that are predicted to occur in an equivalent system with the component genes on separate operons. Quantification of gene expression in the lac operon evolved in growth conditions containing constant lactose, alternating with glucose, or constant glucose, shows characteristic gene expression patterns depending on conditions. We are simulating these conditions to show context-dependent biophysical sources and costs of different lac operon architectures.

  15. Synthetic Biology: Engineering Living Systems from Biophysical Principles.

    Science.gov (United States)

    Bartley, Bryan A; Kim, Kyung; Medley, J Kyle; Sauro, Herbert M

    2017-03-28

    Synthetic biology was founded as a biophysical discipline that sought explanations for the origins of life from chemical and physical first principles. Modern synthetic biology has been reinvented as an engineering discipline to design new organisms as well as to better understand fundamental biological mechanisms. However, success is still largely limited to the laboratory and transformative applications of synthetic biology are still in their infancy. Here, we review six principles of living systems and how they compare and contrast with engineered systems. We cite specific examples from the synthetic biology literature that illustrate these principles and speculate on their implications for further study. To fully realize the promise of synthetic biology, we must be aware of life's unique properties. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  16. From hadron therapy to cosmic rays: a life in biophysics

    CERN Multimedia

    Christine Sutton

    2014-01-01

    In 1954 – the year CERN was founded – another scientific journey began at what is now the Lawrence Berkeley National Laboratory. Beams of protons from a particle accelerator were used for the first time by John Lawrence – a doctor and the brother of Ernest Lawrence, the physicist after whom the Berkeley lab is named – to treat patients with cancer. For many years, Eleanor Blakely has been one of the leaders of that journey. She visited CERN last week and spoke with the Bulletin about her life in biophysics.   Use of the cylcotron beam to mimic "shooting stars" seen by astronauts. Black hood on subject Cornelius Tobias keeps out light during neutron irradiation experiment at the 184-inch accelerator. Helping to position Tobias in the beam line are (left to right) John Lyman of Biomedical Division, and Ralph Thomas of Health Physics. (Photo courtesy of Lawrence Berkeley National Laboratory.) Interested in biophysics, which was still a new...

  17. Achievements and challenges in structural bioinformatics and computational biophysics.

    Science.gov (United States)

    Samish, Ilan; Bourne, Philip E; Najmanovich, Rafael J

    2015-01-01

    The field of structural bioinformatics and computational biophysics has undergone a revolution in the last 10 years. Developments that are captured annually through the 3DSIG meeting, upon which this article reflects. An increase in the accessible data, computational resources and methodology has resulted in an increase in the size and resolution of studied systems and the complexity of the questions amenable to research. Concomitantly, the parameterization and efficiency of the methods have markedly improved along with their cross-validation with other computational and experimental results. The field exhibits an ever-increasing integration with biochemistry, biophysics and other disciplines. In this article, we discuss recent achievements along with current challenges within the field. © The Author 2014. Published by Oxford University Press.

  18. Biophysical climate impacts of recent changes in global forest cover

    Science.gov (United States)

    Alkama, Ramdane; Cescatti, Alessandro

    2016-02-01

    Changes in forest cover affect the local climate by modulating the land-atmosphere fluxes of energy and water. The magnitude of this biophysical effect is still debated in the scientific community and currently ignored in climate treaties. Here we present an observation-driven assessment of the climate impacts of recent forest losses and gains, based on Earth observations of global forest cover and land surface temperatures. Our results show that forest losses amplify the diurnal temperature variation and increase the mean and maximum air temperature, with the largest signal in arid zones, followed by temperate, tropical, and boreal zones. In the decade 2003-2012, variations of forest cover generated a mean biophysical warming on land corresponding to about 18% of the global biogeochemical signal due to CO2 emission from land-use change.

  19. BIOPHYSICAL AND MECH ATTRIBUTES TO LOSSES CAL AND ...

    African Journals Online (AJOL)

    User

    and 150N to crack the rice grain at 22.5mm as w. 125N to crack the rice grain at 20mm, as such 13 crack the rice grain at 23.5mm,as wel the rice grain at 22.5mm respectively. Therefore is advisable to handle a particular rice variety un. Keywords: biophysical, mechanical properties,. 1. Introduction ntroduction ntroduction.

  20. Biophysical and electrochemical studies of protein-nucleic acid interactions

    Czech Academy of Sciences Publication Activity Database

    Bowater, R. P.; Cobb, A:M.; Pivoňková, Hana; Havran, Luděk; Fojta, Miroslav

    2015-01-01

    Roč. 146, č. 5 (2015), s. 723-739 ISSN 0026-9247 R&D Projects: GA ČR(CZ) GBP206/12/G151; GA ČR(CZ) GAP301/11/2076 Institutional support: RVO:68081707 Keywords : ISOTHERMAL TITRATION CALORIMETRY * OSMIUM-TETROXIDE COMPLEXES * SURFACE-PLASMON RESONANCE Subject RIV: BO - Biophysics Impact factor: 1.131, year: 2015

  1. Biophysical research requirements for Beaufort Sea hydrocarbon development

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2008-08-15

    This review identified biophysical research requirements and data gaps for the development of hydrocarbon resources in the Beaufort Sea. The potential major effects of critical activities during each phase of the offshore oil and gas development cycle were identified in order to assess the impacts on local communities and traditional harvesting methods. Baseline environmental conditions were established. Information needs were ranked using 3 criteria: (1) the current understanding of the biophysical component in terms of present status and long-term sustainability, (2) the potential impact of the oil and gas development on the long-term sustainability of the biophysical component, and (3) the timeline for completion of the research relative to the expected development for the Beaufort Sea region. Mitigation and environmental management plans were outlined, and key research, data collection, and data analyses required to address data gaps were identified. Previous gap analyses for the region were reviewed. Data from a series of workshops conducted with various stakeholders were also included in the study. High research priorities include the assessment of the effects of climatic change on the physical oceanography of the region, studies on deepwater plankton, benthos, and fish. It was concluded that studies are needed to determine the effects of development on marine mammals, avifauna, and macroalgae. 207 refs., 49 tabs., 4 figs.

  2. Screening of the aerodynamic and biophysical properties of barley malt

    Science.gov (United States)

    Ghodsvali, Alireza; Farzaneh, Vahid; Bakhshabadi, Hamid; Zare, Zahra; Karami, Zahra; Mokhtarian, Mohsen; Carvalho, Isabel. S.

    2016-10-01

    An understanding of the aerodynamic and biophysical properties of barley malt is necessary for the appropriate design of equipment for the handling, shipping, dehydration, grading, sorting and warehousing of this strategic crop. Malting is a complex biotechnological process that includes steeping; germination and finally, the dehydration of cereal grains under controlled temperature and humidity conditions. In this investigation, the biophysical properties of barley malt were predicted using two models of artificial neural networks as well as response surface methodology. Stepping time and germination time were selected as the independent variables and 1 000 kernel weight, kernel density and terminal velocity were selected as the dependent variables (responses). The obtained outcomes showed that the artificial neural network model, with a logarithmic sigmoid activation function, presents more precise results than the response surface model in the prediction of the aerodynamic and biophysical properties of produced barley malt. This model presented the best result with 8 nodes in the hidden layer and significant correlation coefficient values of 0.783, 0.767 and 0.991 were obtained for responses one thousand kernel weight, kernel density, and terminal velocity, respectively. The outcomes indicated that this novel technique could be successfully applied in quantitative and qualitative monitoring within the malting process.

  3. Modelling benthic biophysical drivers of ecosystem structure and biogeochemical response

    Science.gov (United States)

    Stephens, Nicholas; Bruggeman, Jorn; Lessin, Gennadi; Allen, Icarus

    2016-04-01

    The fate of carbon deposited at the sea floor is ultimately decided by biophysical drivers that control the efficiency of remineralisation and timescale of carbon burial in sediments. Specifically, these drivers include bioturbation through ingestion and movement, burrow-flushing and sediment reworking, which enhance vertical particulate transport and solute diffusion. Unfortunately, these processes are rarely satisfactorily resolved in models. To address this, a benthic model that explicitly describes the vertical position of biology (e.g., habitats) and biogeochemical processes is presented that includes biological functionality and biogeochemical response capturing changes in ecosystem structure, benthic-pelagic fluxes and biodiversity on inter-annual timescales. This is demonstrated by the model's ability to reproduce temporal variability in benthic infauna, vertical pore water nutrients and pelagic-benthic solute fluxes compared to in-situ data. A key advance is the replacement of bulk parameterisation of bioturbation by explicit description of the bio-physical processes responsible. This permits direct comparison with observations and determination of key parameters in experiments. Crucially, the model resolves the two-way interaction between sediment biogeochemistry and ecology, allowing exploration of the benthic response to changing environmental conditions, the importance of infaunal functional traits in shaping benthic ecological structure and the feedback the resulting bio-physical processes exert on pore water nutrient profiles. The model is actively being used to understand shelf sea carbon cycling, the response of the benthos to climatic change, food provision and other societal benefits.

  4. Primordial membranes

    DEFF Research Database (Denmark)

    Hanczyc, Martin M; Monnard, Pierre-Alain

    2017-01-01

    Cellular membranes, which are self-assembled bilayer structures mainly composed of lipids, proteins and conjugated polysaccharides, are the defining feature of cell physiology. It is likely that the complexity of contemporary cells was preceded by simpler chemical systems or protocells during...... the various evolutionary stages that led from inanimate to living matter. It is also likely that primitive membranes played a similar role in protocell 'physiology'. The composition of such ancestral membranes has been proposed as mixtures of single hydrocarbon chain amphiphiles, which are simpler versions...

  5. Principles and biophysical applications of single particle super-localization and rotational tracking

    Energy Technology Data Exchange (ETDEWEB)

    Gu, Yan [Iowa State Univ., Ames, IA (United States)

    2013-01-01

    While conventional Single Particle Tracking (SPT) techniques acquire 2D or 3D trajectories of particle probes, we have developed Single Particle Orientation and Rotational Tracking (SPORT) techniques to extract orientation and rotational information. Combined with DIC microscopy, the SPORT technique has been applied in biophysical studies, including membrane diffusion and intracellular transport. The rotational dynamics of nanoparticle vectors on live cell membranes was recorded and its influence on the fate of these nanoparticle vectors was elucidated. The rotational motions of gold nanorods with various surface modifiers were tracked continuously at a temporal resolution of 5 ms under a DIC microscope. We found that the rotational behaviors of gold nanorod vectors are strongly related to their surface charge, specific surface functional groups, and the availability of receptors on cell membranes. The study of rotational Brownian motion of nanoparticles on cell membranes will lead to a better understanding of the mechanisms of drug delivery and provide guidance in designing surface modification strategies for drug delivery vectors under various circumstances. To characterize the rotation mode of surface functionalized gold nanorods on cell membranes, the SPORT technique is combined with the correlation analysis of the bright and dark DIC intensities. The unique capabilities of visualizing and understanding rotational motions of functionalized nanoparticles on live cell membranes allow us to correlate rotational and translational dynamics in unprecedented detail and provide new insights for complex membrane processes, including electrostatic interactions, ligand-receptor binding, and lateral (confined and hopping) diffusion of membrane receptors. Surface-functionalized nanoparticles interact with the membrane in fundamentally different ways and exhibit distinct rotational modes. The early events of particle-membrane approach and attachment are directly visualized

  6. The USA-National Phenology Network Biophysical Program

    Science.gov (United States)

    Losleben, M. V.; Crimmins, T. M.; Weltzin, J. F.

    2009-12-01

    On January 1, 2009, the USA National Phenology Network (USA-NPN, www.usanpn.org) launched the USA-NPN Biophysical Program. The overarching goal of the Biophysical Program (BP) is to link phenology, the study of recurring plant and animal life cycle stages, with climate through the integration of phenology observations, meteorological, and spectral remote sensing measurements at sites across a broad a spectrum of environments. Phenology is critical for understanding a changing world. Many of the recurring plant and animal life cycle stages such as leafing and flowering of plants, maturation of agricultural crops, emergence of insects, and migration of birds are sensitive to climatic variation and change, and are simple to observe and record. Such changes can effect, for example, timing mismatches between the emergence of food sources and the arrival of migrating populations, or create new disease and invasive species vectors via increasingly suitable growing seasons relative to the climatic life cycle requirements of hosts or the organisms themselves. New vectors or crashing populations can have major repercussions on entire ecosystems and regional economics. Thus, to track phenology and build a national database, the USA-NPN is providing standard phenology monitoring protocols. Further, the integration of weather stations with phenological data provides an opportunity to understand how a changing climate is altering phenology. Thus, the USA-NPN Biophysical Program is developing an integrative biology-climate site template for widespread dissemination, in collaboration with the Rocky Mountain Biological Laboratory (RMBL, http://rmbl.org/rockymountainbiolab/). This poster presents the USA-NPN Biophysical Program, and the results of the collaboration with RMBL during the summer of 2009, including the installation of an elevational network of climate stations. The National Science Foundation’s Major Research Instrumentation (NSF’s MRI) program provides funding

  7. DNA hybridization on membrane-modified carbon electrodes

    Czech Academy of Sciences Publication Activity Database

    Kouřilová, Alena; Babkina, S. S.; Cahová, Kateřina; Havran, Luděk; Jelen, František; Paleček, Emil; Fojta, Miroslav

    2005-01-01

    Roč. 38, - (2005), s. 2493-2507 ISSN 0003-2719 R&D Projects: GA MPO(CZ) 1H-PK/42; GA AV ČR(CZ) IAA4004402; GA AV ČR(CZ) IBS5004355 Institutional research plan: CEZ:AV0Z50040507 Keywords : DNA hybridization * electrochemical DNA sensor * nitrocellulose membrane Subject RIV: BO - Biophysics Impact factor: 1.036, year: 2005

  8. Membrane Surface Nanostructures and Adhesion Property of T Lymphocytes Exploited by AFM

    Directory of Open Access Journals (Sweden)

    Lu Hongsong

    2009-01-01

    Full Text Available Abstract The activation of T lymphocytes plays a very important role in T-cell-mediated immune response. Though there are many related literatures, the changes of membrane surface nanostructures and adhesion property of T lymphocytes at different activation stages have not been reported yet. However, these investigations will help us further understand the biophysical and immunologic function of T lymphocytes in the context of activation. In the present study, the membrane architectures of peripheral blood T lymphocytes were obtained by AFM, and adhesion force of the cell membrane were measured by acquiring force–distance curves. The results indicated that the cell volume increased with the increases of activation time, whereas membrane surface adhesion force decreased, even though the local stiffness for resting and activated cells is similar. The results provided complementary and important data to further understand the variation of biophysical properties of T lymphocytes in the context of in vitro activation.

  9. G protein-membrane interactions II: Effect of G protein-linked lipids on membrane structure and G protein-membrane interactions.

    Science.gov (United States)

    Casas, Jesús; Ibarguren, Maitane; Álvarez, Rafael; Terés, Silvia; Lladó, Victoria; Piotto, Stefano P; Concilio, Simona; Busquets, Xavier; López, David J; Escribá, Pablo V

    2017-09-01

    G proteins often bear myristoyl, palmitoyl and isoprenyl moieties, which favor their association with the membrane and their accumulation in G Protein Coupled Receptor-rich microdomains. These lipids influence the biophysical properties of membranes and thereby modulate G protein binding to bilayers. In this context, we showed here that geranylgeraniol, but neither myristate nor palmitate, increased the inverted hexagonal (H II ) phase propensity of phosphatidylethanolamine-containing membranes. While myristate and palmitate preferentially associated with phosphatidylcholine membranes, geranylgeraniol favored nonlamellar-prone membranes. In addition, Gαi 1 monomers had a higher affinity for lamellar phases, while Gβγ and Gαβγ showed a marked preference for nonlamellar prone membranes. Moreover, geranylgeraniol enhanced the binding of G protein dimers and trimers to phosphatidylethanolamine-containing membranes, yet it decreased that of monomers. By contrast, both myristate and palmitate increased the Gαi 1 preference for lamellar membranes. Palmitoylation reinforced the binding of the monomer to PC membranes and myristoylation decreased its binding to PE-enriched bilayer. Finally, binding of dimers and trimers to lamellar-prone membranes was decreased by palmitate and myristate, but it was increased in nonlamellar-prone bilayers. These results demonstrate that co/post-translational G protein lipid modifications regulate the membrane lipid structure and that they influence the physico-chemical properties of membranes, which in part explains why G protein subunits sort to different plasma membrane domains. This article is part of a Special Issue entitled: Membrane Lipid Therapy: Drugs Targeting Biomembranes edited by Pablo V. Escribá. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Talk to the Hand: U.S. Army Biophysical Testing.

    Science.gov (United States)

    Santee, William R; Potter, Adam W; Friedl, Karl E

    2017-07-01

    Many people are unaware of the science underlying the biophysical properties of Soldier clothing and personal protective equipment, yet there is a well-refined biomedical methodology initiated by Army physiologists in World War II. This involves a methodical progression of systematic material testing technologies, computer modeling, and human testing that enables more efficient development and rapid evaluation of new concepts for Soldier health and performance. Sophisticated manikins that sweat and move are a central part of this testing continuum. This report briefly summarizes the evolution and use of one specialized form of the manikin technologies, the thermal hand model, and its use in research on Soldier hand-wear items that sustain dexterity and protect the hand in extreme environments. Thermal manikin testing methodologies were developed to provide an efficient and consistent analytical tool for the rapid evaluation of new clothing concepts. These methods have been upgraded since the original World War II and Korean War eras to include articulation and sweating capabilities, as characterized and illustrated in this article. The earlier "retired" versions of thermal hand models have now been transferred to the National Museum of Health and Science. The biophysical values from manikin testing are critical inputs to the U.S. Army Research Institute of Environmental Medicine mathematical models that provide predictions of soldier comfort, duration of exposure before loss of manual dexterity, and time to significant risk of freezing (skin temperature Army has been on the forefront of the biophysical analysis of clothing including gloves since environmental research was established at the Armored Medical Research Laboratory and Climatic Research Laboratory during World War II. U.S. Army Research Institute of Environmental Medicine does not make the equipment but works with their Natick Soldier Research, Development, and Engineering Center partners to make the

  11. Biophysical approach to chronic kidney disease management in older patients

    Directory of Open Access Journals (Sweden)

    Alberto Foletti

    2016-06-01

    Full Text Available Chronic kidney disease (CKD and its clinical progression are a critical issue in an aging population. Therefore, strategies aimed at preventing and managing the decline of renal function are warranted. Recent evidence has provided encouraging results for the improvement of renal function achieved through an integrated biophysical approach, but prospective studies on the clinical efficacy of this strategy are still lacking. This was an open-label prospective pilot study to investigate the effect of electromagnetic information transfer through the aqueous system on kidney function of older patients affected by stage 1 or 2 CKD. Patients received biophysical therapy every 3 months over a 1-year period. Estimated glomerular filtration rate (eGFR values were calculated using the CKD–Epidemiology Collaboration formula, and were recorded at baseline and at the end of treatment. Overall, 58 patients (mean age 74.8 ± 3.7 years were included in the study. At baseline, mean eGFR was 64.6 ± 15.5 mL/min, and it significantly increased to 69.9 ± 15.8 mL/min after 1 year (+5.2 ± 10 mL/min, p<0.0002. The same trend was observed among men (+5.7 ± 10.2 mL/min, p<0.0064 and women (+4.7 ± 9.9 mL/min, p<0.014. When results were analyzed by sex, no difference was found between the 2 groups. Although further and larger prospective studies are needed, our findings suggest that an integrated biophysical approach may be feasible in the management of older patients with early-stage CKD, to reduce and prevent the decline of renal function due to aging or comorbidities.

  12. Sphingolipid levels crucially modulate lateral microdomain organization of plasma membrane in living yeast

    Czech Academy of Sciences Publication Activity Database

    Večeř, J.; Veselá, Petra; Malínský, Jan; Herman, P.

    2014-01-01

    Roč. 588, č. 3 (2014), s. 443-449 ISSN 0014-5793 R&D Projects: GA ČR GAP205/12/0720 Institutional support: RVO:68378041 Keywords : membrane microdomain * lipid order * fluidity Subject RIV: BO - Biophysics Impact factor: 3.169, year: 2014

  13. Effect of heavy water on phospholipid membranes: experimental confirmation of molecular dynamics simulations

    Czech Academy of Sciences Publication Activity Database

    Beranová, Lenka; Humpolíčková, Jana; Sýkora, Jan; Benda, Aleš; Cwiklik, Lukasz; Jurkiewicz, Piotr; Gröbner, G.; Hof, Martin

    Roč. 14, č. 42 ( 2012 ), s. 14516-14522 ISSN 1463-9076 R&D Projects: GA AV ČR GEMEM/09/E006; GA ČR GBP208/12/G016 Institutional support: RVO:61388955 Keywords : phospholipid membranes * biophysics * physical chemistry Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.829, year: 2012

  14. Effect of storage duration on the rheological properties of goose liquid egg products and eggshell membranes

    Czech Academy of Sciences Publication Activity Database

    Kumbár, V.; Nedomová, Š.; Trnka, Jan; Buchar, J.; Pytel, R.

    2016-01-01

    Roč. 95, č. 7 (2016), s. 1693-1701 ISSN 0032-5791 Institutional support: RVO:61388998 Keywords : egg yolk * albumen * liquid whole egg * rheology * eggshell membrane Subject RIV: BO - Biophysics Impact factor: 1.908, year: 2016 http://ps.oxfordjournals.org/

  15. Improvement of the accuracy by the measurement of the electrical cell membrane parameters

    Czech Academy of Sciences Publication Activity Database

    Rohlíček, Vojtěch; Rech, František

    2002-01-01

    Roč. 51, č. 2 (2002), s. 169-177 ISSN 0862-8408 Institutional research plan: CEZ:AV0Z5011922 Keywords : patch clamp technique * electrical parameters of the cell membrane * memebrane capacity Subject RIV: BO - Biophysics Impact factor: 0.984, year: 2002

  16. Short-Term Memory and Its Biophysical Model

    Science.gov (United States)

    Wang, Wei; Zhang, Kai; Tang, Xiao-wei

    1996-12-01

    The capacity of short-term memory has been studied using an integrate-and-fire neuronal network model. It is found that the storage of events depend on the manner of the correlation between the events, and the capacity is dominated by the value of after-depolarization potential. There is a monotonic increasing relationship between the value of after-depolarization potential and the memory numbers. The biophysics relevance of the network model is discussed and different kinds of the information processes are studied too.

  17. Large-scale biophysical evaluation of protein PEGylation effects

    DEFF Research Database (Denmark)

    Vernet, Erik; Popa, Gina; Pozdnyakova, Irina

    2016-01-01

    PEGylation is the most widely used method to chemically modify protein biopharmaceuticals, but surprisingly limited public data is available on the biophysical effects of protein PEGylation. Here we report the first large-scale study, with site-specific mono-PEGylation of 15 different proteins...... and characterization of 61 entities in total using a common set of analytical methods. Predictions of molecular size were typically accurate in comparison with actual size determined by size-exclusion chromatography (SEC) or dynamic light scattering (DLS). In contrast, there was no universal trend regarding the effect...

  18. Synthesis and Biophysical Characterization of Chlorambucil Anticancer Ether Lipid Prodrugs

    DEFF Research Database (Denmark)

    Pedersen, Palle Jacob; Christensen, Mikkel Stochkendahl; Ruysschaert, Tristan

    2009-01-01

    The synthesis and biophysical characterization of four prodrug ether phospholipid conjugates are described. The lipids are prepared from the anticancer drug chlorambucil and have C16 and C18 ether chains with phosphatidylcholine or phosphatidylglycerol headgroups. All four prodrugs have the ability...... to form unilamellar liposomes (86-125 nm) and are hydrolyzed by phospholipase A2, resulting in chlorambucil release. Liposomal formulations of prodrug lipids displayed cytotoxicity toward HT-29, MT-3, and ES-2 cancer cell lines in the presence of phospholipase A2, with IC50 values in the 8-36 μM range....

  19. Hydrophobic ampersand hydrophilic: Theoretical models of solvation for molecular biophysics

    International Nuclear Information System (INIS)

    Pratt, L.R.; Tawa, G.J.; Hummer, G.; Garcia, A.E.; Corcelli, S.A.

    1996-01-01

    Molecular statistical thermodynamic models of hydration for chemistry and biophysics have advanced abruptly in recent years. With liquid water as solvent, salvation phenomena are classified as either hydrophobic or hydrophilic effects. Recent progress in treatment of hydrophilic effects have been motivated by continuum dielectric models interpreted as a modelistic implementation of second order perturbation theory. New results testing that perturbation theory of hydrophilic effects are presented and discussed. Recent progress in treatment of hydrophobic effects has been achieved by applying information theory to discover models of packing effects in dense liquids. The simplest models to which those ideas lead are presented and discussed

  20. Surface enhanced raman spectroscopy analytical, biophysical and life science applications

    CERN Document Server

    Schlücker, Sebastian

    2013-01-01

    Covering everything from the basic theoretical and practical knowledge to new exciting developments in the field with a focus on analytical and life science applications, this monograph shows how to apply surface-enhanced Raman scattering (SERS) for solving real world problems. From the contents: * Theory and practice of SERS * Analytical applications * SERS combined with other analytical techniques * Biophysical applications * Life science applications including various microscopies Aimed at analytical, surface and medicinal chemists, spectroscopists, biophysicists and materials scientists. Includes a Foreword by the renowned Raman spectroscopist Professor Wolfgang Kiefer, the former Editor-in-Chief of the Journal of Raman Spectroscopy.

  1. Mathematical and computational modelling of skin biophysics: a review.

    Science.gov (United States)

    Limbert, Georges

    2017-07-01

    The objective of this paper is to provide a review on some aspects of the mathematical and computational modelling of skin biophysics, with special focus on constitutive theories based on nonlinear continuum mechanics from elasticity, through anelasticity, including growth, to thermoelasticity. Microstructural and phenomenological approaches combining imaging techniques are also discussed. Finally, recent research applications on skin wrinkles will be presented to highlight the potential of physics-based modelling of skin in tackling global challenges such as ageing of the population and the associated skin degradation, diseases and traumas.

  2. Use of an integrated biophysical process for the treatment of halo- and nitro- organic wastes

    Directory of Open Access Journals (Sweden)

    Liron Shoshani

    2017-07-01

    Full Text Available This study assessed the use of an integrated biophysical process incorporating the addition of powdered activated carbon (PAC to a dual-sludge biological process, in order to improve the removal of problematic contaminants from complex herbicides production wastewater. The main focus was on the removal of nitrogen compounds, total organic carbon (TOC, and halogenated organics (AOX. The dual-sludge pilot setup comprised a conventional activated sludge (CAS system followed by a membrane bioreactor (MBR system. The dilution ratio of raw wastewater was gradually decreased (with groundwater from 0.8 to 0 (no dilution, and PAC was added in the last phase of the study to maintain an equilibrium concentration of 2000 mg/L. PAC addition stimulated a high and steady removal (98% of the ammoniacal nitrogen, conforming to the sea discharge limit of 5 mg/L. However, the effluent concentrations of total nitrogen, TOC, and AOX were still above the stringent discharge limits of 20, 100 and 0.5 mg/L respectively. Furthermore, it was shown that synergistic effect of various toxic organic compounds, rather than mineral salinity, was the major cause for the acute inhibitions of nitrification and AOX removal. The study showed that the proposed process can function as an efficient treatment system for the complex wastewater typically produced in the herbicide industry, however, it is recommended that complementary physico-chemical treatment steps be added to the treatment process.

  3. Biophysical Analysis of Lipopolysaccharide Formulations for an Understanding of the Low Endotoxin Recovery (LER Phenomenon

    Directory of Open Access Journals (Sweden)

    Wilmar Correa

    2017-12-01

    Full Text Available Lipopolysaccharides (LPS, endotoxin are complex and indispensable components of the outer membrane of most Gram-negative bacteria. They represent stimuli for many biological effects with pathophysiological character. Recombinant therapeutic proteins that are manufactured using biotechnological processes are prone to LPS contaminations due to their ubiquitous occurrence. The maximum endotoxin load of recombinant therapeutic proteins must be below the pyrogenic threshold. Certain matrices that are commonly used for recombinant therapeutic proteins show a phenomenon called “Low Endotoxin Recovery (LER”. LER is defined as the loss of detectable endotoxin activity over time using compendial Limulus amebocyte lysate (LAL assays when undiluted products are spiked with known amount of endotoxin standards. Because LER poses potential risks that endotoxin contaminations in products may be underestimated or undetected by the LAL assay, the United States (U.S. Food and Drug Administration’s (FDA’s Center for Drug Evaluation and Research (CDER has recently started requesting that companies conduct endotoxin spike/hold recovery studies to determine whether a given biological product causes LER. Here, we have performed an analysis of different LPS preparations with relevant detergents studying their acyl chain phase transition, their aggregate structures, their size distributions, and binding affinity with a particular anti-endotoxin peptide, and correlating it with the respective data in the macrophage activation test. In this way, we have worked out biophysical parameters that are important for an understanding of LER.

  4. Comparison of Biophysical and Biologic Properties of α-Helical Enantiomeric Antimicrobial Peptides

    Science.gov (United States)

    Chen, Yuxin; Vasil, Adriana I.; Rehaume, Linda; Mant, Colin T.; Burns, Jane L.; Vasil, Michael L.; Hancock, Robert E. W.; Hodges, Robert S.

    2011-01-01

    In our previous study (Chen et al. J Biol Chem 2005, 280:12316–12329), we utilized an α-helical antimicrobial peptide V681 as the framework to study the effects of peptide hydrophobicity, amphipathicity, and helicity on biologic activities where we obtained several V681 analogs with dramatic improvement in peptide therapeutic indices against gram-negative and gram-positive bacteria. In the present study, the d-enantiomers of three peptides – V681, V13AD and V13KL were synthesized to compare biophysical and biologic properties with their enantiomeric isomers. Each d-enantiomer was shown by circular dichroism spectroscopy to be a mirror image of the corresponding l-isomer in benign conditions and in the presence of 50% trifluoroethanol. l- and d-enantiomers exhibited equivalent antimicrobial activities against a diverse group of Pseudomonas aeruginosa clinical isolates, various gram-negative and gram-positive bacteria and a fungus. In addition, l- and d-enantiomeric peptides were equally active in their ability to lyse human red blood cells. The similar activity of l- and d-enantiomeric peptides on prokaryotic or eukaryotic cell membranes suggests that there are no chiral receptors and the cell membrane is the sole target for these peptides. Peptide d-V13KD showed significant improvements in the therapeutic indices compared with the parent peptide V681 by 53-fold against P. aeruginosa strains, 80-fold against gram-negative bacteria, 69-fold against gram-positive bacteria, and 33-fold against Candida albicans. The excellent stability of d-enantiomers to trypsin digestion (no proteolysis by trypsin) compared with the rapid breakdown of the l-enantiomers highlights the advantage of the d-enantiomers and their potential as clinical therapeutics. PMID:16492164

  5. MODIS-derived Biophysical Parameters for 5-km Land Cover, North America, 2000-2012

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set provides MODIS-derived surface biophysical climatologies of bidirectional distribution function (BRDF), BDRF/albedo, land surface temperature (LST),...

  6. MODIS-derived Biophysical Parameters for 5-km Land Cover, North America, 2000-2012

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: This data set provides MODIS-derived surface biophysical climatologies of bidirectional distribution function (BRDF), BDRF/albedo, land surface temperature...

  7. NACP New England and Sierra National Forests Biophysical Measurements: 2008-2010

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: This data set includes biophysical measurements collected in 2009 from five New England experimental forest stations: Bartlett Experimental Forest, Harvard...

  8. NACP New England and Sierra National Forests Biophysical Measurements: 2008-2010

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set includes biophysical measurements collected in 2009 from five New England experimental forest stations: Bartlett Experimental Forest, Harvard Forest,...

  9. 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

  10. Biophysical regulation of epigenetic state and cell reprogramming

    Science.gov (United States)

    Downing, Timothy L.; Soto, Jennifer; Morez, Constant; Houssin, Timothee; Fritz, Ashley; Yuan, Falei; Chu, Julia; Patel, Shyam; Schaffer, David V.; Li, Song

    2013-12-01

    Biochemical factors can help reprogram somatic cells into pluripotent stem cells, yet the role of biophysical factors during reprogramming is unknown. Here, we show that biophysical cues, in the form of parallel microgrooves on the surface of cell-adhesive substrates, can replace the effects of small-molecule epigenetic modifiers and significantly improve reprogramming efficiency. The mechanism relies on the mechanomodulation of the cells’ epigenetic state. Specifically, decreased histone deacetylase activity and upregulation of the expression of WD repeat domain 5 (WDR5)—a subunit of H3 methyltranferase—by microgrooved surfaces lead to increased histone H3 acetylation and methylation. We also show that microtopography promotes a mesenchymal-to-epithelial transition in adult fibroblasts. Nanofibrous scaffolds with aligned fibre orientation produce effects similar to those produced by microgrooves, suggesting that changes in cell morphology may be responsible for modulation of the epigenetic state. These findings have important implications in cell biology and in the optimization of biomaterials for cell-engineering applications.

  11. Measuring (bio)physical tree properties using accelerometers

    Science.gov (United States)

    van Emmerik, Tim; Steele-Dunne, Susan; Hut, Rolf; Gentine, Pierre; Selker, John; van de Giesen, Nick

    2017-04-01

    Trees play a crucial role in the water, carbon and nitrogen cycle on local, regional and global scales. Understanding the exchange of heat, water, and CO2 between trees and the atmosphere is important to assess the impact of drought, deforestation and climate change. Unfortunately, ground measurements of tree dynamics are often expensive, or difficult due to challenging environments. We demonstrate the potential of measuring (bio)physical properties of trees using robust and affordable acceleration sensors. Tree sway is dependent on e.g. mass and wind energy absorption of the tree. By measuring tree acceleration we can relate the tree motion to external loads (e.g. precipitation), and tree (bio)physical properties (e.g. mass). Using five months of acceleration data of 19 trees in the Brazilian Amazon, we show that the frequency spectrum of tree sway is related to mass, precipitation, and canopy drag. This presentation aims to show the concept of using accelerometers to measure tree dynamics, and we acknowledge that the presented example applications is not an exhaustive list. Further analyses are the scope of current research, and we hope to inspire others to explore additional applications.

  12. Climate Change Effects on Agriculture: Economic Responses to Biophysical Shocks

    Science.gov (United States)

    Nelson, Gerald C.; Valin, Hugo; Sands, Ronald D.; Havlik, Petr; Ahammad, Helal; Deryng, Delphine; Elliott, Joshua; Fujimori, Shinichiro; Hasegawa, Tomoko; Heyhoe, Edwina

    2014-01-01

    Agricultural production is sensitive to weather and thus directly affected by climate change. Plausible estimates of these climate change impacts require combined use of climate, crop, and economic models. Results from previous studies vary substantially due to differences in models, scenarios, and data. This paper is part of a collective effort to systematically integrate these three types of models. We focus on the economic component of the assessment, investigating how nine global economic models of agriculture represent endogenous responses to seven standardized climate change scenarios produced by two climate and five crop models. These responses include adjustments in yields, area, consumption, and international trade. We apply biophysical shocks derived from the Intergovernmental Panel on Climate Change's representative concentration pathway with end-of-century radiative forcing of 8.5 W/m(sup 2). The mean biophysical yield effect with no incremental CO2 fertilization is a 17% reduction globally by 2050 relative to a scenario with unchanging climate. Endogenous economic responses reduce yield loss to 11%, increase area of major crops by 11%, and reduce consumption by 3%. Agricultural production, cropland area, trade, and prices show the greatest degree of variability in response to climate change, and consumption the lowest. The sources of these differences include model structure and specification; in particular, model assumptions about ease of land use conversion, intensification, and trade. This study identifies where models disagree on the relative responses to climate shocks and highlights research activities needed to improve the representation of agricultural adaptation responses to climate change.

  13. Climate change effects on agriculture: economic responses to biophysical shocks.

    Science.gov (United States)

    Nelson, Gerald C; Valin, Hugo; Sands, Ronald D; Havlík, Petr; Ahammad, Helal; Deryng, Delphine; Elliott, Joshua; Fujimori, Shinichiro; Hasegawa, Tomoko; Heyhoe, Edwina; Kyle, Page; Von Lampe, Martin; Lotze-Campen, Hermann; Mason d'Croz, Daniel; van Meijl, Hans; van der Mensbrugghe, Dominique; Müller, Christoph; Popp, Alexander; Robertson, Richard; Robinson, Sherman; Schmid, Erwin; Schmitz, Christoph; Tabeau, Andrzej; Willenbockel, Dirk

    2014-03-04

    Agricultural production is sensitive to weather and thus directly affected by climate change. Plausible estimates of these climate change impacts require combined use of climate, crop, and economic models. Results from previous studies vary substantially due to differences in models, scenarios, and data. This paper is part of a collective effort to systematically integrate these three types of models. We focus on the economic component of the assessment, investigating how nine global economic models of agriculture represent endogenous responses to seven standardized climate change scenarios produced by two climate and five crop models. These responses include adjustments in yields, area, consumption, and international trade. We apply biophysical shocks derived from the Intergovernmental Panel on Climate Change's representative concentration pathway with end-of-century radiative forcing of 8.5 W/m(2). The mean biophysical yield effect with no incremental CO2 fertilization is a 17% reduction globally by 2050 relative to a scenario with unchanging climate. Endogenous economic responses reduce yield loss to 11%, increase area of major crops by 11%, and reduce consumption by 3%. Agricultural production, cropland area, trade, and prices show the greatest degree of variability in response to climate change, and consumption the lowest. The sources of these differences include model structure and specification; in particular, model assumptions about ease of land use conversion, intensification, and trade. This study identifies where models disagree on the relative responses to climate shocks and highlights research activities needed to improve the representation of agricultural adaptation responses to climate change.

  14. Protein Biophysics Explains Why Highly Abundant Proteins Evolve Slowly

    Directory of Open Access Journals (Sweden)

    Adrian W.R. Serohijos

    2012-08-01

    Full Text Available The consistent observation across all kingdoms of life that highly abundant proteins evolve slowly demonstrates that cellular abundance is a key determinant of protein evolutionary rate. However, other empirical findings, such as the broad distribution of evolutionary rates, suggest that additional variables determine the rate of protein evolution. Here, we report that under the global selection against the cytotoxic effects of misfolded proteins, folding stability (ΔG, simultaneous with abundance, is a causal variable of evolutionary rate. Using both theoretical analysis and multiscale simulations, we demonstrate that the anticorrelation between the premutation ΔG and the arising mutational effect (ΔΔG, purely biophysical in origin, is a necessary requirement for abundance–evolutionary rate covariation. Additionally, we predict and demonstrate in bacteria that the strength of abundance–evolutionary rate correlation depends on the divergence time separating reference genomes. Altogether, these results highlight the intrinsic role of protein biophysics in the emerging universal patterns of molecular evolution.

  15. Mechanoresponsive stem cells to target cancer metastases through biophysical cues.

    Science.gov (United States)

    Liu, Linan; Zhang, Shirley X; Liao, Wenbin; Farhoodi, Henry P; Wong, Chi W; Chen, Claire C; Ségaliny, Aude I; Chacko, Jenu V; Nguyen, Lily P; Lu, Mengrou; Polovin, George; Pone, Egest J; Downing, Timothy L; Lawson, Devon A; Digman, Michelle A; Zhao, Weian

    2017-07-26

    Despite decades of effort, little progress has been made to improve the treatment of cancer metastases. To leverage the central role of the mechanoenvironment in cancer metastasis, we present a mechanoresponsive cell system (MRCS) to selectively identify and treat cancer metastases by targeting the specific biophysical cues in the tumor niche in vivo. Our MRCS uses mechanosensitive promoter-driven mesenchymal stem cell (MSC)-based vectors, which selectively home to and target cancer metastases in response to specific mechanical cues to deliver therapeutics to effectively kill cancer cells, as demonstrated in a metastatic breast cancer mouse model. Our data suggest a strong correlation between collagen cross-linking and increased tissue stiffness at the metastatic sites, where our MRCS is specifically activated by the specific cancer-associated mechano-cues. MRCS has markedly reduced deleterious effects compared to MSCs constitutively expressing therapeutics. MRCS indicates that biophysical cues, specifically matrix stiffness, are appealing targets for cancer treatment due to their long persistence in the body (measured in years), making them refractory to the development of resistance to treatment. Our MRCS can serve as a platform for future diagnostics and therapies targeting aberrant tissue stiffness in conditions such as cancer and fibrotic diseases, and it should help to elucidate mechanobiology and reveal what cells "feel" in the microenvironment in vivo. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  16. Biophysical behaviour of the infant Meibomian lipid layer.

    Science.gov (United States)

    Kaercher, T; Möbius, D; Welt, R

    1994-01-01

    Infants have been known occasionally to stare without blinking for almost a minute. This puts great demands on the stability of their tear-film. To verify the stability of infant tears, we performed biophysical experiments on Meibomian gland secretion, which forms the outermost layer of the tear-film. The secretion was taken from infants belonging to one of three age-groups (1.5 years, 4-5 years, 7-10 years). Under in vitro conditions we determined the surface pressure and the surface potential of the film by spreading the secretion over a water surface and subsequently compressing and decompressing it. Sufficient amounts of Meibomian gland secretion were expressed in all age-groups. The surface pressure and the surface potential of the tears in infants corresponded to those in healthy adults. It was also found that the younger the patient was, the better was the consistency of the surface potential under repeated periods of compression and expansion. In comparison with the secretion of healthy adults, the infant Meibomian gland secretion showed better biophysical characteristics and a correspondingly higher stability in the tear-film.

  17. Quantum-Sequencing: Biophysics of quantum tunneling through nucleic acids

    Science.gov (United States)

    Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

    2014-03-01

    Tunneling microscopy and spectroscopy has extensively been used in physical surface sciences to study quantum tunneling to measure electronic local density of states of nanomaterials and to characterize adsorbed species. Quantum-Sequencing (Q-Seq) is a new method based on tunneling microscopy for electronic sequencing of single molecule of nucleic acids. A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free single-molecule sequencing method. Here, we present the unique ``electronic fingerprints'' for all nucleotides on DNA and RNA using Q-Seq along their intrinsic biophysical parameters. We have analyzed tunneling spectra for the nucleotides at different pH conditions and analyzed the HOMO, LUMO and energy gap for all of them. In addition we show a number of biophysical parameters to further characterize all nucleobases (electron and hole transition voltage and energy barriers). These results highlight the robustness of Q-Seq as a technique for next-generation sequencing.

  18. Biophysical aspects of human thermoregulation during heat stress.

    Science.gov (United States)

    Cramer, Matthew N; Jay, Ollie

    2016-04-01

    Humans maintain a relatively constant core temperature through the dynamic balance between endogenous heat production and heat dissipation to the surrounding environment. In response to metabolic or environmental disturbances to heat balance, the autonomic nervous system initiates cutaneous vasodilation and eccrine sweating to facilitate higher rates of dry (primarily convection and radiation) and evaporative transfer from the body surface; however, absolute heat losses are ultimately governed by the properties of the skin and the environment. Over the duration of a heat exposure, the cumulative imbalance between heat production and heat dissipation leads to body heat storage, but the consequent change in core temperature, which has implications for health and safety in occupational and athletic settings particularly among certain clinical populations, involves a complex interaction between changes in body heat content and the body's morphological characteristics (mass, surface area, and tissue composition) that collectively determine the body's thermal inertia. The aim of this review is to highlight the biophysical aspects of human core temperature regulation by outlining the principles of human energy exchange and examining the influence of body morphology during exercise and environmental heat stress. An understanding of the biophysical factors influencing core temperature will enable researchers and practitioners to better identify and treat individuals/populations most vulnerable to heat illness and injury during exercise and extreme heat events. Further, appropriate guidelines may be developed to optimize health, safety, and work performance during heat stress. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Developing a physics expert identity in a biophysics research group

    Science.gov (United States)

    Rodriguez, Idaykis; Goertzen, Renee Michelle; Brewe, Eric; Kramer, Laird H.

    2015-06-01

    We investigate the development of expert identities through the use of the sociocultural perspective of learning as participating in a community of practice. An ethnographic case study of biophysics graduate students focuses on the experiences the students have in their research group meetings. The analysis illustrates how the communities of practice-based identity constructs of competencies characterize student expert membership. A microanalysis of speech, sound, tones, and gestures in video data characterize students' social competencies in the physics community of practice. Results provide evidence that students at different stages of their individual projects have opportunities to develop social competencies such as mutual engagement, negotiability of the repertoire, and accountability to the enterprises as they interact with group members. The biophysics research group purposefully designed a learning trajectory including conducting research and writing it for publication in the larger community of practice as a pathway to expertise. The students of the research group learn to become socially competent as specific experts of their project topic and methodology, ensuring acceptance, agency, and membership in their community of practice. This work expands research on physics expertise beyond the cognitive realm and has implications for how to design graduate learning experiences to promote expert identity development.

  20. Robotic membranes

    DEFF Research Database (Denmark)

    Ramsgaard Thomsen, Mette

    2008-01-01

    , Vivisection and Strange Metabolisms, were developed at the Centre for Information Technology and Architecture (CITA) at the Royal Danish Academy of Fine Arts in Copenhagen as a means of engaging intangible digital data with tactile physical material. As robotic membranes, they are a dual examination...

  1. Social and Biophysical Predictors of Public Perceptions of Extreme Fires

    Science.gov (United States)

    Hall, T. E.; Kooistra, C. M.; Paveglio, T.; Gress, S.; Smith, A. M.

    2013-12-01

    To date, what constitutes an 'extreme' fire has been approached separately by biophysical and social scientists. Research on the biophysical characteristics of fires has identified potential dimensions of extremity, including fire size and vegetation mortality. On the social side, factors such as the degree of immediate impact to one's life and property or the extent of social disruption in the community contribute to a perception of extremity. However, some biophysical characteristics may also contribute to perceptions of extremity, including number of simultaneous ignitions, rapidity of fire spread, atypical fire behavior, and intensity of smoke. Perceptions of these impacts can vary within and across communities, but no studies to date have investigated such perceptions in a comprehensive way. In this study, we address the question, to what extent is the magnitude of impact of fires on WUI residents' well-being explained by measurable biophysical characteristics of the fire and subjective evaluations of the personal and community-level impacts of the fire? We bring together diverse strands of psychological theory, including landscape perception, mental models, risk perception, and community studies. The majority of social science research on fires has been in the form of qualitative case studies, and our study is methodologically unique by using a nested design (hierarchical modeling) to enable generalizable conclusions across a wide range of fires and human communities. We identified fires that burned in 2011 or 2012 in the northern Rocky Mountain region that were at least 1,000 acres and that intersected (within 15 km) urban clusters or identified Census places. For fires where an adequately large number of households was located in proximity to the fire, we drew random samples of approximately 150 individuals for each fire. We used a hybrid internet (Qualtrics) and mail survey, following the Dillman method, to measure individual perceptions. We developed two

  2. RESEARCH ON REDUCING PREMATURITY RUPTURE OF MEMBRANE

    Directory of Open Access Journals (Sweden)

    Maria URSACHI (BOLOTA

    2016-12-01

    -term (3 days and distance (2 years interventional methods applied; clinical investigation of complications arising post intervention; studying behavior synthetic amnion. Conclusions: The cause of PRAS is multifactorial. Traditionally, fetal membrane rupture has been attributed to increased physical stress, which weakens the membranes. At the molecular level PRAS is the result of reducing collagen synthesis, alteration of the structure of collagen to accelerate degradation. In addition, these biochemical changes can be amplified and biophysical stress today. The priorities of this research include elucidation of the normal biological process of fetal membranes, including extracellular matrix remodeling, apoptosis.

  3. Membrane transport mechanism 3D structure and beyond

    CERN Document Server

    Ziegler, Christine

    2014-01-01

    This book provides a molecular view of membrane transport by means of numerous biochemical and biophysical techniques. The rapidly growing number of atomic structures of transporters in different conformations and the constant progress in bioinformatics have recently added deeper insights.   The unifying mechanism of energized solute transport across membranes is assumed to consist of the conformational cycling of a carrier protein to provide access to substrate binding sites from either side of a cellular membrane. Due to the central role of active membrane transport there is considerable interest in deciphering the principles of one of the most fundamental processes in nature: the alternating access mechanism.   This book brings together particularly significant structure-function studies on a variety of carrier systems from different transporter families: Glutamate symporters, LeuT-like fold transporters, MFS transporters and SMR (RND) exporters, as well as ABC-type importers.   The selected examples im...

  4. Defining thermostability of membrane proteins by western blotting.

    Science.gov (United States)

    Ashok, Y; Nanekar, R; Jaakola, V-P

    2015-12-01

    Membrane proteins are relatively challenging targets for structural and other biophysical studies. Insufficient expression in various expression systems, inherent flexibility, and instability in the detergents that are required for membrane extraction are the main reasons for this limited success. Therefore, identification of suitable conditions and membrane protein variants that can help stabilize functional protein for extended periods of time is critical for structural studies. Here, we describe a western blot-based assay that simplifies identification of thermostabilizing conditions for membrane proteins. We show successful testing of a variety of parameters such as additive lipids, ligands and detergents. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  5. A synthesized biophysical and social vulnerability assessment for Taiwan

    Science.gov (United States)

    Lee, Yung-Jaan

    2017-11-01

    Taiwan, located in the Western Pacific, is a country that is one of the most vulnerable to disasters that are associated with the changing climate; it is located within the Ring of Fire, which is the most geologically active region in the world. The environmental and geological conditions in Taiwan are sensitive and vulnerable to such disasters. Owing to increasing urbanization in Taiwan, floods and climate-related disasters have taken an increasing toll on human lives. As global warming accelerates the rising of sea levels and increasing of the frequency of extreme weather events, disasters will continue to affect socioeconomic development and human conditions. Under such circumstances, researchers and policymakers alike must recognize the importance of providing useful knowledge concerning vulnerability, disaster recovery and resilience. Strategies for reducing vulnerability and climate-related disaster risks and for increasing resilience involve preparedness, mitigation and adaptation. In the last two decades, extreme climate events have caused severe flash floods, debris flows, landslides, and other disasters and have had negative effects of many sectors, including agriculture, infrastructure and health. Since climate change is expected to have a continued impact on socio-economic development, this work develops a vulnerability assessment framework that integrates both biophysical and social vulnerability and supports synthesized vulnerability analyses to identify vulnerable areas in Taiwan. Owing to its geographical, geological and climatic features, Taiwan is susceptible to earthquakes, typhoons, droughts and various induced disasters. Therefore, Taiwan has the urgent task of establishing a framework for assessing vulnerability as a planning and policy tool that can be used to identify not only the regions that require special attention but also hotspots in which efforts should be made to reduce vulnerability and the risk of climate-related disaster. To

  6. High-yield membrane protein expression from E. coli using an engineered outer membrane protein F fusion.

    Science.gov (United States)

    Su, Pin-Chuan; Si, William; Baker, Deidre L; Berger, Bryan W

    2013-04-01

    Obtaining high yields of membrane proteins necessary to perform detailed structural study is difficult due to poor solubility and variability in yields from heterologous expression systems. To address this issue, an Escherichia coli-based membrane protein overexpression system utilizing an engineered bacterial outer membrane protein F (pOmpF) fusion has been developed. Full-length human receptor activity-modifying protein 1 (RAMP1) was expressed using pOmpF, solubilized in FC15 and purified to homogeneity. Using circular dichroism and fluorescence spectroscopy, purified full-length RAMP1 is composed of approximately 90% α-helix, and retains its solubility and structure in FC15 over a wide range of temperatures (20-60°C). Thus, our approach provides a useful, complementary approach to achieve high-yield, full-length membrane protein overexpression for biophysical studies. Copyright © 2013 The Protein Society.

  7. Biophysical characterization of antibodies with isothermal titration calorimetry

    Directory of Open Access Journals (Sweden)

    Verna Frasca

    2016-07-01

    Full Text Available Antibodies play a key role in the immune response. Since antibodies bind antigens with high specificity and tight affinity, antibodies are an important reagent in experimental biology, assay development, biomedical research and diagnostics. Monoclonal antibodies are therapeutic drugs and used for vaccine development. Antibody engineering, biophysical characterization, and structural data have provided a deeper understanding of how antibodies function, and how to make better drugs. Isothermal titration calorimetry (ITC is a label-free binding assay, which measures affinity, stoichiometry, and binding thermodynamics for biomolecular interactions. When thermodynamic data are used together with structural and kinetic data from other assays, a complete structure-activity-thermodynamics profile can be constructed. This review article describes ITC, and discusses several applications on how data from ITC provides insights into how antibodies function, guide antibody engineering, and aid design of new therapeutic drugs.

  8. TOPICAL REVIEW: The physics, biophysics and technology of photodynamic therapy

    Science.gov (United States)

    Wilson, Brian C.; Patterson, Michael S.

    2008-05-01

    Photodynamic therapy (PDT) uses light-activated drugs to treat diseases ranging from cancer to age-related macular degeneration and antibiotic-resistant infections. This paper reviews the current status of PDT with an emphasis on the contributions of physics, biophysics and technology, and the challenges remaining in the optimization and adoption of this treatment modality. A theme of the review is the complexity of PDT dosimetry due to the dynamic nature of the three essential components—light, photosensitizer and oxygen. Considerable progress has been made in understanding the problem and in developing instruments to measure all three, so that optimization of individual PDT treatments is becoming a feasible target. The final section of the review introduces some new frontiers of research including low dose rate (metronomic) PDT, two-photon PDT, activatable PDT molecular beacons and nanoparticle-based PDT.

  9. The physics, biophysics and technology of photodynamic therapy

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, Brian C [Division of Biophysics and Bioimaging, Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, ON M5G 2M9 (Canada); Patterson, Michael S [Department of Medical Physics, Juravinski Cancer Centre and Department of Medical Physics and Applied Radiation Sciences, McMaster University, 699 Concession Street, Hamilton, ON L8V 5C2 (Canada)], E-mail: wilson@uhnres.utoronto.ca, E-mail: mike.patterson@jcc.hhsc.ca

    2008-05-07

    Photodynamic therapy (PDT) uses light-activated drugs to treat diseases ranging from cancer to age-related macular degeneration and antibiotic-resistant infections. This paper reviews the current status of PDT with an emphasis on the contributions of physics, biophysics and technology, and the challenges remaining in the optimization and adoption of this treatment modality. A theme of the review is the complexity of PDT dosimetry due to the dynamic nature of the three essential components-light, photosensitizer and oxygen. Considerable progress has been made in understanding the problem and in developing instruments to measure all three, so that optimization of individual PDT treatments is becoming a feasible target. The final section of the review introduces some new frontiers of research including low dose rate (metronomic) PDT, two-photon PDT, activatable PDT molecular beacons and nanoparticle-based PDT. (topical review)

  10. The physics, biophysics and technology of photodynamic therapy

    International Nuclear Information System (INIS)

    Wilson, Brian C; Patterson, Michael S

    2008-01-01

    Photodynamic therapy (PDT) uses light-activated drugs to treat diseases ranging from cancer to age-related macular degeneration and antibiotic-resistant infections. This paper reviews the current status of PDT with an emphasis on the contributions of physics, biophysics and technology, and the challenges remaining in the optimization and adoption of this treatment modality. A theme of the review is the complexity of PDT dosimetry due to the dynamic nature of the three essential components-light, photosensitizer and oxygen. Considerable progress has been made in understanding the problem and in developing instruments to measure all three, so that optimization of individual PDT treatments is becoming a feasible target. The final section of the review introduces some new frontiers of research including low dose rate (metronomic) PDT, two-photon PDT, activatable PDT molecular beacons and nanoparticle-based PDT. (topical review)

  11. Biophysical information in asymmetric and symmetric diurnal bidirectional canopy reflectance

    Science.gov (United States)

    Vanderbilt, Vern C.; Caldwell, William F.; Pettigrew, Rita E.; Ustin, Susan L.; Martens, Scott N.; Rousseau, Robert A.; Berger, Kevin M.; Ganapol, B. D.; Kasischke, Eric S.; Clark, Jenny A.

    1991-01-01

    The authors present a theory for partitioning the information content in diurnal bidirectional reflectance measurements in order to detect differences potentially related to biophysical variables. The theory, which divides the canopy reflectance into asymmetric and symmetric functions of solar azimuth angle, attributes asymmetric variation to diurnal changes in the canopy biphysical properties. The symmetric function is attributed to the effects of sunlight interacting with a hypothetical average canopy which would display the average diurnal properties of the actual canopy. The authors analyzed radiometer data collected diurnally in the Thematic Mapper wavelength bands from two walnut canopies that received differing irrigation treatments. The reflectance of the canopies varied with sun and view angles and across seven bands in the visible, near-infrared, and middle infrared wavelength regions. Although one of the canopies was permanently water stressed and the other was stressed in mid-afternoon each day, no water stress signature was unambiguously evident in the reflectance data.

  12. The physics, biophysics and technology of photodynamic therapy.

    Science.gov (United States)

    Wilson, Brian C; Patterson, Michael S

    2008-05-07

    Photodynamic therapy (PDT) uses light-activated drugs to treat diseases ranging from cancer to age-related macular degeneration and antibiotic-resistant infections. This paper reviews the current status of PDT with an emphasis on the contributions of physics, biophysics and technology, and the challenges remaining in the optimization and adoption of this treatment modality. A theme of the review is the complexity of PDT dosimetry due to the dynamic nature of the three essential components -- light, photosensitizer and oxygen. Considerable progress has been made in understanding the problem and in developing instruments to measure all three, so that optimization of individual PDT treatments is becoming a feasible target. The final section of the review introduces some new frontiers of research including low dose rate (metronomic) PDT, two-photon PDT, activatable PDT molecular beacons and nanoparticle-based PDT.

  13. Fragility of complexity biophysical systems by neutron scattering

    International Nuclear Information System (INIS)

    Magazu, Salvatore; Migliardo, Federica; Bellocco, Ersilia; Lagana, Giuseppina; Mondelli, Claudia

    2006-01-01

    Neutron scattering is an exceptional tool to investigate structural and dynamical properties of systems of biophysical interest, such as proteins, enzymes, lipids and sugars. Moreover, elastic neutron scattering enhances the investigation of atomic motions in hydrated proteins in a wide temperature range and on the picosecond timescale. Homologous disaccharides, such as trehalose, maltose and sucrose, are cryptobiotic substances, since they allow to many organisms to undergo in a 'suspended life' state, known as cryptobiosis in extreme environmental conditions. The present paper is aimed to discuss the fragility degree of disaccharides, as evaluated of the temperature dependence of the mean square displacement by elastic neutron scattering, in order to link this feature with their bioprotective functions

  14. Irrigation Requirement Estimation Using Vegetation Indices and Inverse Biophysical Modeling

    Science.gov (United States)

    Bounoua, Lahouari; Imhoff, Marc L.; Franks, Shannon

    2010-01-01

    We explore an inverse biophysical modeling process forced by satellite and climatological data to quantify irrigation requirements in semi-arid agricultural areas. We constrain the carbon and water cycles modeled under both equilibrium, balance between vegetation and climate, and non-equilibrium, water added through irrigation. We postulate that the degree to which irrigated dry lands vary from equilibrium climate conditions is related to the amount of irrigation. The amount of water required over and above precipitation is considered as an irrigation requirement. For July, results show that spray irrigation resulted in an additional amount of water of 1.3 mm per occurrence with a frequency of 24.6 hours. In contrast, the drip irrigation required only 0.6 mm every 45.6 hours or 46% of that simulated by the spray irrigation. The modeled estimates account for 87% of the total reported irrigation water use, when soil salinity is not important and 66% in saline lands.

  15. Biophysics at the Boundaries: The Next Problem Sets

    Science.gov (United States)

    Skolnick, Malcolm

    2009-03-01

    The interface between physics and biology is one of the fastest growing subfields of physics. As knowledge of such topics as cellular processes and complex ecological systems advances, researchers have found that progress in understanding these and other systems requires application of more quantitative approaches. Today, there is a growing demand for quantitative and computational skills in biological research and the commercialization of that research. The fragmented teaching of science in our universities still leaves biology outside the quantitative and mathematical culture that is the foundation of physics. This is particularly inopportune at a time when the needs for quantitative thinking about biological systems are exploding. More physicists should be encouraged to become active in research and development in the growing application fields of biophysics including molecular genetics, biomedical imaging, tissue generation and regeneration, drug development, prosthetics, neural and brain function, kinetics of nonequilibrium open biological systems, metabolic networks, biological transport processes, large-scale biochemical networks and stochastic processes in biochemical systems to name a few. In addition to moving into basic research in these areas, there is increasing opportunity for physicists in industry beginning with entrepreneurial roles in taking research results out of the laboratory and in the industries who perfect and market the inventions and developments that physicists produce. In this talk we will identify and discuss emerging opportunities for physicists in biophysical and biotechnological pursuits ranging from basic research through development of applications and commercialization of results. This will include discussion of the roles of physicists in non-traditional areas apart from academia such as patent law, financial analysis and regulatory science and the problem sets assigned in education and training that will enable future

  16. Climate change effects on agriculture: Economic responses to biophysical shocks

    Science.gov (United States)

    Nelson, Gerald C.; Valin, Hugo; Sands, Ronald D.; Havlík, Petr; Ahammad, Helal; Deryng, Delphine; Elliott, Joshua; Fujimori, Shinichiro; Hasegawa, Tomoko; Heyhoe, Edwina; Kyle, Page; Von Lampe, Martin; Lotze-Campen, Hermann; Mason d’Croz, Daniel; van Meijl, Hans; van der Mensbrugghe, Dominique; Müller, Christoph; Popp, Alexander; Robertson, Richard; Robinson, Sherman; Schmid, Erwin; Schmitz, Christoph; Tabeau, Andrzej; Willenbockel, Dirk

    2014-01-01

    Agricultural production is sensitive to weather and thus directly affected by climate change. Plausible estimates of these climate change impacts require combined use of climate, crop, and economic models. Results from previous studies vary substantially due to differences in models, scenarios, and data. This paper is part of a collective effort to systematically integrate these three types of models. We focus on the economic component of the assessment, investigating how nine global economic models of agriculture represent endogenous responses to seven standardized climate change scenarios produced by two climate and five crop models. These responses include adjustments in yields, area, consumption, and international trade. We apply biophysical shocks derived from the Intergovernmental Panel on Climate Change’s representative concentration pathway with end-of-century radiative forcing of 8.5 W/m2. The mean biophysical yield effect with no incremental CO2 fertilization is a 17% reduction globally by 2050 relative to a scenario with unchanging climate. Endogenous economic responses reduce yield loss to 11%, increase area of major crops by 11%, and reduce consumption by 3%. Agricultural production, cropland area, trade, and prices show the greatest degree of variability in response to climate change, and consumption the lowest. The sources of these differences include model structure and specification; in particular, model assumptions about ease of land use conversion, intensification, and trade. This study identifies where models disagree on the relative responses to climate shocks and highlights research activities needed to improve the representation of agricultural adaptation responses to climate change. PMID:24344285

  17. Climate change effects on agriculture: Economic responses to biophysical shocks

    Energy Technology Data Exchange (ETDEWEB)

    Nelson, Gerald; Valin, Hugo; Sands, Ronald; Havlik, Petr; Ahammad, Helal; Deryng, Delphine; Elliott, Joshua; Fujimori, Shinichiro; Hasegawa, Tomoko; Heyhoe, Edwina; Kyle, G. Page; von Lampe, Martin; Lotze-Campen, Hermann; Mason d' Croz, Daniel; van Meijl, Hans; van der Mensbrugghe, Dominique; Mueller, C.; Popp, Alexander; Robertson, Richard; Robinson, Sherman; Schmid, E.; Schmitz, Christoph; Tabeau, Andrzej; Willenbockel, Dirk

    2013-12-16

    Agricultural production is sensitive to weather and will thus be directly affected by climate change. Plausible estimates of these climate change impacts require combined use of climate, crop, and economic models. Results from previous studies vary substantially due to differences in models, scenarios, and data. This paper is part of a collective effort to systematically integrate these three types of models. We focus on the economic component of the assessment, investigating how nine global economic models of agriculture represent endogenous responses to seven standardized climate change scenarios produced by two climate and five crop models. These responses include adjustments in yields, area, consumption, and international trade. We apply biophysical shocks derived from the IPCC’s Representative Concentration Pathway that result in end-of-century radiative forcing of 8.5 watts per square meter. The mean biophysical impact on crop yield with no incremental CO2 fertilization is a 17 percent reduction globally by 2050 relative to a scenario with unchanging climate. Endogenous economic responses reduce yield loss to 11 percent, increase area of major crops by 12 percent, and reduce consumption by 2 percent. Agricultural production, cropland area, trade, and prices show the greatest degree of variability in response to climate change, and consumption the lowest. The sources of these differences includes model structure and specification; in particular, model assumptions about ease of land use conversion, intensification, and trade. This study identifies where models disagree on the relative responses to climate shocks and highlights research activities needed to improve the representation of agricultural adaptation responses to climate change.

  18. Biophysical and structural considerations for protein sequence evolution

    Directory of Open Access Journals (Sweden)

    Grahnen Johan A

    2011-12-01

    Full Text Available Abstract Background Protein sequence evolution is constrained by the biophysics of folding and function, causing interdependence between interacting sites in the sequence. However, current site-independent models of sequence evolutions do not take this into account. Recent attempts to integrate the influence of structure and biophysics into phylogenetic models via statistical/informational approaches have not resulted in expected improvements in model performance. This suggests that further innovations are needed for progress in this field. Results Here we develop a coarse-grained physics-based model of protein folding and binding function, and compare it to a popular informational model. We find that both models violate the assumption of the native sequence being close to a thermodynamic optimum, causing directional selection away from the native state. Sampling and simulation show that the physics-based model is more specific for fold-defining interactions that vary less among residue type. The informational model diffuses further in sequence space with fewer barriers and tends to provide less support for an invariant sites model, although amino acid substitutions are generally conservative. Both approaches produce sequences with natural features like dN/dS Conclusions Simple coarse-grained models of protein folding can describe some natural features of evolving proteins but are currently not accurate enough to use in evolutionary inference. This is partly due to improper packing of the hydrophobic core. We suggest possible improvements on the representation of structure, folding energy, and binding function, as regards both native and non-native conformations, and describe a large number of possible applications for such a model.

  19. Hyperspectral dimensionality reduction for biophysical variable statistical retrieval

    Science.gov (United States)

    Rivera-Caicedo, Juan Pablo; Verrelst, Jochem; Muñoz-Marí, Jordi; Camps-Valls, Gustau; Moreno, José

    2017-10-01

    Current and upcoming airborne and spaceborne imaging spectrometers lead to vast hyperspectral data streams. This scenario calls for automated and optimized spectral dimensionality reduction techniques to enable fast and efficient hyperspectral data processing, such as inferring vegetation properties. In preparation of next generation biophysical variable retrieval methods applicable to hyperspectral data, we present the evaluation of 11 dimensionality reduction (DR) methods in combination with advanced machine learning regression algorithms (MLRAs) for statistical variable retrieval. Two unique hyperspectral datasets were analyzed on the predictive power of DR + MLRA methods to retrieve leaf area index (LAI): (1) a simulated PROSAIL reflectance data (2101 bands), and (2) a field dataset from airborne HyMap data (125 bands). For the majority of MLRAs, applying first a DR method leads to superior retrieval accuracies and substantial gains in processing speed as opposed to using all bands into the regression algorithm. This was especially noticeable for the PROSAIL dataset: in the most extreme case, using the classical linear regression (LR), validation results RCV2 (RMSECV) improved from 0.06 (12.23) without a DR method to 0.93 (0.53) when combining it with a best performing DR method (i.e., CCA or OPLS). However, these DR methods no longer excelled when applied to noisy or real sensor data such as HyMap. Then the combination of kernel CCA (KCCA) with LR, or a classical PCA and PLS with a MLRA showed more robust performances (RCV2 of 0.93). Gaussian processes regression (GPR) uncertainty estimates revealed that LAI maps as trained in combination with a DR method can lead to lower uncertainties, as opposed to using all HyMap bands. The obtained results demonstrated that, in general, biophysical variable retrieval from hyperspectral data can largely benefit from dimensionality reduction in both accuracy and computational efficiency.

  20. Membrane Transition Temperature Determines Cisplatin Response

    Science.gov (United States)

    Raghunathan, Krishnan; Ahsan, Aarif; Ray, Dipankar; Nyati, Mukesh K.; Veatch, Sarah L.

    2015-01-01

    Cisplatin is a classical chemotherapeutic agent used in treating several forms of cancer including head and neck. However, cells develop resistance to the drug in some patients through a range of mechanisms, some of which are poorly understood. Using isolated plasma membrane vesicles as a model system, we present evidence suggesting that cisplatin induced resistance may be due to certain changes in the bio-physical properties of plasma membranes. Giant plasma membrane vesicles (GPMVs) isolated from cortical cytoskeleton exhibit a miscibility transition between a single liquid phase at high temperature and two distinct coexisting liquid phases at low temperature. The temperature at which this transition occurs is hypothesized to reflect the magnitude of membrane heterogeneity at physiological temperature. We find that addition of cisplatin to vesicles isolated from cisplatin-sensitive cells result in a lowering of this miscibility transition temperature, whereas in cisplatin-resistant cells such treatment does not affect the transition temperature. To explore if this is a cause or consequence of cisplatin resistance, we tested if addition of cisplatin in combination with agents that modulate GPMV transition temperatures can affect cisplatin sensitivity. We found that cells become more sensitive to cisplatin when isopropanol, an agent that lowers GPMV transition temperature, was combined with cisplatin. Conversely, cells became resistant to cisplatin when added in combination with menthol that raises GPMV transition temperatures. These data suggest that changes in plasma membrane heterogeneity augments or suppresses signaling events initiated in the plasma membranes that can determine response to cisplatin. We postulate that desired perturbations of membrane heterogeneity could provide an effective therapeutic strategy to overcome cisplatin resistance for certain patients. PMID:26484687

  1. Effects of single amino acid substitution on the biophysical properties and biological activities of an amphipathic α-helical antibacterial peptide against Gram-negative bacteria.

    Science.gov (United States)

    Tan, Juanjuan; Huang, Jinfeng; Huang, Yibing; Chen, Yuxin

    2014-07-24

    An antimicrobial peptide, known as V13K, was utilized as the framework to study the effects of charge, hydrophobicity and helicity on the biophysical properties and biological activities of α-helical peptides. Six amino acids (Lys, Glu, Gly, Ser, Ala, and Leu) were individually used to substitute the original hydrophobic valine at the selected sixteenth location on the non-polar face of V13K. The results showed that the single amino acid substitutions changed the hydrophobicity of peptide analogs as monitored by RP-HPLC, but did not cause significant changes on peptide secondary structures both in a benign buffer and in a hydrophobic environment. The biological activities of the analogs exhibited a hydrophobicity-dependent behavior. The mechanism of peptide interaction with the outer membrane and cytoplasmic membrane of Gram-negative bacteria was investigated. We demonstrated that this single amino acid substitution method has valuable potential for the rational design of antimicrobial peptides with enhanced activities.

  2. Chemically Stable Lipids for Membrane Protein Crystallization

    Energy Technology Data Exchange (ETDEWEB)

    Ishchenko, Andrii; Peng, Lingling; Zinovev, Egor; Vlasov, Alexey; Lee, Sung Chang; Kuklin, Alexander; Mishin, Alexey; Borshchevskiy, Valentin; Zhang, Qinghai; Cherezov, Vadim (MIPT); (USC); (Scripps)

    2017-05-01

    The lipidic cubic phase (LCP) has been widely recognized as a promising membrane-mimicking matrix for biophysical studies of membrane proteins and their crystallization in a lipidic environment. Application of this material to a wide variety of membrane proteins, however, is hindered due to a limited number of available host lipids, mostly monoacylglycerols (MAGs). Here, we designed, synthesized, and characterized a series of chemically stable lipids resistant to hydrolysis, with properties complementary to the widely used MAGs. In order to assess their potential to serve as host lipids for crystallization, we characterized the phase properties and lattice parameters of mesophases made of two most promising lipids at a variety of different conditions by polarized light microscopy and small-angle X-ray scattering. Both lipids showed remarkable chemical stability and an extended LCP region in the phase diagram covering a wide range of temperatures down to 4 °C. One of these lipids has been used for crystallization and structure determination of a prototypical membrane protein bacteriorhodopsin at 4 and 20 °C.

  3. Toxin studies using an integrated biophysical and structural biology approach.

    Energy Technology Data Exchange (ETDEWEB)

    Last, Julie A.; Schroeder, Anne E.; Slade, Andrea Lynn; Sasaki, Darryl Yoshio; Yip, Christopher M. (University of Toronto, Toronto, Ontario, Canada); Schoeniger, Joseph S. (Sandia National Laboratories, Livermore, CA)

    2005-03-01

    Clostridial neurotoxins, such as botulinum and tetanus, are generally thought to invade neural cells through a process of high affinity binding mediated by gangliosides, internalization via endosome formation, and subsequent membrane penetration of the catalytic domain activated by a pH drop in the endosome. This surface recognition and internalization process is still not well understood with regard to what specific membrane features the toxins target, the intermolecular interactions between bound toxins, and the molecular conformational changes that occur as a result of pH lowering. In an effort to elucidate the mechanism of tetanus toxin binding and permeation through the membrane a simple yet representative model was developed that consisted of the ganglioside G{sub tlb} incorporated in a bilayer of cholesterol and DPPC (dipalmitoylphosphatidyl choline). The bilayers were stable over time yet sensitive towards the binding and activity of whole toxin. A liposome leakage study at constant pH as well as with a pH gradient, to mimic the processes of the endosome, was used to elucidate the effect of pH on the toxin's membrane binding and permeation capability. Topographic imaging of the membrane surface, via in situ tapping mode AFM, provided nanoscale characterization of the toxin's binding location and pore formation activity.

  4. Fatty acids are rapidly delivered to and extracted from membranes by methyl-β-cyclodextrin

    OpenAIRE

    Brunaldi, Kellen; Huang, Nasi; Hamilton, James A.

    2010-01-01

    We performed detailed biophysical studies of transfer of long-chain fatty acids (FAs) from methyl-β-CD (MBCD) to model membranes (egg-PC vesicles) and cells and the extraction of FA from membranes by MBCD. We used i) fluorescein phosphatidylethanolamine to detect transfer of FA anions arriving in the outer membrane leaflet; ii) entrapped pH dyes to measure pH changes after FA diffusion (flip-flop) across the lipid bilayer; and iii) soluble fluorescent-labeled FA binding protein to measure the...

  5. Contributions of adaptation currents to dynamic spike threshold on slow timescales: Biophysical insights from conductance-based models

    Science.gov (United States)

    Yi, Guosheng; Wang, Jiang; Wei, Xile; Deng, Bin; Li, Huiyan; Che, Yanqiu

    2017-06-01

    Spike-frequency adaptation (SFA) mediated by various adaptation currents, such as voltage-gated K+ current (IM), Ca2+-gated K+ current (IAHP), or Na+-activated K+ current (IKNa), exists in many types of neurons, which has been shown to effectively shape their information transmission properties on slow timescales. Here we use conductance-based models to investigate how the activation of three adaptation currents regulates the threshold voltage for action potential (AP) initiation during the course of SFA. It is observed that the spike threshold gets depolarized and the rate of membrane depolarization (dV/dt) preceding AP is reduced as adaptation currents reduce firing rate. It is indicated that the presence of inhibitory adaptation currents enables the neuron to generate a dynamic threshold inversely correlated with preceding dV/dt on slower timescales than fast dynamics of AP generation. By analyzing the interactions of ionic currents at subthreshold potentials, we find that the activation of adaptation currents increase the outward level of net membrane current prior to AP initiation, which antagonizes inward Na+ to result in a depolarized threshold and lower dV/dt from one AP to the next. Our simulations demonstrate that the threshold dynamics on slow timescales is a secondary effect caused by the activation of adaptation currents. These findings have provided a biophysical interpretation of the relationship between adaptation currents and spike threshold.

  6. Soil functional types: surveying the biophysical dimensions of soil security

    Science.gov (United States)

    Cécillon, Lauric; Barré, Pierre

    2015-04-01

    Soil is a natural capital that can deliver key ecosystem services (ES) to humans through the realization of a series of soil processes controlling ecosystem functioning. Soil is also a diverse and endangered natural resource. A huge pedodiversity has been described at all scales, which is strongly altered by global change. The multidimensional concept soil security, encompassing biophysical, economic, social, policy and legal frameworks of soils has recently been proposed, recognizing the role of soils in global environmental sustainability challenges. The biophysical dimensions of soil security focus on the functionality of a given soil that can be viewed as the combination of its capability and its condition [1]. Indeed, all soils are not equal in term of functionality. They show different processes, provide different ES to humans and respond specifically to global change. Knowledge of soil functionality in space and time is thus a crucial step towards the achievement soil security. All soil classification systems incorporate some functional information, but soil taxonomy alone cannot fully describe the functioning, limitations, resistance and resilience of soils. Droogers and Bouma [2] introduced functional variants (phenoforms) for each soil type (genoform) so as to fit more closely to soil functionality. However, different genoforms can have the same functionality. As stated by McBratney and colleagues [1], there is a great need of an agreed methodology for defining the reference state of soil functionality. Here, we propose soil functional types (SFT) as a relevant classification system for the biophysical dimensions of soil security. Following the definition of plant functional types widely used in ecology, we define a soil functional type as "a set of soil taxons or phenoforms sharing similar processes (e.g. soil respiration), similar effects on ecosystem functioning (e.g. primary productivity) and similar responses to global change (land-use, management or

  7. Applications of thermal neutron scattering in biology, biochemistry and biophysics

    International Nuclear Information System (INIS)

    Worcester, D.L.

    1977-01-01

    Biological applications of thermal neutron scattering have increased rapidly in recent years. The following categories of biological research with thermal neutron scattering are presently identified: crystallography of biological molecules; neutron small-angle scattering of biological molecules in solution (these studies have already included numerous measurements of proteins, lippoproteins, viruses, ribosomal subunits and chromatin subunit particles); neutron small-angle diffraction and scattering from biological membranes and membrane components; and neutron quasielastic and inelastic scattering studies of the dynamic properties of biological molecules and materials. (author)

  8. CREB Overexpression Ameliorates Age-related Behavioral and Biophysical Deficits

    Science.gov (United States)

    Yu, Xiao-Wen

    Age-related cognitive deficits are observed in both humans and animals. Yet, the molecular mechanisms underlying these deficits are not yet fully elucidated. In aged animals, a decrease in intrinsic excitability of pyramidal neurons from the CA1 sub-region of hippocampus is believed to contribute to age-related cognitive impairments, but the molecular mechanism(s) that modulate both these factors has yet to be identified. Increasing activity of the transcription factor cAMP response element-binding protein (CREB) in young adult rodents has been shown to facilitate cognition, and increase intrinsic excitability of their neurons. However, how CREB changes with age, and how that impacts cognition in aged animals, is not clear. Therefore, we first systematically characterized age- and training-related changes in CREB levels in dorsal hippocampus. At a remote time point after undergoing behavioral training, levels of total CREB and activated CREB (phosphorylated at S133, pCREB) were measured in both young and aged rats. We found that pCREB, but not total CREB was significantly reduced in dorsal CA1 of aged rats. Importantly, levels of pCREB were found to be positively correlated with short-term spatial memory in both young and aged rats i.e. higher pCREB in dorsal CA1 was associated with better spatial memory. These findings indicate that an age-related deficit in CREB activity may contribute to the development of age-related cognitive deficits. However, it was still unclear if increasing CREB activity would be sufficient to ameliorate age-related cognitive, and biophysical deficits. To address this question, we virally overexpressed CREB in CA1, where we found the age-related deficit. Young and aged rats received control or CREB virus, and underwent water maze training. While control aged animals exhibited deficits in long-term spatial memory, aged animals with CREB overexpression performed at levels comparable to young animals. Concurrently, aged neurons

  9. Biophysical Aspects of Radiation Quality. Second Panel Report

    International Nuclear Information System (INIS)

    1968-01-01

    If a living system is exposed to ionizing radiation a sequence of events follows. It starts with the absorption and dissipation of radiation energy, and continues through various physico-chemical and biochemical reactions up to the final biological end point observed. One of the aims of research in quantitative radiation biology is to understand the mechanism of this sequence of actions and to explore the differences in quality of different kinds of radiations. Because of its complexity, progress in this work requires the combined efforts of physicists, biochemists, biologists and physicians. It should, however, be done in very close collaboration rather than in following isolated lines in any one direction. For this reason, and because of the growing importance of the field for almost all applications of ionizing radiations, it was felt desirable to bring together a group of scientists engaged in research on radiation quality who represented a wide range of interests. The first panel on Biophysical Aspects of Radiation Quality, convened by the International Atomic Energy Agency in Vienna and held from 29 March to 2 April 1965, proved to be a successful beginning, stimulating a useful exchange of ideas and information. By this meeting, and the resulting collection of papers, published in 1966 as No. 58 of the Agency's Technical Reports Series, the importance of research on radiation quality was highlighted and the field itself became more clearly defined. The Agency held a second Panel on the same subject in Vienna from 14 to 18 April 1967. This meeting was attended by 18 experts from 10 countries, and representatives from Euratom and WHO. The Czechoslovak Socialist Republic, France, India and Poland were represented for the first time. Fourteen papers were presented and discussed in some detail. It became evident that much progress had been made since the previous meeting in certain areas such as microdosimetry, the dependence of the oxygen effect on radiation

  10. Characterizing the structure of lipodisq nanoparticles for membrane protein spectroscopic studies.

    Science.gov (United States)

    Zhang, Rongfu; Sahu, Indra D; Liu, Lishan; Osatuke, Anna; Comer, Raven G; Dabney-Smith, Carole; Lorigan, Gary A

    2015-01-01

    Membrane protein spectroscopic studies are challenging due to the difficulty introduced in preparing homogenous and functional hydrophobic proteins incorporated into a lipid bilayer system. Traditional membrane mimics such as micelles or liposomes have proved to be powerful in solubilizing membrane proteins for biophysical studies, however, several drawbacks have limited their applications. Recently, a nanosized complex termed lipodisq nanoparticles was utilized as an alternative membrane mimic to overcome these caveats by providing a homogeneous lipid bilayer environment. Despite all the benefits that lipodisq nanoparticles could provide to enhance the biophysical studies of membrane proteins, structural characterization in different lipid compositions that closely mimic the native membrane environment is still lacking. In this study, the formation of lipodisq nanoparticles using different weight ratios of POPC/POPG lipids to SMA polymers was characterized via solid-state nuclear magnetic resonance (SSNMR) spectroscopy and dynamic light scattering (DLS). A critical weight ratio of (1/1.25) for the complete solubilization of POPC/POPG vesicles has been observed and POPC/POPG vesicles turned clear instantaneously upon the addition of the SMA polymer. The size of lipodisq nanoparticles formed from POPC/POPG lipids at this weight ratio of (1/1.25) was found to be about 30 nm in radius. We also showed that upon the complete solubilization of POPC/POPG vesicles by SMA polymers, the average size of the lipodisq nanoparticles is weight ratio dependent, when more SMA polymers were introduced, smaller lipodisq nanoparticles were obtained. The results of this study will be helpful for a variety of biophysical experiments when specific size of lipid disc is required. Further, this study will provide a proper path for researchers working on membrane proteins to obtain pertinent structure and dynamic information in a physiologically relevant membrane mimetic environment

  11. A Biophysical Neural Model To Describe Spatial Visual Attention

    International Nuclear Information System (INIS)

    Hugues, Etienne; Jose, Jorge V.

    2008-01-01

    Visual scenes have enormous spatial and temporal information that are transduced into neural spike trains. Psychophysical experiments indicate that only a small portion of a spatial image is consciously accessible. Electrophysiological experiments in behaving monkeys have revealed a number of modulations of the neural activity in special visual area known as V4, when the animal is paying attention directly towards a particular stimulus location. The nature of the attentional input to V4, however, remains unknown as well as to the mechanisms responsible for these modulations. We use a biophysical neural network model of V4 to address these issues. We first constrain our model to reproduce the experimental results obtained for different external stimulus configurations and without paying attention. To reproduce the known neuronal response variability, we found that the neurons should receive about equal, or balanced, levels of excitatory and inhibitory inputs and whose levels are high as they are in in vivo conditions. Next we consider attentional inputs that can induce and reproduce the observed spiking modulations. We also elucidate the role played by the neural network to generate these modulations

  12. Ecosystem biophysical memory in the southwestern North America climate system

    International Nuclear Information System (INIS)

    Forzieri, G; Feyen, L; Vivoni, E R

    2013-01-01

    To elucidate the potential role of vegetation to act as a memory source in the southwestern North America climate system, we explore correlation structures of remotely sensed vegetation dynamics with precipitation, temperature and teleconnection indices over 1982–2006 for six ecoregions. We found that lagged correlations between vegetation dynamics and climate variables are modulated by the dominance of monsoonal or Mediterranean regimes and ecosystem-specific physiological processes. Subtropical and tropical ecosystems exhibit a one month lag positive correlation with precipitation, a zero- to one-month lag negative correlation with temperature, and modest negative effects of sea surface temperature (SST). Mountain forests have a zero month lag negative correlation with precipitation, a zero–one month lag negative correlation with temperature, and no significant correlation with SSTs. Deserts show a strong one–four month lag positive correlation with precipitation, a low zero–two month lag negative correlation with temperature, and a high four–eight month lag positive correlation with SSTs. The ecoregion-specific biophysical memories identified offer an opportunity to improve the predictability of land–atmosphere interactions and vegetation feedbacks onto climate. (letter)

  13. Biophysical induction of vascular smooth muscle cell podosomes.

    Directory of Open Access Journals (Sweden)

    Na Young Kim

    Full Text Available Vascular smooth muscle cell (VSMC migration and matrix degradation occurs with intimal hyperplasia associated with atherosclerosis, vascular injury, and restenosis. One proposed mechanism by which VSMCs degrade matrix is through the use of podosomes, transient actin-based structures that are thought to play a role in extracellular matrix degradation by creating localized sites of matrix metalloproteinase (MMP secretion. To date, podosomes in VSMCs have largely been studied by stimulating cells with phorbol esters, such as phorbol 12,13-dibutyrate (PDBu, however little is known about the physiological cues that drive podosome formation. We present the first evidence that physiological, physical stimuli mimicking cues present within the microenvironment of diseased arteries can induce podosome formation in VSMCs. Both microtopographical cues and imposed pressure mimicking stage II hypertension induce podosome formation in A7R5 rat aortic smooth muscle cells. Moreover, wounding using a scratch assay induces podosomes at the leading edge of VSMCs. Notably the effect of each of these biophysical stimuli on podosome stimulation can be inhibited using a Src inhibitor. Together, these data indicate that physical cues can induce podosome formation in VSMCs.

  14. Biochemical and biophysical methods for studying mitochondrial iron metabolism.

    Science.gov (United States)

    Holmes-Hampton, Gregory P; Tong, Wing-Hang; Rouault, Tracey A

    2014-01-01

    Iron is a heavily utilized element in organisms and numerous mechanisms accordingly regulate the trafficking, metabolism, and storage of iron. Despite the high regulation of iron homeostasis, several diseases and mutations can lead to the misregulation and often accumulation of iron in the cytosol or mitochondria of tissues. To understand the genesis of iron overload, it is necessary to employ various techniques to quantify iron in organisms and mitochondria. This chapter discusses techniques for determining the total iron content of tissue samples, ranging from colorimetric determination of iron concentrations, atomic absorption spectroscopy, inductively coupled plasma-optical emission spectroscopy, and inductively coupled plasma-mass spectrometry. In addition, we discuss in situ techniques for analyzing iron including electron microscopic nonheme iron histochemistry, electron energy loss spectroscopy, synchrotron X-ray fluorescence imaging, and confocal Raman microscopy. Finally, we discuss biophysical methods for studying iron in isolated mitochondria, including ultraviolet-visible, electron paramagnetic resonance, X-ray absorbance, and Mössbauer spectroscopies. This chapter should aid researchers to select and interpret mitochondrial iron quantifications.

  15. Time-resolved biophysical approaches to nucleocytoplasmic transport

    Directory of Open Access Journals (Sweden)

    Francesco Cardarelli

    2017-01-01

    Full Text Available Molecules are continuously shuttling across the nuclear envelope barrier that separates the nucleus from the cytoplasm. Instead of being just a barrier to diffusion, the nuclear envelope is rather a complex filter that provides eukaryotes with an elaborate spatiotemporal regulation of fundamental molecular processes, such as gene expression and protein translation. Given the highly dynamic nature of nucleocytoplasmic transport, during the past few decades large efforts were devoted to the development and application of time resolved, fluorescence-based, biophysical methods to capture the details of molecular motion across the nuclear envelope. These methods are here divided into three major classes, according to the differences in the way they report on the molecular process of nucleocytoplasmic transport. In detail, the first class encompasses those methods based on the perturbation of the fluorescence signal, also known as ensemble-averaging methods, which average the behavior of many molecules (across many pores. The second class comprises those methods based on the localization of single fluorescently-labelled molecules and tracking of their position in space and time, potentially across single pores. Finally, the third class encompasses methods based on the statistical analysis of spontaneous fluorescence fluctuations out of the equilibrium or stationary state of the system. In this case, the behavior of single molecules is probed in presence of many similarly-labelled molecules, without dwelling on any of them. Here these three classes, with their respective pros and cons as well as their main applications to nucleocytoplasmic shuttling will be briefly reviewed and discussed.

  16. Biophysical insight into the anti-amyloidogenic behavior of taurine.

    Science.gov (United States)

    Chaturvedi, Sumit Kumar; Alam, Parvez; Khan, Javed Masood; Siddiqui, Mohd Khursheed; Kalaiarasan, Ponnusamy; Subbarao, Naidu; Ahmad, Zeeshan; Khan, Rizwan Hasan

    2015-09-01

    In this work, we investigated the inhibitory ability of taurine on the aggregation of Human serum albumin (HSA) and also examined how it controls the kinetic parameters of the aggregation process. We demonstrated the structural alterations in the HSA after binding to the taurine at 65 °C by exploiting various biophysical techniques. UV-vis spectroscopy was used to check the turbidometric changes in the protein. Thioflavin T fluorescence kinetics was subjected to explore kinetic parameters comparing the amyloid formation in the presence of varying concentration of taurine. Further, Congo red binding and ANS binding assays were performed to determine the inhibitory effect of taurine on HSA fibrillation process and surface hydrophobicity modifications occurring before and after the addition of taurine with protein, respectively. Far UV CD and Dynamic Light Scattering (DLS) confirmed that taurine stabilized the protein α-helical structure and formed complex with HSA which is further supported by differential scanning calorimetry (DSC). Moreover, microscopic imaging techniques were also done to analyze the morphology of aggregation formed. Taurine is also capable of altering the cytotoxicity of the proteinaceous aggregates. Molecular docking study also deciphered the possible residues involved in protein and drug interaction. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Biophysical model of prokaryotic diversity in geothermal hot springs.

    Science.gov (United States)

    Klales, Anna; Duncan, James; Nett, Elizabeth Janus; Kane, Suzanne Amador

    2012-02-01

    Recent studies of photosynthetic bacteria living in geothermal hot spring environments have revealed surprisingly complex ecosystems with an unexpected level of genetic diversity. One case of particular interest involves the distribution along hot spring thermal gradients of genetically distinct bacterial strains that differ in their preferred temperatures for reproduction and photosynthesis. In such systems, a single variable, temperature, defines the relevant environmental variation. In spite of this, each region along the thermal gradient exhibits multiple strains of photosynthetic bacteria adapted to several distinct thermal optima, rather than a single thermal strain adapted to the local environmental temperature. Here we analyze microbiology data from several ecological studies to show that the thermal distribution data exhibit several universal features independent of location and specific bacterial strain. These include the distribution of optimal temperatures of different thermal strains and the functional dependence of the net population density on temperature. We present a simple population dynamics model of these systems that is highly constrained by biophysical data and by physical features of the environment. This model can explain in detail the observed thermal population distributions, as well as certain features of population dynamics observed in laboratory studies of the same organisms. © 2012 American Physical Society

  18. Editorial: The Sackler International Prize in Biophysical Sciences

    Science.gov (United States)

    Frydman, Lucio

    2018-02-01

    The Raymond and Beverly Sackler International Prize is awarded alternatively in the fields of Biophysics, Chemistry and Physics on a yearly basis, by Tel Aviv University. The price is intended to encourage dedication to science, originality and excellence, by rewarding outstanding scientists under 45 years of age, with a total purse of 100,000. The 2016 Raymond and Beverly Sackler Prize was awarded in the field of Magnetic Resonance last February in a festive symposium, to three excellent researchers: Professor John Morton (University College London), Professor Guido Pintacuda (Ecole Normale Supérieure de Lyon and CNRS), and Professor Charalampos Kalodimos (at the time at the University of Minnesota). John was recognized for his novel contributions to quantum information processing, by means of a range of highly elegant physical phenomena involving both NMR and EPR. Guido was recognized for his methodological advances in solid state NMR spectroscopy, including advances in proton detection under ultrafast MAS at ultrahigh magnetic field, and for his insightful applications to challenging biological systems. While Charalampos (Babis) was recognized for beautifully detailed characterizations of structure, function, and dynamics in challenging and important biological systems through solution NMR spectroscopy.

  19. Universal buffers for use in biochemistry and biophysical experiments

    Directory of Open Access Journals (Sweden)

    Dewey Brooke

    2015-08-01

    Full Text Available The use of buffers that mimic biological solutions is a foundation of biochemical and biophysical studies. However, buffering agents have both specific and nonspecific interactions with proteins. Buffer molecules can induce changes in conformational equilibria, dynamic behavior, and catalytic properties merely by their presence in solution. This effect is of concern because many of the standard experiments used to investigate protein structure and function involve changing solution conditions such as pH and/or temperature. In experiments in which pH is varied, it is common practice to switch buffering agents so that the pH is within the working range of the weak acid and conjugate base. If multiple buffers are used, it is not always possible to decouple buffer induced change from pH or temperature induced change. We have developed a series of mixed biological buffers for protein analysis that can be used across a broad pH range, are compatible with biologically relevant metal ions, and avoid complications that may arise from changing the small molecule composition of buffers when pH is used as an experimental variable.

  20. The biophysical bases of will-less behaviours

    Directory of Open Access Journals (Sweden)

    Jose Luis ePerez Velazquez

    2012-10-01

    Full Text Available Are there distinctions at the neurophysiological level that correlate with voluntary and involuntary actions? Whereas the wide variety of involuntary behaviours (and here mostly the deviant or pathological ones will be considered will necessarily be represented at some biophysical level in nervous system activity, for after all those cellular activity patterns manifest themselves as behaviours and thus there will be a multiplicity of them, there could be some general tendencies to be discerned amongst that assortment. Collecting observations derived from neurophysiological activity associated with several pathological conditions characterised by presenting will-less actions such as Parkinson’s disease, seizures, alien hand syndrome and tics, it is proposed that a general neurophysiologic tendency of brain activity that correlates with involuntary actions is higher than normal synchrony in specific brain cell networks, depending upon the behaviour in question. Wilful, considered normal behaviour, depends on precise coordination of the collective activity in cell ensembles that may be lost, or diminished, when there are tendencies towards more than normal or aberrant synchronization of cellular activity. Hence, rapid fluctuations in synchrony is associated with normal actions and cognition while less variability in brain recordings particularly with regards to synchronization could be a signature of unconscious and deviant behaviours in general.

  1. Biophysical Studies of Function and Stability in Adenylosuccinate Lyase

    Science.gov (United States)

    Ray, Stephen; Duval, Nathan; Wilkinson, Terry, II; Shaheen, Sean; Ghosh, Kinshuk; Patterson, David

    2012-10-01

    Adenylosuccinate Lyase (ADSL) is a homotetrameric protein with four active sites that accommodate two reactions in the de novo purine biosynthesis pathway. It catalyzes the conversion of SAICAR to AICAR and AMPS to AMP. Point mutations in the gene encoding the protein ADSL lead to ADSL deficiency, a disorder characterized by serious neurological and physiological symptoms. Two leading hypotheses regarding the pathogenesis are ``Loss of Function'' or ``Gain in Toxic Function.'' These hypotheses can be related to the reduction of either the enzyme kinetics or the stability of the tetramer structure. Enzymatic studies can be used to provide a quantitative measure of the extent to which the enzyme acts on its designated substrates, SAICAR and AMPS. Recent kinetic studies have measured activity only on the substrates independently. Here we present characterization of enzyme kinetics for the biophysically interesting and physiologically relevant case where two substrates exhibit competitive binding to the enzyme, for both wild type and disease causing mutants of ADSL. Preliminary data suggest equivalent specific activities may be necessary to suppress severe phenotypes from expressing. Additionally, we will present results on the role of mutations on the thermodynamic stability of the enzyme. We will discuss thermodynamic analysis that gives a direct quantitative measure of the propensity of formation of folded and unfolded states of the protein, which influence the functionality of the protein and may also influence aggregation.

  2. IS THERE ANY ASSOCIATION BETWEEN MATERNAL DEPRESSION AND BIOPHYSICAL PROFILE?

    Directory of Open Access Journals (Sweden)

    M Z Pezeshki

    2008-11-01

    Full Text Available "nMother's mental health status during pregnancy has important effects on fetal growth and development. However, there are few studies concerning association of maternal depression and biophysical profile (BPP of the fetus. We performed this research to know if maternal depression has any association with fetal BPP score. For measuring depression, Farsi version of Patient Health Questionnaire-9 (PHQ-9 was completed. A total of 100 pregnant women in their third trimester (>24 weeks who had not hyperthyroidism, hypothyroidism, eclampsia and preeclampsia, fever, infection, diabetes or a fetus with intrauterine growth retardation (IUGR and were not using any medication entered the study. Spearman correlation coefficient between the score of PHQ-9 questionnaire and BPP score was -0.08 (P = 0.43. Based on Kruskal Wallis test, there was no difference in BPP score of depressed and nondepressed women (P = 0.65. We found no relationship between maternal depression and BPP score in third trimester of pregnancy. Further studies for elucidating neuro-hormonal mechanisms related to the result of our study are suggested

  3. Biophysical and biological meanings of healthspan from C. elegans cohort

    Energy Technology Data Exchange (ETDEWEB)

    Suda, Hitoshi, E-mail: suda@tsc.u-tokai.ac.jp

    2014-09-12

    Highlights: • We focus on a third factor, noise, as well as on genetic and environmental factors. • C. elegans fed a healthy food had an extended healthspan as compared to those fed a conventional diet. • An amplification of ATP noise was clearly evident from around the onset of biodemographic aging. • The extension of timing of noise amplification may contribute to effectively extending the healthspan. • The same mechanism of the mean lifespan extension in C. elegans may be realized in humans. - Abstract: Lifespan among individuals ranges widely in organisms from yeast to mammals, even in an isogenic cohort born in a nearly uniform environment. Needless to say, genetic and environmental factors are essential for aging and lifespan, but in addition, a third factor or the existence of a stochastic element must be reflected in aging and lifespan. An essential point is that lifespan or aging is an unpredictable phenomenon. The present study focuses on elucidating the biophysical and biological meanings of healthspan that latently indwells a stochastic nature. To perform this purpose, the nematode Caenorhabditis elegans served as a model animal. C. elegans fed a healthy food had an extended healthspan as compared to those fed a conventional diet. Then, utilizing this phenomenon, we clarified a mechanism of healthspan extension by measuring the single-worm ATP and estimating the ATP noise (or the variability of the ATP content) among individual worms and by quantitatively analyzing biodemographic data with the lifespan equation that was derived from a fluctuation theory.

  4. An approach to membrane protein structure without crystals

    Science.gov (United States)

    Sorgen, Paul L.; Hu, Yonglin; Guan, Lan; Kaback, H. Ronald; Girvin, Mark E.

    2002-01-01

    The lactose permease of Escherichia coli catalyzes coupled translocation of galactosides and H+ across the cell membrane. It is the best-characterized member of the Major Facilitator Superfamily, a related group of membrane proteins with 12 transmembrane domains that mediate transport of various substrates across cell membranes. Despite decades of effort and their functional importance in all kingdoms of life, no high-resolution structures have been solved for any member of this family. However, extensive biochemical, genetic, and biophysical studies on lactose permease have established its transmembrane topology, secondary structure, and numerous interhelical contacts. Here we demonstrate that this information is sufficient to calculate a structural model at the level of helix packing or better. PMID:12391320

  5. From biological membranes to biomimetic model membranes

    Directory of Open Access Journals (Sweden)

    Eeman, M.

    2010-01-01

    Full Text Available Biological membranes play an essential role in the cellular protection as well as in the control and the transport of nutrients. Many mechanisms such as molecular recognition, enzymatic catalysis, cellular adhesion and membrane fusion take place into the biological membranes. In 1972, Singer et al. provided a membrane model, called fluid mosaic model, in which each leaflet of the bilayer is formed by a homogeneous environment of lipids in a fluid state including globular assembling of proteins and glycoproteins. Since its conception in 1972, many developments were brought to this model in terms of composition and molecular organization. The main development of the fluid mosaic model was made by Simons et al. (1997 and Brown et al. (1997 who suggested that membrane lipids are organized into lateral microdomains (or lipid rafts with a specific composition and a molecular dynamic that are different to the composition and the dynamic of the surrounding liquid crystalline phase. The discovery of a phase separation in the plane of the membrane has induced an explosion in the research efforts related to the biology of cell membranes but also in the development of new technologies for the study of these biological systems. Due to the high complexity of biological membranes and in order to investigate the biological processes that occur on the membrane surface or within the membrane lipid bilayer, a large number of studies are performed using biomimicking model membranes. This paper aims at revisiting the fundamental properties of biological membranes in terms of membrane composition, membrane dynamic and molecular organization, as well as at describing the most common biomimicking models that are frequently used for investigating biological processes such as membrane fusion, membrane trafficking, pore formation as well as membrane interactions at a molecular level.

  6. Membrane Protein Properties Revealed through Data-Rich Electrostatics Calculations.

    Science.gov (United States)

    Marcoline, Frank V; Bethel, Neville; Guerriero, Christopher J; Brodsky, Jeffrey L; Grabe, Michael

    2015-08-04

    The electrostatic properties of membrane proteins often reveal many of their key biophysical characteristics, such as ion channel selectivity and the stability of charged membrane-spanning segments. The Poisson-Boltzmann (PB) equation is the gold standard for calculating protein electrostatics, and the software APBSmem enables the solution of the PB equation in the presence of a membrane. Here, we describe significant advances to APBSmem, including full automation of system setup, per-residue energy decomposition, incorporation of PDB2PQR, calculation of membrane-induced pKa shifts, calculation of non-polar energies, and command-line scripting for large-scale calculations. We highlight these new features with calculations carried out on a number of membrane proteins, including the recently solved structure of the ion channel TRPV1 and a large survey of 1,614 membrane proteins of known structure. This survey provides a comprehensive list of residues with large electrostatic penalties for being embedded in the membrane, potentially revealing interesting functional information. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Towards understanding the Tat translocation mechanism through structural and biophysical studies of the amphipathic region of TatA from Escherichia coli.

    Science.gov (United States)

    Chan, Catherine S; Haney, Evan F; Vogel, Hans J; Turner, Raymond J

    2011-09-01

    The twin-arginine translocase (Tat) system is used by many bacteria and plants to move folded proteins across the cytoplasmic or thylakoid membrane. In most bacteria, the TatA protein is believed to form a defined pore in the membrane through homo-oligomerization with other TatA protomers. The predicted secondary structure of TatA includes a transmembrane helix, an amphipathic helix, and an unstructured C-terminal region. Here biophysical and structural investigations were performed on a synthetic peptide representing the amphipathic region of TatA (residues 22 to 44, abbreviated TatAH2). The C-terminal region of TatA (residues 44-89) was previously shown to be accessible from both the cytoplasmic and periplasmic sides of the membrane only when the membrane potential was intact, suggesting dependence of its topology on an energized membrane (Chan et al. 2007 Biochemistry 46: 7396-404). Such observation suggests that the TatAH2 region would have unique lipid interactions that may be related to the function of TatA during translocation and thus warranted further investigations. NMR and CD spectroscopy of TatAH2 show that it adopts a predominantly helical structure in a membrane environment while remaining unstructured in aqueous solution. Differential scanning calorimetry studies also reveal that TatAH2 interacts with DPPG lipids but not with DPPC, suggesting that negatively charged phospholipid head groups contribute to the membrane interactions with TatA. Copyright © 2011 Elsevier B.V. All rights reserved.

  8. Toxoplasma gondii: Biochemical and biophysical characterization of recombinant soluble dense granule proteins GRA2 and GRA6

    Energy Technology Data Exchange (ETDEWEB)

    Bittame, Amina [CNRS, UMR 5163, 38042 Grenoble (France); Université Grenoble Alpes, 38042 Grenoble (France); Effantin, Grégory [Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 38044 Grenoble (France); CNRS, IBS, 38044 Grenoble (France); CEA, IBS, 38044 Grenoble (France); Unit for Virus Host-Cell Interactions (UVHCI), UMI 3265 (UJF-EMBL-CNRS), 38027 Grenoble (France); Pètre, Graciane; Ruffiot, Pauline; Travier, Laetitia [CNRS, UMR 5163, 38042 Grenoble (France); Université Grenoble Alpes, 38042 Grenoble (France); Schoehn, Guy; Weissenhorn, Winfried [Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 38044 Grenoble (France); CNRS, IBS, 38044 Grenoble (France); CEA, IBS, 38044 Grenoble (France); Unit for Virus Host-Cell Interactions (UVHCI), UMI 3265 (UJF-EMBL-CNRS), 38027 Grenoble (France); Cesbron-Delauw, Marie-France; Gagnon, Jean [CNRS, UMR 5163, 38042 Grenoble (France); Université Grenoble Alpes, 38042 Grenoble (France); Mercier, Corinne, E-mail: corinne.mercier@ujf-grenoble.fr [CNRS, UMR 5163, 38042 Grenoble (France); Université Grenoble Alpes, 38042 Grenoble (France)

    2015-03-27

    The most prominent structural feature of the parasitophorous vacuole (PV) in which the intracellular parasite Toxoplasma gondii proliferates is a membranous nanotubular network (MNN), which interconnects the parasites and the PV membrane. The MNN function remains unclear. The GRA2 and GRA6 proteins secreted from the parasite dense granules into the PV have been implicated in the MNN biogenesis. Amphipathic alpha-helices (AAHs) predicted in GRA2 and an alpha-helical hydrophobic domain predicted in GRA6 have been proposed to be responsible for their membrane association, thereby potentially molding the MMN in its structure. Here we report an analysis of the recombinant proteins (expressed in detergent-free conditions) by circular dichroism, which showed that full length GRA2 displays an alpha-helical secondary structure while recombinant GRA6 and GRA2 truncated of its AAHs are mainly random coiled. Dynamic light scattering and transmission electron microscopy showed that recombinant GRA6 and truncated GRA2 constitute a homogenous population of small particles (6–8 nm in diameter) while recombinant GRA2 corresponds to 2 populations of particles (∼8–15 nm and up to 40 nm in diameter, respectively). The unusual properties of GRA2 due to its AAHs are discussed. - Highlights: • Toxoplasma gondii: soluble GRA2 forms 2 populations of particles. • T. gondii: the dense granule protein GRA2 folds intrinsically as an alpha-helix. • T. gondii: monomeric soluble GRA6 forms particles of 6–8 nm in diameter. • T. gondii: monomeric soluble GRA6 is random coiled. • Unusual biophysical properties of the dense granule protein GRA2 from T. gondii.

  9. G-protein coupled receptor solubilization and purification for biophysical analysis and functional studies, in the total absence of detergent.

    Science.gov (United States)

    Jamshad, Mohammed; Charlton, Jack; Lin, Yu-Pin; Routledge, Sarah J; Bawa, Zharain; Knowles, Timothy J; Overduin, Michael; Dekker, Niek; Dafforn, Tim R; Bill, Roslyn M; Poyner, David R; Wheatley, Mark

    2015-04-16

    G-protein coupled receptors (GPCRs) constitute the largest class of membrane proteins and are a major drug target. A serious obstacle to studying GPCR structure/function characteristics is the requirement to extract the receptors from their native environment in the plasma membrane, coupled with the inherent instability of GPCRs in the detergents required for their solubilization. In the present study, we report the first solubilization and purification of a functional GPCR [human adenosine A2A receptor (A2AR)], in the total absence of detergent at any stage, by exploiting spontaneous encapsulation by styrene maleic acid (SMA) co-polymer direct from the membrane into a nanoscale SMA lipid particle (SMALP). Furthermore, the A2AR-SMALP, generated from yeast (Pichia pastoris) or mammalian cells, exhibited increased thermostability (~5°C) compared with detergent [DDM (n-dodecyl-β-D-maltopyranoside)]-solubilized A2AR controls. The A2AR-SMALP was also stable when stored for prolonged periods at 4°C and was resistant to multiple freeze-thaw cycles, in marked contrast with the detergent-solubilized receptor. These properties establish the potential for using GPCR-SMALP in receptor-based drug discovery assays. Moreover, in contrast with nanodiscs stabilized by scaffold proteins, the non-proteinaceous nature of the SMA polymer allowed unobscured biophysical characterization of the embedded receptor. Consequently, CD spectroscopy was used to relate changes in secondary structure to loss of ligand binding ([(3)H]ZM241385) capability. SMALP-solubilization of GPCRs, retaining the annular lipid environment, will enable a wide range of therapeutic targets to be prepared in native-like state to aid drug discovery and understanding of GPCR molecular mechanisms.

  10. The Use of Photoelectric Cells as Sources of Power for Anti fly Biophysical Devices

    International Nuclear Information System (INIS)

    Aliev, R.; Aliboev, M.; Bazarov, O.; Tulanova, B.

    2011-01-01

    An anti fly biophysical device is developed and optimized. It has a luminescent bulb, solid emitters, and a photoelectric power source. Promising uses of industrial photoelectric batteries are proposed, and the feasibility of their adoption in agriculture is shown. (authors)

  11. LBA-ECO ND-01 Reflectance and Biophysical Measures, Grass Pastures: Rondonia, Brazil

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set provides the results of spectral reflectance (350 to 2,500 nm at 1-nm increments) and biophysical measurements on grass pastures in eight cattle...

  12. Novel biophysical determination of miRNAs related to prostate and head and neck cancers

    Czech Academy of Sciences Publication Activity Database

    Hudcová, K.; Trnková, L.; Kejnovská, Iva; Vorlíčková, Michaela; Gumulec, J.; Kizek, R.; Masarik, M.

    2015-01-01

    Roč. 44, č. 3 (2015), s. 131-138 ISSN 0175-7571 Institutional support: RVO:68081707 Keywords : SQUAMOUS-CELL CARCINOMA * ELIMINATION VOLTAMMETRY * CYTOSINE SIGNALS Subject RIV: BO - Biophysics Impact factor: 1.444, year: 2015

  13. LBA-ECO LC-14 Biophysical Measurements, Rainfall Exclusion, Tapajos National Forest

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set reports forest biophysical measurements from a rainfall exclusion experiment conducted at the km 67 Seca Floresta site, Tapajos National Forest, Brazil...

  14. LBA-ECO ND-01 Reflectance and Biophysical Measures, Grass Pastures: Rondonia, Brazil

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: This data set provides the results of spectral reflectance (350 to 2,500 nm at 1-nm increments) and biophysical measurements on grass pastures in eight...

  15. LBA-ECO LC-14 Biophysical Measurements, Rainfall Exclusion, Tapajos National Forest

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: This data set reports forest biophysical measurements from a rainfall exclusion experiment conducted at the km 67 Seca Floresta site, Tapajos National...

  16. Lab-on-a-Chip Platforms for Biophysical Studies of Cancer with Single-Cell Resolution.

    Science.gov (United States)

    Shukla, Vasudha C; Kuang, Tai-Rong; Senthilvelan, Abirami; Higuita-Castro, Natalia; Duarte-Sanmiguel, Silvia; Ghadiali, Samir N; Gallego-Perez, Daniel

    2018-03-17

    Recent cancer research has more strongly emphasized the biophysical aspects of tumor development, progression, and microenvironment. In addition to genetic modifications and mutations in cancer cells, it is now well accepted that the physical properties of cancer cells such as stiffness, electrical impedance, and refractive index vary with tumor progression and can identify a malignant phenotype. Moreover, cancer heterogeneity renders population-based characterization techniques inadequate, as individual cellular features are lost in the average. Hence, platforms for fast and accurate characterization of biophysical properties of cancer cells at the single-cell level are required. Here, we highlight some of the recent advances in the field of cancer biophysics and the development of lab-on-a-chip platforms for single-cell biophysical analyses of cancer cells. Copyright © 2018 Elsevier Ltd. All rights reserved.

  17. EDITORIAL: Focus on Heavy Ions in Biophysics and Medical Physics FOCUS ON HEAVY IONS IN BIOPHYSICS AND MEDICAL PHYSICS

    Science.gov (United States)

    Durante, Marco

    2008-07-01

    Interest in energetic heavy ions is rapidly increasing in the field of biomedicine. Heavy ions are normally excluded from radiation protection, because they are not normally experienced by humans on Earth. However, knowledge of heavy ion biophysics is necessary in two fields: charged particle cancer therapy (hadrontherapy), and radiation protection in space missions. The possibility to cure tumours using accelerated heavy charged particles was first tested in Berkeley in the sixties, but results were not satisfactory. However, about 15 years ago therapy with carbon ions was resumed first in Japan and then in Europe. Heavy ions are preferable to photons for both physical and biological characteristics: the Bragg peak and limited lateral diffusion ensure a conformal dose distribution, while the high relative biological effectiveness and low oxygen enhancement ration in the Bragg peak region make the beam very effective in treating radioresistant and hypoxic tumours. Recent results coming from the National Institute of Radiological Sciences in Chiba (see the paper by Dr Tsujii and co-workers in this issue) and GSI (Germany) provide strong clinical evidence that heavy ions are indeed an extremely effective weapon in the fight against cancer. However, more research is needed in the field, especially on optimization of the treatment planning and risk of late effects in normal tissue, including secondary cancers. On the other hand, high-energy heavy ions are present in galactic cosmic radiation and, although they are rare as compared to protons, they give a major contribution in terms of equivalent dose to the crews of manned space exploratory-class missions. Exploration of the Solar System is now the main goal of the space program, and the risk caused by exposure to galactic cosmic radiation is considered a serious hindrance toward this goal, because of the high uncertainty on late effects of energetic heavy nuclei, and the lack of effective countermeasures. Risks

  18. Biophysical approaches to G protein-coupled receptors: Structure, function and dynamics

    Science.gov (United States)

    Chollet, André; Turcatti, Gerardo

    1999-05-01

    G protein-coupled receptors (GPCR) represent a large family of drug targets for which there is no high-resolution structural information. In order to understand the mechanisms of ligand recognition and receptor activation, there is a strong need for novel biophysical methods. In this Perspective we provide an overview of recent experimental approaches used to explore the molecular architecture and dynamics of GPCR and their interactions with ligands and G proteins using biophysical, non-crystallographic, methods.

  19. Cellular normoxic biophysical markers of hydroxyurea treatment in sickle cell disease

    OpenAIRE

    Hosseini, Poorya; Abidi, Sabia Z.; Du, E; Papageorgiou, Dimitrios P.; Choi, Youngwoon; Park, YongKeun; Higgins, John M.; Kato, Gregory J.; Suresh, Subra; Dao, Ming; Yaqoob, Zahid; So, Peter T. C.

    2016-01-01

    There exists a critical need for developing biomarkers reflecting clinical outcomes and for evaluating the effectiveness of treatments for sickle cell disease patients. Prior attempts to find such patient-specific markers have mostly relied upon chemical biomarkers or biophysical properties at hypoxia with limited success. We introduce unique biomarkers based on characterization of cellular biophysical properties at normoxia and show that these markers correlate sensitively with treatment usi...

  20. Volterra dendritic stimulus processors and biophysical spike generators with intrinsic noise sources

    OpenAIRE

    Lazar, Aurel A.; Zhou, Yiyin

    2014-01-01

    We consider a class of neural circuit models with internal noise sources arising in sensory systems. The basic neuron model in these circuits consists of a nonlinear dendritic stimulus processor (DSP) cascaded with a biophysical spike generator (BSG). The nonlinear dendritic processor is modeled as a set of nonlinear operators that are assumed to have a Volterra series representation. Biophysical point neuron models, such as the Hodgkin-Huxley neuron, are used to model the spike generator. We...

  1. Sonographic biophysical profile in detection of foetal hypoxia in 100 cases of suspected high risk pregnancy

    International Nuclear Information System (INIS)

    Ullah, N.; Khan, A.R.; Usman, M.

    2010-01-01

    Background: The foetus has become increasingly accessible and visible as a patient over the last two decades. Ultrasound imaging has broadened the scope of foetal assessment. Dynamic real time B-Mode ultrasound is used to monitor cluster of biophysical variables, both dynamic and static collectively termed as biophysical profile. The purpose of this study was to determine the effect of sonographic biophysical profile score on perinatal outcome in terms of mortality and morbidity. Methods: This descriptive study was carried on 100 randomly select ed high risk pregnant patients in Radiology Department PGMI, Government Lady Reading Hospital, Peshawar from December 2007 to June 2008. Manning biophysical profile including non-stress was employed for foetal screening, using Toshiba ultrasound machine model Nemio SSA-550A and 7.5 MHZ probe. Results: Out of 100 cases 79 (79%) had a normal biophysical profile in the last scan of 10/10 and had a normal perinatal outcome with 5 minutes Apgar score >7/10. In 13 (13%) cases Apgar score at 5 minute was < 7/10 and babies were shifted to nursery. There were 2 (2%) false positive cases that showed abnormal biophysical profile scores of 6/10 but babies were born with an Apgar score of 8/10 at 5 minutes. There were 2 (2%) neonatal deaths in this study group. The sensitivity of biophysical profile was 79.1%, specificity 92.9%. Predictive value for a positive test was 98.55%; predictive value for a negative test was 41.93%. Conclusion: Biophysical profile is highly accurate and reliable test of diagnosing foetal hypoxia. (author)

  2. Biophysical impacts of climate-smart agriculture in the Midwest United States.

    Science.gov (United States)

    Bagley, Justin E; Miller, Jesse; Bernacchi, Carl J

    2015-09-01

    The potential impacts of climate change in the Midwest United States present unprecedented challenges to regional agriculture. In response to these challenges, a variety of climate-smart agricultural methodologies have been proposed to retain or improve crop yields, reduce agricultural greenhouse gas emissions, retain soil quality and increase climate resilience of agricultural systems. One component that is commonly neglected when assessing the environmental impacts of climate-smart agriculture is the biophysical impacts, where changes in ecosystem fluxes and storage of moisture and energy lead to perturbations in local climate and water availability. Using a combination of observational data and an agroecosystem model, a series of climate-smart agricultural scenarios were assessed to determine the biophysical impacts these techniques have in the Midwest United States. The first scenario extended the growing season for existing crops using future temperature and CO2 concentrations. The second scenario examined the biophysical impacts of no-till agriculture and the impacts of annually retaining crop debris. Finally, the third scenario evaluated the potential impacts that the adoption of perennial cultivars had on biophysical quantities. Each of these scenarios was found to have significant biophysical impacts. However, the timing and magnitude of the biophysical impacts differed between scenarios. © 2014 John Wiley & Sons Ltd.

  3. Atomic force microscopy of model lipid membranes.

    Science.gov (United States)

    Morandat, Sandrine; Azouzi, Slim; Beauvais, Estelle; Mastouri, Amira; El Kirat, Karim

    2013-02-01

    Supported lipid bilayers (SLBs) are biomimetic model systems that are now widely used to address the biophysical and biochemical properties of biological membranes. Two main methods are usually employed to form SLBs: the transfer of two successive monolayers by Langmuir-Blodgett or Langmuir-Schaefer techniques, and the fusion of preformed lipid vesicles. The transfer of lipid films on flat solid substrates offers the possibility to apply a wide range of surface analytical techniques that are very sensitive. Among them, atomic force microscopy (AFM) has opened new opportunities for determining the nanoscale organization of SLBs under physiological conditions. In this review, we first focus on the different protocols generally employed to prepare SLBs. Then, we describe AFM studies on the nanoscale lateral organization and mechanical properties of SLBs. Lastly, we survey recent developments in the AFM monitoring of bilayer alteration, remodeling, or digestion, by incubation with exogenous agents such as drugs, proteins, peptides, and nanoparticles.

  4. Biophysics, Pathophysiology and Pharmacology of Ion Channel Gating Pores

    Directory of Open Access Journals (Sweden)

    Adrien eMoreau

    2014-04-01

    Full Text Available Voltage sensor domain (VSDs are a feature of voltage gated ion channel (VGICs and voltage sensitive proteins. They are composed of four transmembrane (TM segments (S1 to S4. Currents leaking through VSDs are called omega or gating pore currents.Gating pores are caused by mutations of the highly conserved positively charged amino acids in the S4 segment that disrupt interactions between the S4 segment and the gating charge transfer center (GCTC. The GCTC separates the intracellular and extracellular water crevices. The disruption of S4–GCTC interactions allows these crevices to communicate and create a fast activating and non-inactivating alternative cation-selective permeation pathway of low conductance, or a gating pore.Gating pore currents have recently been shown to cause periodic paralysis phenotypes. There is also increasing evidence that gating pores are linked to several other familial diseases. For example, gating pores in Nav1.5 and Kv7.2 channels may underlie mixed arrhythmias associated with dilated cardiomyopathy (DCM phenotypes and peripheral nerve hyperexcitability (PNH respectively. There is little evidence for the existence of gating pore blockers. Moreover, it is known that a number of toxins bind to the VSD of a specific domain of Na+ channels. These toxins may thus modulate gating pore currents. This focus on the VSD motif opens up a new area of research centered on developing molecules to treat a number of cell excitability disorders such as epilepsy, cardiac arrhythmias, and pain.The purpose of the present review is to summarize existing knowledge of the pathophysiology, biophysics, and pharmacology of gating pore currents and to serve as a guide for future studies aimed at improving our understanding of gating pores and their pathophysiological roles.

  5. Electron paramagnetic resonance biophysical radiation dosimetry with tooth enamel

    Science.gov (United States)

    Khan, Rao F. H.

    This thesis deals with advancements made in the field of Electron Paramagnetic Resonance (EPR) for biophysical dosimetry with tooth enamel for accident, emergency and retrospective radiation dose reconstruction. A methodology has been developed to measure retrospective radiation exposures in human tooth enamel. This entails novel sample preparation procedures with minimum mechanical treatment to reduce the preparation induced uncertainties, establish optimum measurement conditions inside the EPR cavity, post process the measured spectrum with functional simulation of dosimetric and other interfering signals, and reconstruct dose. By using this technique, retrospective gamma radiation exposures as low as 80 +/- 30 mGy have been successfully deciphered. The notion of dose modifier was introduced in EPR biodosimetry for low dose measurements. It has been demonstrated that by using the modified zero added dose (MZAD) technique for low radiation exposures, doses in the 100 mGy range can be easily reconstructed in teeth which were previously thought useless for EPR dosimetry. Also the use of a dose modifier makes robust dose reconstruction possible for higher radiation exposures. The EPR dosimetry technique was also developed for tooth samples extracted from rodents, which represent small tooth sizing. EPR doses in the molars, extracted from mice irradiated with whole body exposures, were reassessed and shown to be correct within the experimental uncertainty. The sensitivity of human tooth enamel for neutron irradiation, obtained from the 3 MV McMaster K. N. Van de Graaff accelerator, was also studied. For the first time this work has shown that the neutron sensitivity of the tooth enamel is approximately 1/10th of the equivalent gamma sensitivity. Parametric studies for neutron dose rate and neutron energy within the available range of the accelerator, showed no impact on the sensitivity of the tooth enamel. Therefore, tooth enamel can be used as a dosimeter for both

  6. Biophysical fitness landscapes for transcription factor binding sites.

    Directory of Open Access Journals (Sweden)

    Allan Haldane

    2014-07-01

    Full Text Available Phenotypic states and evolutionary trajectories available to cell populations are ultimately dictated by complex interactions among DNA, RNA, proteins, and other molecular species. Here we study how evolution of gene regulation in a single-cell eukaryote S. cerevisiae is affected by interactions between transcription factors (TFs and their cognate DNA sites. Our study is informed by a comprehensive collection of genomic binding sites and high-throughput in vitro measurements of TF-DNA binding interactions. Using an evolutionary model for monomorphic populations evolving on a fitness landscape, we infer fitness as a function of TF-DNA binding to show that the shape of the inferred fitness functions is in broad agreement with a simple functional form inspired by a thermodynamic model of two-state TF-DNA binding. However, the effective parameters of the model are not always consistent with physical values, indicating selection pressures beyond the biophysical constraints imposed by TF-DNA interactions. We find little statistical support for the fitness landscape in which each position in the binding site evolves independently, indicating that epistasis is common in the evolution of gene regulation. Finally, by correlating TF-DNA binding energies with biological properties of the sites or the genes they regulate, we are able to rule out several scenarios of site-specific selection, under which binding sites of the same TF would experience different selection pressures depending on their position in the genome. These findings support the existence of universal fitness landscapes which shape evolution of all sites for a given TF, and whose properties are determined in part by the physics of protein-DNA interactions.

  7. Biophysical fitness landscapes for transcription factor binding sites.

    Science.gov (United States)

    Haldane, Allan; Manhart, Michael; Morozov, Alexandre V

    2014-07-01

    Phenotypic states and evolutionary trajectories available to cell populations are ultimately dictated by complex interactions among DNA, RNA, proteins, and other molecular species. Here we study how evolution of gene regulation in a single-cell eukaryote S. cerevisiae is affected by interactions between transcription factors (TFs) and their cognate DNA sites. Our study is informed by a comprehensive collection of genomic binding sites and high-throughput in vitro measurements of TF-DNA binding interactions. Using an evolutionary model for monomorphic populations evolving on a fitness landscape, we infer fitness as a function of TF-DNA binding to show that the shape of the inferred fitness functions is in broad agreement with a simple functional form inspired by a thermodynamic model of two-state TF-DNA binding. However, the effective parameters of the model are not always consistent with physical values, indicating selection pressures beyond the biophysical constraints imposed by TF-DNA interactions. We find little statistical support for the fitness landscape in which each position in the binding site evolves independently, indicating that epistasis is common in the evolution of gene regulation. Finally, by correlating TF-DNA binding energies with biological properties of the sites or the genes they regulate, we are able to rule out several scenarios of site-specific selection, under which binding sites of the same TF would experience different selection pressures depending on their position in the genome. These findings support the existence of universal fitness landscapes which shape evolution of all sites for a given TF, and whose properties are determined in part by the physics of protein-DNA interactions.

  8. The Colorado Plateau II: biophysical, socioeconomic, and cultural research

    Science.gov (United States)

    Mattson, David J.; van Riper, Charles

    2005-01-01

    The publication of The Colorado Plateau: Cultural, Biological, and Physical Research in 2004 marked a timely summation of current research in the Four Corners states. This new volume, derived from the seventh Biennial Conference on the Colorado Plateau in 2003, complements the previous book by focusing on the integration of science into resource management issues. The 32 chapters range in content from measuring human impacts on cultural resources, through grazing and the wildland-urban interface issues, to parameters of climate change on the Plateau. The book also introduces economic perspectives by considering shifting patterns and regional disparities in the Colorado Plateau economy. A series of chapters on mountain lions explores the human-wildland interface. These chapters deal with the entire spectrum of challenges associated with managing this large mammal species in Arizona and on the Colorado Plateau, conveying a wealth of timely information of interest to wildlife managers and enthusiasts. Another provocative set of chapters on biophysical resources explores the management of forest restoration, from the micro scale all the way up to large-scale GIS analyses of ponderosa pine ecosystems on the Colorado Plateau. Given recent concerns for forest health in the wake of fires, severe drought, and bark-beetle infestation, these chapters will prove enlightening for forest service, park service, and land management professionals at both the federal and state level, as well as general readers interested in how forest management practices will ultimately affect their recreation activities. With broad coverage that touches on topics as diverse as movement patterns of rattlesnakes, calculating watersheds, and rescuing looted rockshelters, this volume stands as a compendium of cutting-edge research on the Colorado Plateau that offers a wealth of insights for many scholars.

  9. Biophysical Assessment and Predicted Thermophysiologic Effects of Body Armor.

    Directory of Open Access Journals (Sweden)

    Adam W Potter

    Full Text Available Military personnel are often required to wear ballistic protection in order to defend against enemies. However, this added protection increases mass carried and imposes additional thermal burden on the individual. Body armor (BA is known to reduce combat casualties, but the effects of BA mass and insulation on the physical performance of soldiers are less well documented. Until recently, the emphasis has been increasing personal protection, with little consideration of the adverse impacts on human performance.The purpose of this work was to use sweating thermal manikin and mathematical modeling techniques to quantify the tradeoff between increased BA protection, the accompanying mass, and thermal effects on human performance.Using a sweating thermal manikin, total insulation (IT, clo and vapor permeability indexes (im were measured for a baseline clothing ensemble with and without one of seven increasingly protective U.S. Army BA configurations. Using mathematical modeling, predictions were made of thermal impact on humans wearing each configuration while working in hot/dry (desert, hot/humid (jungle, and temperate environmental conditions.In nearly still air (0.4 m/s, IT ranged from 1.57 to 1.63 clo and im from 0.35 to 0.42 for the seven BA conditions, compared to IT and im values of 1.37 clo and 0.45 respectively, for the baseline condition (no BA.Biophysical assessments and predictive modeling show a quantifiable relationship exists among increased protection and increased thermal burden and decreased work capacity. This approach enables quantitative analysis of the tradeoffs between ballistic protection, thermal-work strain, and physical work performance.

  10. Mechanisms of Soil Aggregation: a biophysical modeling framework

    Science.gov (United States)

    Ghezzehei, T. A.; Or, D.

    2016-12-01

    Soil aggregation is one of the main crosscutting concepts in all sub-disciplines and applications of soil science from agriculture to climate regulation. The concept generally refers to adhesion of primary soil particles into distinct units that remain stable when subjected to disruptive forces. It is one of the most sensitive soil qualities that readily respond to disturbances such as cultivation, fire, drought, flooding, and changes in vegetation. These changes are commonly quantified and incorporated in soil models indirectly as alterations in carbon content and type, bulk density, aeration, permeability, as well as water retention characteristics. Soil aggregation that is primarily controlled by organic matter generally exhibits hierarchical organization of soil constituents into stable units that range in size from a few microns to centimeters. However, this conceptual model of soil aggregation as the key unifying mechanism remains poorly quantified and is rarely included in predictive soil models. Here we provide a biophysical framework for quantitative and predictive modeling of soil aggregation and its attendant soil characteristics. The framework treats aggregates as hotspots of biological, chemical and physical processes centered around roots and root residue. We keep track of the life cycle of an individual aggregate from it genesis in the rhizosphere, fueled by rhizodeposition and mediated by vigorous microbial activity, until its disappearance when the root-derived resources are depleted. The framework synthesizes current understanding of microbial life in porous media; water holding and soil binding capacity of biopolymers; and environmental controls on soil organic matter dynamics. The framework paves a way for integration of processes that are presently modeled as disparate or poorly coupled processes, including storage and protection of carbon, microbial activity, greenhouse gas fluxes, movement and storage of water, resistance of soils against

  11. Biophysical Assessment and Predicted Thermophysiologic Effects of Body Armor.

    Science.gov (United States)

    Potter, Adam W; Gonzalez, Julio A; Karis, Anthony J; Xu, Xiaojiang

    2015-01-01

    Military personnel are often required to wear ballistic protection in order to defend against enemies. However, this added protection increases mass carried and imposes additional thermal burden on the individual. Body armor (BA) is known to reduce combat casualties, but the effects of BA mass and insulation on the physical performance of soldiers are less well documented. Until recently, the emphasis has been increasing personal protection, with little consideration of the adverse impacts on human performance. The purpose of this work was to use sweating thermal manikin and mathematical modeling techniques to quantify the tradeoff between increased BA protection, the accompanying mass, and thermal effects on human performance. Using a sweating thermal manikin, total insulation (IT, clo) and vapor permeability indexes (im) were measured for a baseline clothing ensemble with and without one of seven increasingly protective U.S. Army BA configurations. Using mathematical modeling, predictions were made of thermal impact on humans wearing each configuration while working in hot/dry (desert), hot/humid (jungle), and temperate environmental conditions. In nearly still air (0.4 m/s), IT ranged from 1.57 to 1.63 clo and im from 0.35 to 0.42 for the seven BA conditions, compared to IT and im values of 1.37 clo and 0.45 respectively, for the baseline condition (no BA). Biophysical assessments and predictive modeling show a quantifiable relationship exists among increased protection and increased thermal burden and decreased work capacity. This approach enables quantitative analysis of the tradeoffs between ballistic protection, thermal-work strain, and physical work performance.

  12. Gravitropism of cucumber hypocotyls: biophysical mechanism of altered growth

    Science.gov (United States)

    Cosgrove, D. J.

    1990-01-01

    The biophysical basis for the changes in cell elongation rate during gravitropism was examined in aetiolated cucumber (Cucumis sativus L.) hypocotyls. Bulk osmotic pressures on the two sides of the stem and in the epidermal cells were not altered during the early time course of gravitropism. By the pressure-probe technique, a small increase in turgor (0.3 bar, 30 kPa) was detected on the upper (inhibited) side, whereas there was a negligible decrease in turgor on the lower (stimulated) side. These small changes in turgor and water potential appeared to be indirect, passive consequences of the altered growth and the small resistance for water movement from the xylem, and indicated that the change in growth was principally due to changes in wall properties. The results indicate that the hydraulic conductance of the water-transport pathway was large (.25 h-1 bar-1) and the water potential difference supporting cell expansion was no greater than 0.3 bar (30 kPa). From pressure-block experiments, it appeared that upon gravitropic stimulation (1) the yield threshold of the lower half of the stem did not decrease and (2) the wall on the upper side of the stem was not made more rigid by a cross-linking process. Mechanical measurements of the stress/strain properties of the walls showed that the initial development of gravitropism did not involve an alteration of the mechanical behaviour of the isolated walls. Thus, gravitropism in cucumber hypocotyls occurs principally by an alteration of the wall relaxation process, without a necessary change in wall mechanical properties.

  13. Derivation of global vegetation biophysical parameters from EUMETSAT Polar System

    Science.gov (United States)

    García-Haro, Francisco Javier; Campos-Taberner, Manuel; Muñoz-Marí, Jordi; Laparra, Valero; Camacho, Fernando; Sánchez-Zapero, Jorge; Camps-Valls, Gustau

    2018-05-01

    This paper presents the algorithm developed in LSA-SAF (Satellite Application Facility for Land Surface Analysis) for the derivation of global vegetation parameters from the AVHRR (Advanced Very High Resolution Radiometer) sensor on board MetOp (Meteorological-Operational) satellites forming the EUMETSAT (European Organization for the Exploitation of Meteorological Satellites) Polar System (EPS). The suite of LSA-SAF EPS vegetation products includes the leaf area index (LAI), the fractional vegetation cover (FVC), and the fraction of absorbed photosynthetically active radiation (FAPAR). LAI, FAPAR, and FVC characterize the structure and the functioning of vegetation and are key parameters for a wide range of land-biosphere applications. The algorithm is based on a hybrid approach that blends the generalization capabilities offered by physical radiative transfer models with the accuracy and computational efficiency of machine learning methods. One major feature is the implementation of multi-output retrieval methods able to jointly and more consistently estimate all the biophysical parameters at the same time. We propose a multi-output Gaussian process regression (GPRmulti), which outperforms other considered methods over PROSAIL (coupling of PROSPECT and SAIL (Scattering by Arbitrary Inclined Leaves) radiative transfer models) EPS simulations. The global EPS products include uncertainty estimates taking into account the uncertainty captured by the retrieval method and input errors propagation. A sensitivity analysis is performed to assess several sources of uncertainties in retrievals and maximize the positive impact of modeling the noise in training simulations. The paper discusses initial validation studies and provides details about the characteristics and overall quality of the products, which can be of interest to assist the successful use of the data by a broad user's community. The consistent generation and distribution of the EPS vegetation products will

  14. Biophysical landscape interactions: Bridging disciplines and scale with connectivity

    Science.gov (United States)

    van der Ploeg, Martine; Baartman, Jantiene; Robinson, David

    2017-04-01

    The combination of climate change, population growth and soil threats, such as carbon loss, biodiversity decline or erosion amongst others , increasingly confront the global community [1]. One of the major challenges in studying processes involved in soil threats, landscape resilience, ecosystem stability, sustainable land management and the economic consequences, is that it is an interdisciplinary field [2], that needs less stringent scientific disciplinary boundaries [3]. As a result of disciplinary focus, ambiguity may arise on the understanding of landscape interactions, and this is especially true in the interaction between a landscape's physical and biological processes [4]. Another important aspect in biophysical landscape interactions are the differences in scale related to the various processes that play a role in these systems. While scaling of environmental processes is possible, as long as the phenomena at hand can be described by the same set of differential equations [5], biophysical landscape interactions pose problems for scaling approaches. Landscape position and land use impact the coupled processes in soil and vegetation. Differences in micro-behavior, driven by the interplay of heterogeneous soil and vegetation dynamics, impact emergent characteristics across a landscape. A complicating factor is the response of vegetation to changing environmental conditions, including a possible and often unknown time-lag. By altering soil conditions, plants may leave an imprint in the landscape that remains even after vegetation has disappeared due to e.g. drought, wildfire or overgrazing. Plants also respond biochemically to their environment, while the models used for hydrology are often based on physical interactions. Gene-expression and genotype adaptation may further complicate our modelling efforts in for example climate change impacts. What are we missing by not having more connectivity in our thinking, and what we can solve? We think that integrated

  15. Biophysical Properties of Irradiated Erythrocytes and Role of Antioxidants

    International Nuclear Information System (INIS)

    Eman Mohammed Elbakrawy, E.M.

    2010-01-01

    Irradiation of blood and blood components with gamma-irradiation is recommended for the inactivation of T-lymphocytes and prevention of transfusion-associated graft versus host diseases. The aim of the present work is to ensure that the currently applied irradiation dose 25 Gy is a safe dose based on the study of the electrical behavior, rheological properties, membrane solubilization, membrane hemolysis and scanning electron microscope of stored erythrocytes. In addition it aims to study the possibility of increasing the irradiation doses to 50 and 100 Gy. Moreover Alpha lipoic acid (a potent natural antioxidant) was added to the stored erythrocytes before irradiation for radioprotection. Irradiation of erythrocytes with 25 Gy did not show significant changes for the calculated dielectric parameters. However, increasing the irradiation doses resulted in significant decrease in the calculated dielectric parameters reflecting the damaging effects of radiation on the membrane structure. The obtained results showed that α lipoic acid can play an important role in minimizing the radiation-induced damage to the erythrocytes and conserve their electrical properties. There were non-significant changes in viscosity after exposure to 25 Gy, while a significant increase at 50 Gy and a significant decrease at 100 Gy were observed. The study found that α lipoic acid (ALA) resulted in non-significant change in viscosity after exposure to 50 Gy and 100 Gy. A significant increase in the yield stress was observed after exposure to 25 and 50 Gy while at 100 Gy, the yield stress showed a remarkable decrease. Addition of .-lipoic acid before irradiation resulted in non-significant changes in the yield stress at doses 25, 50, 100 Gy.The obtained results of the average membrane solubilization (D 50 ) and the average membrane hemolysis (H 50 ) showed non-significant change at 25 Gy; while an observable decrease was observed at 50 Gy and 100 Gy. The addition of lipoic acid did not

  16. A combined kinetic push and thermodynamic pull as driving forces for outer membrane protein sorting and folding in bacteria.

    Science.gov (United States)

    Fleming, Karen G

    2015-10-05

    In vitro folding studies of outer membrane beta-barrels have been invaluable in revealing the lipid effects on folding rates and efficiencies as well as folding free energies. Here, the biophysical results are summarized, and these kinetic and thermodynamic findings are considered in terms of the requirements for folding in the context of the cellular environment. Because the periplasm lacks an external energy source the only driving forces for sorting and folding available within this compartment are binding or folding free energies and their associated rates. These values define functions for periplasmic chaperones and suggest a biophysical mechanism for the BAM complex. © 2015 The Author(s).

  17. Coiled-coil oligomerization controls localization of the plasma membrane REMORINs.

    Science.gov (United States)

    Martinez, Denis; Legrand, Anthony; Gronnier, Julien; Decossas, Marion; Gouguet, Paul; Lambert, Olivier; Berbon, Mélanie; Verron, Loris; Grélard, Axelle; Germain, Veronique; Loquet, Antoine; Mongrand, Sébastien; Habenstein, Birgit

    2018-02-23

    REMORINs are nanodomain-organized proteins located in the plasma membrane and involved in cellular responses in plants. The dynamic assembly of the membrane nanodomains represents an essential tool of the versatile membrane barriers to control and modulate cellular functions. Nevertheless, the assembly mechanisms and protein organization strategies of nanodomains are poorly understood and many structural aspects are difficult to visualize. Using an ensemble of biophysical approaches, including solid-state nuclear magnetic resonance, cryo-electron microscopy and in vivo confocal imaging, we provide first insights on the role and the structural mechanisms of REMORIN trimerization. Our results suggest that the formation of REMORIN coiled-coil trimers is essential for membrane recruitment and promotes REMORIN assembly in vitro into long filaments by trimer-trimer interactions that might participate in nanoclustering into membrane domains in vivo. Copyright © 2018. Published by Elsevier Inc.

  18. Self-assembly of nanoscale particles with biosurfactants and membrane scaffold proteins.

    Science.gov (United States)

    Faas, Ramona; Pohle, Annelie; Moß, Karin; Henkel, Marius; Hausmann, Rudolf

    2017-12-01

    Nanodiscs are membrane mimetics which may be used as tools for biochemical and biophysical studies of a variety of membrane proteins. These nanoscale structures are composed of a phospholipid bilayer held together by an amphipathic membrane scaffold protein (MSP). In the past, nanodiscs were successfully assembled with membrane scaffold protein 1D1 and 1,2-dipalmitoyl- sn -glycero-3-phosphorylcholine with a homogeneous diameter of ∼10 nm. In this study, the formation of nanoscale particles from MSP1D1 and rhamnolipid biosurfactants is investigated. Different protein to lipid ratios of 1:80, 1:90 and 1:100 were used for the assembly reaction, which were consecutively separated, purified and analyzed by size-exclusion chromatography (SEC) and dynamic light scattering (DLS). Size distributions were measured to determine homogeneity and confirm size dimensions. In this study, first evidence is presented on the formation of nanoscale particles with rhamnolipid biosurfactants and membrane scaffold proteins.

  19. Fluorescence correlation spectroscopy for the characterization of membranes : A short review

    Directory of Open Access Journals (Sweden)

    Hwang, L.C.

    2002-01-01

    Full Text Available Fluorescence correlation spectroscopy (FCS is a highly sensitive fluorescence microscopy technique that can be used to probe a wide range of biophysical processes including diffusion, Ligand-receptor binding and molecular aggregation on artificial and cell membranes. FCS is able to measure very small volumes at nanomolar concentrations. In this work, we review the different types of diffusion on cell membranes,describe the theory of FCS and illustrate several of its applications for the characterization of membranes and membrane associated proteins. For comparison with other techniques we discuss the differences of FCS and fluorescence recovery after photobleaching (FRAP,a widely used technique for diffusion measurements on membranes, in detail

  20. Cell-geometry-dependent changes in plasma membrane order direct stem cell signalling and fate.

    Science.gov (United States)

    von Erlach, Thomas C; Bertazzo, Sergio; Wozniak, Michele A; Horejs, Christine-Maria; Maynard, Stephanie A; Attwood, Simon; Robinson, Benjamin K; Autefage, Hélène; Kallepitis, Charalambos; Del Río Hernández, Armando; Chen, Christopher S; Goldoni, Silvia; Stevens, Molly M

    2018-03-01

    Cell size and shape affect cellular processes such as cell survival, growth and differentiation 1-4 , thus establishing cell geometry as a fundamental regulator of cell physiology. The contributions of the cytoskeleton, specifically actomyosin tension, to these effects have been described, but the exact biophysical mechanisms that translate changes in cell geometry to changes in cell behaviour remain mostly unresolved. Using a variety of innovative materials techniques, we demonstrate that the nanostructure and lipid assembly within the cell plasma membrane are regulated by cell geometry in a ligand-independent manner. These biophysical changes trigger signalling events involving the serine/threonine kinase Akt/protein kinase B (PKB) that direct cell-geometry-dependent mesenchymal stem cell differentiation. Our study defines a central regulatory role by plasma membrane ordered lipid raft microdomains in modulating stem cell differentiation with potential translational applications.

  1. Red Blood Cell Susceptibility to Pneumolysin: CORRELATION WITH MEMBRANE BIOCHEMICAL AND PHYSICAL PROPERTIES.

    Science.gov (United States)

    Bokori-Brown, Monika; Petrov, Peter G; Khafaji, Mawya A; Mughal, Muhammad K; Naylor, Claire E; Shore, Angela C; Gooding, Kim M; Casanova, Francesco; Mitchell, Tim J; Titball, Richard W; Winlove, C Peter

    2016-05-06

    This study investigated the effect of the biochemical and biophysical properties of the plasma membrane as well as membrane morphology on the susceptibility of human red blood cells to the cholesterol-dependent cytolysin pneumolysin, a key virulence factor of Streptococcus pneumoniae, using single cell studies. We show a correlation between the physical properties of the membrane (bending rigidity and surface and dipole electrostatic potentials) and the susceptibility of red blood cells to pneumolysin-induced hemolysis. We demonstrate that biochemical modifications of the membrane induced by oxidative stress, lipid scrambling, and artificial cell aging modulate the cell response to the toxin. We provide evidence that the diversity of response to pneumolysin in diabetic red blood cells correlates with levels of glycated hemoglobin and that the mechanical properties of the red blood cell plasma membrane are altered in diabetes. Finally, we show that diabetic red blood cells are more resistant to pneumolysin and the related toxin perfringolysin O relative to healthy red blood cells. Taken together, these studies indicate that the diversity of cell response to pneumolysin within a population of human red blood cells is influenced by the biophysical and biochemical status of the plasma membrane and the chemical and/or oxidative stress pre-history of the cell. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  2. Magnetically controlled permeability membranes

    KAUST Repository

    Kosel, Jurgen

    2013-10-31

    A bioactive material delivery system can include a thermoresponsive polymer membrane and nanowires distributed within the thermoresponsive polymer membrane. Magnetic activation of a thermoresponsive polymer membrane can take place via altering the magnetization or dimensions of nanowires dispersed or ordered within the membrane matrix.

  3. Membrane cholesterol strongly influences confined diffusion of prestin.

    Science.gov (United States)

    Kamar, R I; Organ-Darling, L E; Raphael, R M

    2012-10-17

    Prestin is the membrane motor protein that drives outer hair cell (OHC) electromotility, a process that is essential for mammalian hearing. Prestin function is sensitive to membrane cholesterol levels, and numerous studies have suggested that prestin localizes in cholesterol-rich membrane microdomains. Previously, fluorescence recovery after photobleaching experiments were performed in HEK cells expressing prestin-GFP after cholesterol manipulations, and revealed evidence of transient confinement. To further characterize this apparent confined diffusion of prestin, we conjugated prestin to a photostable fluorophore (tetramethylrhodamine) and performed single-molecule fluorescence microscopy. Using single-particle tracking, we determined the microscopic diffusion coefficient from the full time course of the mean-squared deviation. Our results indicate that prestin undergoes diffusion in confinement regions, and that depletion of membrane cholesterol increases confinement size and decreases confinement strength. By interpreting the data in terms of a mathematical model of hop-diffusion, we quantified these cholesterol-induced changes in membrane organization. A complementary analysis of the distribution of squared displacements confirmed that cholesterol depletion reduces prestin confinement. These findings support the hypothesis that prestin function is intimately linked to membrane organization, and further promote a regulatory role for cholesterol in OHC and auditory function. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  4. Replacing natural wetlands with stormwater management facilities: Biophysical and perceived social values.

    Science.gov (United States)

    Rooney, R C; Foote, L; Krogman, N; Pattison, J K; Wilson, M J; Bayley, S E

    2015-04-15

    Urban expansion replaces wetlands of natural origin with artificial stormwater management facilities. The literature suggests that efforts to mimic natural wetlands in the design of stormwater facilities can expand the provision of ecosystem services. Policy developments seek to capitalize on these improvements, encouraging developers to build stormwater wetlands in place of stormwater ponds; however, few have compared the biophysical values and social perceptions of these created wetlands to those of the natural wetlands they are replacing. We compared four types of wetlands: natural references sites, natural wetlands impacted by agriculture, created stormwater wetlands, and created stormwater ponds. We anticipated that they would exhibit a gradient in biodiversity, ecological integrity, chemical and hydrologic stress. We further anticipated that perceived values would mirror measured biophysical values. We found higher biophysical values associated with wetlands of natural origin (both reference and agriculturally impacted). The biophysical values of stormwater wetlands and stormwater ponds were lower and indistinguishable from one another. The perceived wetland values assessed by the public differed from the observed biophysical values. This has important policy implications, as the public are not likely to perceive the loss of values associated with the replacement of natural wetlands with created stormwater management facilities. We conclude that 1) agriculturally impacted wetlands provide biophysical values equivalent to those of natural wetlands, meaning that land use alone is not a great predictor of wetland value; 2) stormwater wetlands are not a substantive improvement over stormwater ponds, relative to wetlands of natural origin; 3) stormwater wetlands are poor mimics of natural wetlands, likely due to fundamental distinctions in terms of basin morphology, temporal variation in hydrology, ground water connectivity, and landscape position; 4) these

  5. Reconstitution of lysosomal ion channels into artificial membranes.

    Science.gov (United States)

    Venturi, Elisa; Sitsapesan, Rebecca

    2015-01-01

    Ion channels that are located on intracellular organelles have always posed challenges for biophysicists seeking to measure their ion conduction, selectivity, and gating kinetics. Unlike cell surface ion channels, intracellular ion channels cannot be accessed for biophysical single-channel recordings using the patch-clamp technique while remaining in a physiological setting. Disruption of the cell is always necessary and hence experiments inevitably have a certain "artificial" nature about them. This drawback is turned to considerable advantage if the internal membranes containing the channels of interest can be isolated or if the channels can be purified because they can then be incorporated into artificial membranes of controlled composition. This approach guarantees a tight but flexible control over the biophysical and biochemical environment of the ion channel molecules. This includes the lipid composition of the membrane and the ionic solutions on both sides of the channel, thus allowing the conductance properties of the channel to be accurately measured. Since the influence of multiple unknown regulators of channel function (that could be present within the physiological membrane or in cytosolic, or intraorganelle compartments) is removed, the identification and characterization of physiological and pharmacological regulators that directly affect channel gating can also be achieved. This cannot be performed in a cellular environment. These techniques have typically been used to study the properties of channels located on endoplasmic/sarcoplasmic reticulum (ER/SR) membranes but in this chapter we describe how the techniques are also suited for ion channels of the acidic lysosomal and endolysosomal Ca(2+) stores. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. The Na+,K+/H+-antiporter Nha1 influences the plasma membrane potential of Saccharomyces cerevisiae

    Czech Academy of Sciences Publication Activity Database

    Zimmermannová, Olga; Gášková, D.; Sychrová, Hana

    2006-01-01

    Roč. 6, č. 5 (2006), s. 792-800 ISSN 1567-1356 R&D Projects: GA AV ČR(CZ) IAA5011407; GA ČR(CZ) GP204/02/D092 Institutional research plan: CEZ:AV0Z50110509 Keywords : membrane potential * Na+,K+/H+ antiporter * diS-C3(3) assay Subject RIV: BO - Biophysics Impact factor: 2.274, year: 2006

  7. Polymeric Membrane Reactors

    OpenAIRE

    José M. Sousa; Luís M. Madeira; João C. Santos; Adélio Mendes

    2008-01-01

    The aim of this chapter is the study of membrane reactors with polymeric membranes, particularly catalytic polymeric membranes. After an introduction where the main advantages and disadvantages of the use of polymeric membranes are summarised, a review of the main areas where they have been applied, integrated in chemical reactors, is presented. This excludes the field of bio-membranes processes, which is analysed in a specific chapter of this book. Particular attention is then given to model...

  8. Lifecycle of a Lipoprotein from a Biophysical Perspective

    Science.gov (United States)

    Rutledge, John C.; Huser, Thomas; Voss, John; Chan, James; Parikh, Atul

    The goal of our project was to understand how lipids and lipoproteins interact with cell membranes. This chapter will present the five major areas in which we have focused our attention on understanding how lipids and lipoproteins interact with cell membranes (Fig. 11.1): (1) triglycerides and vascular injury, (2) single lipoprotein analysis, (3) apolipoprotein E (apoE) conformation changes in the postprandial state, (4) triglyceride-rich lipoproteins (TGRLs) and endothelial cell inflammation, and (5) TGRL lipolysis products and monocyte activation. For over a hundred years, Western civilization has questioned how the food we eat translates into disease, and specifically atherosclerotic cardiovascular disease. Although most information indicates that this basic pathophysiological process is mediated through consumption of excess saturated fats, much remains unknown. After humans eat a meal, there is an elevation of triglycerides in the blood in the postprandial state. In normal individuals, triglycerides can rise after a meal by 50 to 100%. This has been documented many times in the past, including a paper by Hyson et al, (1998) [1]. In that study, normal healthy individuals were given a 40%-fat meal. Plasma triglycerides, which were modestly elevated initially, rose about 60% higher three to four hours after ingestion of the meal. Subsequently plasma triglycerides fell to baseline levels six hours after the meal. Even in these healthy individuals, a significant elevation of triglycerides was noted after ingestion of a moder ately high-fat meal.

  9. How To Tackle the Issues in Free Energy Simulations of Long Amphiphiles Interacting with Lipid Membranes: Convergence and Local Membrane Deformations

    DEFF Research Database (Denmark)

    Filipe, H. A. L.; Moreno, M. J.; Rog, T.

    2014-01-01

    One of the great challenges in membrane biophysics is to find a means to foster the transport of drugs across complex membrane structures. In this spirit, we elucidate methodological challenges associated with free energy computations of complex chainlike molecules across lipid membranes....... As an appropriate standard molecule to this end, we consider 7-nitrobenz-2-oxa-1,3-diazol-4-yl-labeled fatty amine, NBD-C-n, which is here dealt with as a homologous series with varying chain lengths. We found the membrane-water interface region to be highly sensitive to details in free energy computations. Despite...... of radius 1.7 nm from the amphiphile. Importantly, the free energy results given by PGC were found to be qualitatively consistent with experimental data, while the PGD results were not. We conclude that with long amphiphiles there is reason for concern with regard to computations of their free energy...

  10. Biophysical and ion channel functional characterization of the Torpedo californica nicotinic acetylcholine receptor in varying detergent-lipid environments

    Science.gov (United States)

    Asmar-Rovira, Guillermo A.; Asseo-García, Aloysha M.; Quesada, Orestes; Hanson, Michael A.; Nogueras, Carlos; Lasalde-Dominicci, José A.; Stevens, Raymond C.

    2009-01-01

    detergents. These results highlight the importance of careful biophysical characterization of membrane proteins for future functional or structural studies in the detergent-solubilized state. PMID:18581036

  11. Biotic games and cloud experimentation as novel media for biophysics education

    Science.gov (United States)

    Riedel-Kruse, Ingmar; Blikstein, Paulo

    2014-03-01

    First-hand, open-ended experimentation is key for effective formal and informal biophysics education. We developed, tested and assessed multiple new platforms that enable students and children to directly interact with and learn about microscopic biophysical processes: (1) Biotic games that enable local and online play using galvano- and photo-tactic stimulation of micro-swimmers, illustrating concepts such as biased random walks, Low Reynolds number hydrodynamics, and Brownian motion; (2) an undergraduate course where students learn optics, electronics, micro-fluidics, real time image analysis, and instrument control by building biotic games; and (3) a graduate class on the biophysics of multi-cellular systems that contains a cloud experimentation lab enabling students to execute open-ended chemotaxis experiments on slimemolds online, analyze their data, and build biophysical models. Our work aims to generate the equivalent excitement and educational impact for biophysics as robotics and video games have had for mechatronics and computer science, respectively. We also discuss how scaled-up cloud experimentation systems can support MOOCs with true lab components and life-science research in general.

  12. Functional and biophysical studies on four ceratoplatanins from the fungus Moniliophthora perniciosa, causal agent of the Witche's broom disease

    International Nuclear Information System (INIS)

    Barsottini, M.; Zaparoli, G.; Garcia, O.; Pereira, G.A.G.; Oliveira, J.F.; Tiezzi, H.O.; Ambrosio, A.L.B.; Dias, S.M.G.

    2012-01-01

    Full text: Ceratoplatanin (CP) is a secreted protein of 12.4 kDa initially identified in culture filtrates of the disease ascomycete Ceratocystis fimbriata f. sp. platani, etiological agent of the canker stain disease. CP is also the founding member of the namesake protein family, which contains fungal-secreted proteins involved in various stages of the host-fungus interaction and may act as phytotoxins or elicitors of defense response. Besides the low molecular weight, CPs have a high percentage of hydrophobic residues and share two conserved intramolecular disulfide bonds. It has been suggested that CPs have important physiological functions, including interaction with cell wall or cell membrane and manipulation of the host's defense system. Furthermore, a recent work showed that the ceratoplatanin from C. fimbriata has some degree of affinity for the saccharide 4-N-acetylglucosamine. However, its precise molecular function remains elusive. Five putative CPs have been identified in Moniliophthora perniciosa a basidiomycete fungus responsible for great economic losses in cocoa industry in the form of Witches' broom disease (WBD) , four of which had their crystal structures resolved by our group. In this work we report biophysical and functional studies on these MpCPs aiming at understanding their role and importance during the WBD progression. (author)

  13. “Exosomics”—A Review of Biophysics, Biology and Biochemistry of Exosomes With a Focus on Human Breast Milk

    Directory of Open Access Journals (Sweden)

    Carolina de la Torre Gomez

    2018-03-01

    Full Text Available Exosomes are biomolecular nanostructures released from cells. They carry specific biomolecular information and are mainly researched for their exquisite properties as a biomarker source and delivery system. We introduce exosomes in the context of other extracellular vesicles, describe their biophysical isolation and characterisation and discuss their biochemical profiling. Motivated by our interest in early-life nutrition and health, and corresponding studies enrolling lactating mothers and their infants, we zoom into exosomes derived from human breast milk. We argue that these should be more extensively studied at proteomic and micronutrient profiling level, because breast milk exosomes provide a more specific window into breast milk quality from an immunological (proteomics and nutritional (micronutrient perspective. Such enhanced breast milk exosome profiling would thereby complement and enrich the more classical whole breast milk analysis and is expected to deliver more functional insights than the rather descriptive analysis of human milk, or larger fractions thereof, such as milk fat globule membrane. We substantiate our arguments by a bioinformatic analysis of two published proteomic data sets of human breast milk exosomes.

  14. Sheet Membrane Spacesuit Water Membrane Evaporator

    Science.gov (United States)

    Bue, Grant; Trevino, Luis; Zapata, Felipe; Dillion, Paul; Castillo, Juan; Vonau, Walter; Wilkes, Robert; Vogel, Matthew; Frodge, Curtis

    2013-01-01

    A document describes a sheet membrane spacesuit water membrane evaporator (SWME), which allows for the use of one common water tank that can supply cooling water to the astronaut and to the evaporator. Test data showed that heat rejection performance dropped only 6 percent after being subjected to highly contaminated water. It also exhibited robustness with respect to freezing and Martian atmospheric simulation testing. Water was allowed to freeze in the water channels during testing that simulated a water loop failure and vapor backpressure valve failure. Upon closing the backpressure valve and energizing the pump, the ice eventually thawed and water began to flow with no apparent damage to the sheet membrane. The membrane evaporator also serves to de-gas the water loop from entrained gases, thereby eliminating the need for special degassing equipment such as is needed by the current spacesuit system. As water flows through the three annular water channels, water evaporates with the vapor flowing across the hydrophobic, porous sheet membrane to the vacuum side of the membrane. The rate at which water evaporates, and therefore, the rate at which the flowing water is cooled, is a function of the difference between the water saturation pressure on the water side of the membrane, and the pressure on the vacuum side of the membrane. The primary theory is that the hydrophobic sheet membrane retains water, but permits vapor pass-through when the vapor side pressure is less than the water saturation pressure. This results in evaporative cooling of the remaining water.

  15. Biophysical characterization and functional studies on calbindin-D28K: A vitamin D-induced calcium-binding protein

    International Nuclear Information System (INIS)

    Leathers, V.L.

    1989-01-01

    Vitamin D dependent calcium binding protein, or calbindin-D, is the principal protein induced in the intestine in response to the steroid hormone 1,25(OH) 2 -vitamin D 3 . A definitive role for calbindin-D in vitamin D 3 mediated biological responses remains unclear. Biophysical and functional studies on chick intestinal calbindin-D 28K (CaBP) were initiated so that some insight might be gained into its relevance to the process of intestinal calcium transport. Calbindin-D belongs to a class of high affinity calcium binding proteins which includes calmodulin, parvalbumin and troponin C. The Ca 2+ binding stoichiometry and binding constants for calbindin-D 28K were quantitated by Quin 2 titration analysis. The protein was found to bind 5-6 Ca 2+ ions with a K D on the order of 10 -8 , in agreement with the 6 domains identified from the amino acid sequence. A slow Ca 2+ exchange rate (80 s -1 ) as assessed by 43 Ca NMR and extensive calcium dependent conformational changes in 1 H NMR spectra were also observed. Functional studies on chick intestinal CaBP were carried out by two different methods. Interactions between CaBP and intestinal cellular components were assessed via photoaffinity labeling techniques. Specific calcium dependent complexes for CaBP were identified with bovine intestinal alkaline phosphatase and brush border membrane proteins of 60 and 150 kD. CaBP was also found to co-migrate with the alkaline phosphatase activity of chick intestinal brush border membranes as evaluated by gel filtration chromatography. The second procedure for evaluating CaBP functionality has involved the quantitation of CaBP association with vesicular transport components as assessed by ELISA. CaBP, immunoreactivity was observed in purified lysosomes, microsomes and microtubules

  16. Effect of ambient light on the time needed to complete a fetal biophysical profile: A randomized controlled trial.

    Science.gov (United States)

    Said, Heather M; Gupta, Shweta; Vricella, Laura K; Wand, Katy; Nguyen, Thinh; Gross, Gilad

    2017-10-01

    The objective of this study is to determine whether ambient light serves as a fetal stimulus to decrease the amount of time needed to complete a biophysical profile. This is a randomized controlled trial of singleton gestations undergoing a biophysical profile. Patients were randomized to either ambient light or a darkened room. The primary outcome was the time needed to complete the biophysical profile. Secondary outcomes included total and individual component biophysical profile scores and scores less than 8. A subgroup analysis of different maternal body mass indices was also performed. 357 biophysical profile studies were analyzed. 182 studies were performed with ambient light and 175 were performed in a darkened room. There was no difference in the median time needed to complete the biophysical profile based on exposure to ambient light (6.1min in darkened room versus 6.6min with ambient light; P=0.73). No difference was found in total or individual component biophysical profile scores. Subgroup analysis by maternal body mass index did not demonstrate shorter study times with ambient light exposure in women who were normal weight, overweight or obese. Ambient light exposure did not decrease the time needed to complete the biophysical profile. There was no evidence that ambient light altered fetal behavior observed during the biophysical profile. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Biophysical Adaptations of Prokaryotic Voltage-Gated Sodium Channels.

    Science.gov (United States)

    Vien, T N; DeCaen, P G

    2016-01-01

    This chapter describes the adaptive features found in voltage-gated sodium channels (NaVs) of prokaryotes and eukaryotes. These two families are distinct, having diverged early in evolutionary history but maintain a surprising degree of convergence in function. While prokaryotic NaVs are required for growth and motility, eukaryotic NaVs selectively conduct fast electrical currents for short- and long-range signaling across cell membranes in mammalian organs. Current interest in prokaryotic NaVs is stoked by their resolved high-resolution structures and functional features which are reminiscent of eukaryotic NaVs. In this chapter, comparisons between eukaryotic and prokaryotic NaVs are made to highlight the shared and unique aspects of ion selectivity, voltage sensitivity, and pharmacology. Examples of prokaryotic and eukaryotic NaV convergent evolution will be discussed within the context of their structural features. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Voltage-Sensitive Ion Channels Biophysics of Molecular Excitability

    CERN Document Server

    Leuchtag, H. Richard

    2008-01-01

    Voltage-sensitive ion channels are macromolecules embedded in the membranes of nerve and muscle fibers of animals. Because of their physiological functions, biochemical structures and electrical switching properties, they are at an intersection of biology, chemistry and physics. Despite decades of intensive research under the traditional approach of gated structural pores, the relation between the structure of these molecules and their function remains enigmatic. This book critically examines physically oriented approaches not covered in other ion-channel books. It looks at optical and thermal as well as electrical data, and at studies in the frequency domain as well as in the time domain. Rather than presenting the reader with only an option of mechanistic models at an inappropriate pseudo-macroscopic scale, it emphasizes concepts established in organic chemistry and condensed state physics. The book’s approach to the understanding of these unique structures breaks with the unproven view of ion channels as...

  19. Surface code—biophysical signals for apoptotic cell clearance

    International Nuclear Information System (INIS)

    Biermann, Mona; Maueröder, Christian; Brauner, Jan M; Chaurio, Ricardo; Herrmann, Martin; Muñoz, Luis E; Janko, Christina

    2013-01-01

    Apoptotic cell death and the clearance of dying cells play an important and physiological role in embryonic development and normal tissue turnover. In contrast to necrosis, apoptosis proceeds in an anti-inflammatory manner. It is orchestrated by the timed release and/or exposure of so-called ‘find-me’, ‘eat me’ and ‘tolerate me’ signals. Mononuclear phagocytes are attracted by various ‘find-me’ signals, including proteins, nucleotides, and phospholipids released by the dying cell, whereas the involvement of granulocytes is prevented via ‘stay away’ signals. The exposure of anionic phospholipids like phosphatidylserine (PS) by apoptotic cells on the outer leaflet of the plasma membrane is one of the main ‘eat me’ signals. PS is recognized by a number of innate receptors as well as by soluble bridging molecules on the surface of phagocytes. Importantly, phagocytes are able to discriminate between viable and apoptotic cells both exposing PS. Due to cytoskeleton remodeling PS has a higher lateral mobility on the surfaces of apoptotic cells thereby promoting receptor clustering on the phagocyte. PS not only plays an important role in the engulfment process, but also acts as ‘tolerate me’ signal inducing the release of anti-inflammatory cytokines by phagocytes. An efficient and fast clearance of apoptotic cells is required to prevent secondary necrosis and leakage of intracellular danger signals into the surrounding tissue. Failure or prolongation of the clearance process leads to the release of intracellular antigens into the periphery provoking inflammation and development of systemic inflammatory autoimmune disease like systemic lupus erythematosus. Here we review the current findings concerning apoptosis-inducing pathways, important players of apoptotic cell recognition and clearance as well as the role of membrane remodeling in the engulfment of apoptotic cells by phagocytes. (paper)

  20. Novel Acoustic Wave Microsystems for Biophysical Studies of Cells

    Science.gov (United States)

    Senveli, Sukru Ufuk

    biocompatible polymer, for dispensing cells into microcavities. A high frequency PCB including a matching circuit was designed for the SAW devices. 3D printed housing was also prepared for demonstrating the integration capability. Experimental results were collected first for analysis of high glycerin content in deionized water. Furthermore, polystyrene microbeads were counted with the system, and their sizes were differentiated experimentally to demonstrate the operation with solid media. Ultimately, biological cells were sensed and characterized. After tumor cells in media were transported to and trapped in microcavities, the proposed platform used SAW interaction between the substrate and the cells to extract their mechanical stiffness based on the ultrasound velocity. Measurements showed that output phase information is an indicator of the stiffness modulus of the trapped cells. Small populations of various types of cells such as MCF7, MDA-MB-231, SKBR3, and JJ012 were characterized and characteristic moduli were estimated for each cell population. In conclusion, the results indicate that high frequency stiffness modulus is a possible biomarker for aggressiveness of the tumor and that microcavity coupled SAW devices are a good candidate for non-invasive interrogation and high frequency biophysical studies of single cells. The proposed system is a successfully miniaturized ultrasonic biosensor and can be integrated with microchannels to obtain higher throughput upon refinement of the design as evidenced by the initial results with microfluidics. Improvement in performance and signal strength is also shown to be possible through matching circuits as demonstrated.

  1. Membrane protein nanoclustering as a functional unit of immune cells : from nanoscopy to single molecule dynamics

    OpenAIRE

    Torreño Piña, Juan Andrés

    2015-01-01

    Premi Extraordinari de Doctorat, promoció 2014-2015. Àmbit de Ciències State-of-the-art biophysical techniques featuring high temporal and spatial resolution have allowed for the first time the direct visualization of individual transmembrane proteins on the cell membrane. These techniques have revealed that a large amount of molecular components of the cell membrane do not organize in a random manner but they rather grouped together forming so-called clusters at the nanoscale. Moreover, t...

  2. Electrophysiological Data and the Biophysical Modelling of Local Cortical Circuits

    Directory of Open Access Journals (Sweden)

    Dimitris Pinotsis

    2014-03-01

    Full Text Available This paper shows how recordings of gamma oscillations – under different experimental conditions or from different subjects – can be combined with a class of population models called neural fields and dynamic causal modeling (DCM to distinguish among alternative hypotheses regarding cortical structure and function. This approach exploits inter-subject variability and trial-specific effects associated with modulations in the peak frequency of gamma oscillations. It draws on the computational power of Bayesian model inversion, when applied to neural field models of cortical dynamics. Bayesian model comparison allows one to adjudicate among different mechanistic hypotheses about cortical excitability, synaptic kinetics and the cardinal topographic features of local cortical circuits. It also provides optimal parameter estimates that quantify neuromodulation and the spatial dispersion of axonal connections or summation of receptive fields in the visual cortex. This paper provides an overview of a family of neural field models that have been recently implemented using the DCM toolbox of the academic freeware Statistical Parametric Mapping (SPM. The SPM software is a popular platform for analyzing neuroimaging data, used by several neuroscience communities worldwide. DCM allows for a formal (Bayesian statistical analysis of cortical network connectivity, based upon realistic biophysical models of brain responses. It is this particular feature of DCM – the unique combination of generative models with optimization techniques based upon (variational Bayesian principles – that furnishes a novel way to characterize functional brain architectures. In particular, it provides answers to questions about how the brain is wired and how it responds to different experimental manipulations. For a review of the general role of neural fields in SPM the reader can consult e.g. see [1]. Neural fields have a long and illustrious history in mathematical

  3. X-Ray structure and biophysical properties of rabbit fibroblast growth factor 1

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jihun; Blaber, Sachiko I.; Irsigler, Andre; Aspinwall, Eric; Blaber, Michael; (FSU)

    2010-01-14

    The rabbit is an important and de facto animal model in the study of ischemic disease and angiogenic therapy. Additionally, fibroblast growth factor 1 (FGF-1) is emerging as one of the most important growth factors for novel pro-angiogenic and pro-arteriogenic therapy. However, despite its significance, the fundamental biophysical properties of rabbit FGF-1, including its X-ray structure, have never been reported. Here, the cloning, crystallization, X-ray structure and determination of the biophysical properties of rabbit FGF-1 are described. The X-ray structure shows that the amino-acid differences between human and rabbit FGF-1 are solvent-exposed and therefore potentially immunogenic, while the biophysical studies identify differences in thermostability and receptor-binding affinity that distinguish rabbit FGF-1 from human FGF-1.

  4. Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution

    Science.gov (United States)

    Zur, Hadas; Tuller, Tamir

    2016-01-01

    mRNA translation is the fundamental process of decoding the information encoded in mRNA molecules by the ribosome for the synthesis of proteins. The centrality of this process in various biomedical disciplines such as cell biology, evolution and biotechnology, encouraged the development of dozens of mathematical and computational models of translation in recent years. These models aimed at capturing various biophysical aspects of the process. The objective of this review is to survey these models, focusing on those based and/or validated on real large-scale genomic data. We consider aspects such as the complexity of the models, the biophysical aspects they regard and the predictions they may provide. Furthermore, we survey the central systems biology discoveries reported on their basis. This review demonstrates the fundamental advantages of employing computational biophysical translation models in general, and discusses the relative advantages of the different approaches and the challenges in the field. PMID:27591251

  5. Materials science and biophysics applications at the ISOLDE radioactive ion beam facility

    CERN Document Server

    Wahl, U

    2011-01-01

    The ISOLDE isotope separator facility at CERN provides a variety of radioactive ion beams, currently more than 800 different isotopes from ~65 chemical elements. The radioisotopes are produced on-line by nuclear reactions from a 1.4 GeV proton beam with various types of targets, outdiffusion of the reaction products and, if possible, chemically selective ionisation, followed by 60 kV acceleration and mass separation. While ISOLDE is mainly used for nuclear and atomic physics studies, applications in materials science and biophysics account for a significant part (currently ~15%) of the delivered beam time, requested by 18 different experiments. The ISOLDE materials science and biophysics community currently consists of ~80 scientists from more than 40 participating institutes and 21 countries. In the field of materials science, investigations focus on the study of semiconductors and oxides, with the recent additions of nanoparticles and metals, while the biophysics studies address the toxicity of metal ions i...

  6. Biophysical Variation within the M1 Type of Ganglion Cell Photoreceptor

    Directory of Open Access Journals (Sweden)

    Alan J. Emanuel

    2017-10-01

    Full Text Available Intrinsically photosensitive retinal ganglion cells of the M1 type encode environmental irradiance for functions that include circadian and pupillary regulation. Their distinct role, morphology, and molecular markers indicate that they are stereotyped circuit elements, but their physiological uniformity has not been investigated in a systematic fashion. We have profiled the biophysical parameters of mouse M1s and found that extreme variation is their hallmark. Most parameters span 1–3 log units, and the full range is evident in M1s that innervate brain regions serving divergent functions. Biophysical profiles differ among cells possessing similar morphology and between neighboring M1s recorded simultaneously. Variation in each parameter is largely independent of that in others, allowing for flexible individualization. Accordingly, a common stimulus drives heterogeneous spike outputs across cells. By contrast, a population of directionally selective retinal ganglion cells appeared physiologically uniform under similar conditions. Thus, M1s lack biophysical constancy and send diverse signals downstream.

  7. Cellular normoxic biophysical markers of hydroxyurea treatment in sickle cell disease.

    Science.gov (United States)

    Hosseini, Poorya; Abidi, Sabia Z; Du, E; Papageorgiou, Dimitrios P; Choi, Youngwoon; Park, YongKeun; Higgins, John M; Kato, Gregory J; Suresh, Subra; Dao, Ming; Yaqoob, Zahid; So, Peter T C

    2016-08-23

    Hydroxyurea (HU) has been used clinically to reduce the frequency of painful crisis and the need for blood transfusion in sickle cell disease (SCD) patients. However, the mechanisms underlying such beneficial effects of HU treatment are still not fully understood. Studies have indicated a weak correlation between clinical outcome and molecular markers, and the scientific quest to develop companion biophysical markers have mostly targeted studies of blood properties under hypoxia. Using a common-path interferometric technique, we measure biomechanical and morphological properties of individual red blood cells in SCD patients as a function of cell density, and investigate the correlation of these biophysical properties with drug intake as well as other clinically measured parameters. Our results show that patient-specific HU effects on the cellular biophysical properties are detectable at normoxia, and that these properties are strongly correlated with the clinically measured mean cellular volume rather than fetal hemoglobin level.

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

    CERN Document Server

    Chung, Shin-Ho; Krishnamurthy, Vikram

    2007-01-01

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

  9. Effect of Hydrodynamic Interactions on Reaction Rates in Membranes.

    Science.gov (United States)

    Oppenheimer, Naomi; Stone, Howard A

    2017-07-25

    The Brownian motion of two particles in three dimensions serves as a model for predicting the diffusion-limited reaction rate, as first discussed by von Smoluchowski. Deutch and Felderhof extended the calculation to account for hydrodynamic interactions between the particles and the target, which results in a reduction of the rate coefficient by about half. Many chemical reactions take place in quasi-two-dimensional systems, such as on the membrane or surface of a cell. We perform a Smoluchowski-like calculation in a quasi-two-dimensional geometry, i.e., a membrane surrounded by fluid, and account for hydrodynamic interactions between the particles. We show that rate coefficients are reduced relative to the case of no interactions. The reduction is more pronounced than the three-dimensional case due to the long-range nature of two-dimensional flows. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  10. The biophysical link between climate, water, and vegetation in bioenergy agro-ecosystems

    International Nuclear Information System (INIS)

    Bagley, Justin E.; Davis, Sarah C.; Georgescu, Matei; Hussain, Mir Zaman; Miller, Jesse; Nesbitt, Stephen W.; VanLoocke, Andy; Bernacchi, Carl J.

    2014-01-01

    Land use change for bioenergy feedstocks is likely to intensify as energy demand rises simultaneously with increased pressure to minimize greenhouse gas emissions. Initial assessments of the impact of adopting bioenergy crops as a significant energy source have largely focused on the potential for bioenergy agroecosystems to provide global-scale climate regulating ecosystem services via biogeochemical processes. Such as those processes associated with carbon uptake, conversion, and storage that have the potential to reduce global greenhouse gas emissions (GHG). However, the expansion of bioenergy crops can also lead to direct biophysical impacts on climate through water regulating services. Perturbations of processes influencing terrestrial energy fluxes can result in impacts on climate and water across a spectrum of spatial and temporal scales. Here, we review the current state of knowledge about biophysical feedbacks between vegetation, water, and climate that would be affected by bioenergy-related land use change. The physical mechanisms involved in biophysical feedbacks are detailed, and interactions at leaf, field, regional, and global spatial scales are described. Locally, impacts on climate of biophysical changes associated with land use change for bioenergy crops can meet or exceed the biogeochemical changes in climate associated with rising GHG's, but these impacts have received far less attention. Realization of the importance of ecosystems in providing services that extend beyond biogeochemical GHG regulation and harvestable yields has led to significant debate regarding the viability of various feedstocks in many locations. The lack of data, and in some cases gaps in knowledge associated with biophysical and biochemical influences on land–atmosphere interactions, can lead to premature policy decisions. - Highlights: • The physical basis for biophysical impacts of expanding bioenergy agroecosystems on climate and water is described. • We

  11. Nuclear envelope remnants: fluid membranes enriched in sterols and polyphosphoinositides.

    Directory of Open Access Journals (Sweden)

    Marie Garnier-Lhomme

    Full Text Available The cytoplasm of eukaryotic cells is a highly dynamic compartment where membranes readily undergo fission and fusion to reorganize the cytoplasmic architecture, and to import, export and transport various cargos within the cell. The double membrane of the nuclear envelope that surrounds the nucleus, segregates the chromosomes from cytoplasm and regulates nucleocytoplasmic transport through pores. Many details of its formation are still unclear. At fertilization the sperm devoid of nuclear envelope pores enters the egg. Although most of the sperm nuclear envelope disassembles, remnants of the envelope at the acrosomal and centriolar fossae do not and are subsequently incorporated into the newly forming male pronuclear envelope. Remnants are conserved from annelid to mammalian sperm.Using lipid mass spectrometry and a new application of deuterium solid-state NMR spectroscopy we have characterized the lipid composition and membrane dynamics of the sperm nuclear envelope remnants in isolated sperm nuclei.We report nuclear envelope remnants are relatively fluid membranes rich in sterols, devoid of sphingomyelin, and highly enriched in polyphosphoinositides and polyunsaturated phospholipids. The localization of the polybasic effector domain of MARCKS illustrates the non-nuclear aspect of the polyphosphoinositides. Based on their atypical biophysical characteristics and phospholipid composition, we suggest a possible role for nuclear envelope remnants in membrane fusion leading to nuclear envelope assembly.

  12. Synthetic Molecular Evolution of Membrane-Active Peptides

    Science.gov (United States)

    Wimley, William

    The physical chemistry of membrane partitioning largely determines the function of membrane active peptides. Membrane-active peptides have potential utility in many areas, including in the cellular delivery of polar compounds, cancer therapy, biosensor design, and in antibacterial, antiviral and antifungal therapies. Yet, despite decades of research on thousands of known examples, useful sequence-structure-function relationships are essentially unknown. Because peptide-membrane interactions within the highly fluid bilayer are dynamic and heterogeneous, accounts of mechanism are necessarily vague and descriptive, and have little predictive power. This creates a significant roadblock to advances in the field. We are bypassing that roadblock with synthetic molecular evolution: iterative peptide library design and orthogonal high-throughput screening. We start with template sequences that have at least some useful activity, and create small, focused libraries using structural and biophysical principles to design the sequence space around the template. Orthogonal high-throughput screening is used to identify gain-of-function peptides by simultaneously selecting for several different properties (e.g. solubility, activity and toxicity). Multiple generations of iterative library design and screening have enabled the identification of membrane-active sequences with heretofore unknown properties, including clinically relevant, broad-spectrum activity against drug-resistant bacteria and enveloped viruses as well as pH-triggered macromolecular poration.

  13. Synthetic Biological Membrane (SBM)

    Data.gov (United States)

    National Aeronautics and Space Administration — The ultimate goal of the Synthetic Biological Membrane project is to develop a new type of membrane that will enable the wastewater treatment system required on...

  14. Oxygen transport membrane

    DEFF Research Database (Denmark)

    2015-01-01

    The present invention relates to a novel composite oxygen transport membrane as well as its preparation and uses thereof.......The present invention relates to a novel composite oxygen transport membrane as well as its preparation and uses thereof....

  15. Hybrid adsorptive membrane reactor

    Science.gov (United States)

    Tsotsis, Theodore T [Huntington Beach, CA; Sahimi, Muhammad [Altadena, CA; Fayyaz-Najafi, Babak [Richmond, CA; Harale, Aadesh [Los Angeles, CA; Park, Byoung-Gi [Yeosu, KR; Liu, Paul K. T. [Lafayette Hill, PA

    2011-03-01

    A hybrid adsorbent-membrane reactor in which the chemical reaction, membrane separation, and product adsorption are coupled. Also disclosed are a dual-reactor apparatus and a process using the reactor or the apparatus.

  16. Premature rupture of membranes

    Science.gov (United States)

    ... gov/ency/patientinstructions/000512.htm Premature rupture of membranes To use the sharing features on this page, ... water that surrounds your baby in the womb. Membranes or layers of tissue hold in this fluid. ...

  17. Transmembrane Signalling: Membrane messengers

    Science.gov (United States)

    Cockroft, Scott L.

    2017-05-01

    Life has evolved elaborate means of communicating essential chemical information across cell membranes. Inspired by biology, two new artificial mechanisms have now been developed that use synthetic messenger molecules to relay chemical signals into or across lipid membranes.

  18. Sphingolipid Organization in the Plasma Membrane and the Mechanisms That Influence It.

    Science.gov (United States)

    Kraft, Mary L

    2016-01-01

    Sphingolipids are structural components in the plasma membranes of eukaryotic cells. Their metabolism produces bioactive signaling molecules that modulate fundamental cellular processes. The segregation of sphingolipids into distinct membrane domains is likely essential for cellular function. This review presents the early studies of sphingolipid distribution in the plasma membranes of mammalian cells that shaped the most popular current model of plasma membrane organization. The results of traditional imaging studies of sphingolipid distribution in stimulated and resting cells are described. These data are compared with recent results obtained with advanced imaging techniques, including super-resolution fluorescence detection and high-resolution secondary ion mass spectrometry (SIMS). Emphasis is placed on the new insight into the sphingolipid organization within the plasma membrane that has resulted from the direct imaging of stable isotope-labeled lipids in actual cell membranes with high-resolution SIMS. Super-resolution fluorescence techniques have recently revealed the biophysical behaviors of sphingolipids and the unhindered diffusion of cholesterol analogs in the membranes of living cells are ultimately in contrast to the prevailing hypothetical model of plasma membrane organization. High-resolution SIMS studies also conflicted with the prevailing hypothesis, showing sphingolipids are concentrated in micrometer-scale membrane domains, but cholesterol is evenly distributed within the plasma membrane. Reductions in cellular cholesterol decreased the number of sphingolipid domains in the plasma membrane, whereas disruption of the cytoskeleton eliminated them. In addition, hemagglutinin, a transmembrane protein that is thought to be a putative raft marker, did not cluster within sphingolipid-enriched regions in the plasma membrane. Thus, sphingolipid distribution in the plasma membrane is dependent on the cytoskeleton, but not on favorable interactions with

  19. Membrane Mechanics of Primary Afferent Neurons in the Dorsal Root Ganglia of Rats.

    Science.gov (United States)

    Kanda, Hirosato; Gu, Jianguo G

    2017-04-25

    Membrane mechanics is an important biological factor regulating many cellular functions including cell motility, intercellular and intracellular signaling, gene expression, and membrane ion channel activity. Primary afferent neurons transduce sensory information about temperature, touch, and pain. These sensory functions may be profoundly affected by the states of primary afferent neuron mechanics. However, membrane mechanics of primary afferent neurons is largely unknown. In this study, we established the optical trapping technique for determining membrane mechanics of cultured primary afferent neurons of the dorsal root ganglia (DRG). We further determined the roles of cytoskeleton and membrane lipids in DRG neuron mechanics. We found that DRG neurons had a plasma membrane tension of ∼54 pN/μm, and the tension was significantly decreased to ∼29 pN/μm by cytochalasin D treatment to disrupt actin cytoskeleton and increased to ∼79 pN/μm by methyl-β-cyclodextrin treatment to sequester membrane cholesterol. DRG neuron membrane stiffness was not significantly affected by the cytoskeleton disruption but was significantly increased after cholesterol sequestration. Our findings elucidate membrane mechanical properties of primary afferent neurons, which provide, to our knowledge, a new perspective on their sensory functions. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  20. Measuring the Viscosity of the Escherichia coli Plasma Membrane Using Molecular Rotors.

    Science.gov (United States)

    Mika, Jacek T; Thompson, Alexander J; Dent, Michael R; Brooks, Nicholas J; Michiels, Jan; Hofkens, Johan; Kuimova, Marina K

    2016-10-04

    The viscosity is a highly important parameter within the cell membrane, affecting the diffusion of small molecules and, hence, controlling the rates of intracellular reactions. There is significant interest in the direct, quantitative assessment of membrane viscosity. Here we report the use of fluorescence lifetime imaging microscopy of the molecular rotor BODIPY C10 in the membranes of live Escherichia coli bacteria to permit direct quantification of the viscosity. Using this approach, we investigated the viscosity in live E. coli cells, spheroplasts, and liposomes made from E. coli membrane extracts. For live cells and spheroplasts, the viscosity was measured at both room temperature (23°C) and the E. coli growth temperature (37°C), while the membrane extract liposomes were studied over a range of measurement temperatures (5-40°C). At 37°C, we recorded a membrane viscosity in live E. coli cells of 950 cP, which is considerably higher than that previously observed in other live cell membranes (e.g., eukaryotic cells, membranes of Bacillus vegetative cells). Interestingly, this indicates that E. coli cells exhibit a high degree of lipid ordering within their liquid-phase plasma membranes. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  1. Idiopathic epiretinal membrane

    NARCIS (Netherlands)

    Bu, Shao-Chong; Kuijer, Roelof; Li, Xiao-Rong; Hooymans, Johanna M M; Los, Leonoor I

    2014-01-01

    Background: Idiopathic epiretinal membrane (iERM) is a fibrocellular membrane that proliferates on the inner surface of the retina at the macular area. Membrane contraction is an important sight-threatening event and is due to fibrotic remodeling. Methods: Analysis of the current literature

  2. Membrane contactor applications

    NARCIS (Netherlands)

    Klaassen, R.; Feron, P.H.M.; Jansen, A.

    2008-01-01

    In a membrane contactor the membrane separation is completely integrated with an extraction or absorption operation in order to exploit the benefits of both technologies fully. Membrane contactor applications that have been developed can be found in both water and gas treatment. Several recently

  3. On "spinning" membrane models

    NARCIS (Netherlands)

    Bergshoeff, E.; Sezgin, E.; Townsend, P.K.

    1988-01-01

    Several alternative actions for a bosonic membrane have recently been proposed. We show that a linearly realized locally world-volume-supersymmetric (spinning membrane) extension of any of these actions implies an analogous extension of the standard Dirac membrane action. We further show that a

  4. Meniscus Membranes For Separation

    Science.gov (United States)

    Dye, Robert C.; Jorgensen, Betty; Pesiri, David R.

    2005-09-20

    Gas separation membranes, especially meniscus-shaped membranes for gas separations are disclosed together with the use of such meniscus-shaped membranes for applications such as thermal gas valves, pre-concentration of a gas stream, and selective pre-screening of a gas stream. In addition, a rapid screening system for simultaneously screening polymer materials for effectiveness in gas separation is provided.

  5. Meniscus membranes for separations

    Science.gov (United States)

    Dye, Robert C [Irvine, CA; Jorgensen, Betty [Jemez Springs, NM; Pesiri, David R [Aliso Viejo, CA

    2004-01-27

    Gas separation membranes, especially meniscus-shaped membranes for gas separations are disclosed together with the use of such meniscus-shaped membranes for applications such as thermal gas valves, pre-concentration of a gas stream, and selective pre-screening of a gas stream. In addition, a rapid screening system for simultaneously screening polymer materials for effectiveness in gas separation is provided.

  6. Plasma membrane ATPases

    DEFF Research Database (Denmark)

    Palmgren, Michael Broberg; Bækgaard, Lone; Lopez Marques, Rosa Laura

    2011-01-01

    membrane include ABC transporters, vacuolar (V-type) H+ pumps, and P-type pumps. These pumps all utilize ATP as a fuel for energizing pumping. This review focuses on the physiological roles of plasma membrane P-type pumps, as they represent the major ATP hydrolytic activity in this membrane....

  7. Biophysics at the intersection of health science and nuclear technology

    International Nuclear Information System (INIS)

    Marquardt, D.; Alsop, R.J.; Rheinstadter, M.C.; Harroun, T.A.

    2014-01-01

    We're all on a quest for improved heart health, but what do we really know about it? A daily regimen of aspirin can help some people with heart disease. We need to lower our cholesterol, and increase our intake of omega fatty acids. There is simply no health benefit to taking extra vitamin E, and it's not known why. Apart from cardiac tests with radiopharmaceuticals, what role does nuclear technology play in this story? It turns out that cold and thermal neutrons are important tools for the biophysicists studying these topics. We will review some recently published studies that are advancing our understanding of how cholesterol, vitamin E, and aspirin all work at the molecular level, inside the membrane of our cells. These insights could not have been learned without access to research reactor neutron beams such as those at the Canadian Neutron Beam Centre, and how this new knowledge has really engaged the broader health science community into new ways of thinking about these molecules. (author)

  8. Biophysics at the intersection of health science and nuclear technology

    International Nuclear Information System (INIS)

    Marquardt, D.; Alsop, R.J.; Rheinstadter, M.C.; Harroun, T.A.

    2014-01-01

    We're all on a quest for improved heart health, but what do we really know about it? A daily regimen of aspirin can help some people with heart disease. We need to lower our cholesterol, and increase our intake of omega fatty acids. There is simply no health bene t to taking extra vitamin E, and it's not known why. Apart from cardiac tests with radiopharmaceuticals, what role does nuclear technology play in this story? It turns out that cold and thermal neutrons are important tools for the biophysicists studying these topics. We will review some recently published studies that are advancing our understanding of how cholesterol, vitamin E, and aspirin all work at the molecular level, inside the membrane of our cells. These insights could not have been learned without access to research reactor neutron beams such as those at the Canadian Neutron Beam Centre, and how this new knowledge has really engaged the broader health science community into new ways of thinking about these molecules. (author)

  9. Biophysics at the intersection of health science and nuclear technology

    Energy Technology Data Exchange (ETDEWEB)

    Marquardt, D. [Brock Univ., Dept. of Physics, St. Catharines, Ontario (Canada); Alsop, R.J.; Rheinstadter, M.C. [McMaster Univ., Dept. of Physics and Astronomy, Hamilton, Ontario (Canada); Harroun, T.A. [Brock Univ., Dept. of Physics, St. Catharines, Ontario (Canada)

    2014-12-15

    We're all on a quest for improved heart health, but what do we really know about it? A daily regimen of aspirin can help some people with heart disease. We need to lower our cholesterol, and increase our intake of omega fatty acids. There is simply no health benefit to taking extra vitamin E, and it's not known why. Apart from cardiac tests with radiopharmaceuticals, what role does nuclear technology play in this story? It turns out that cold and thermal neutrons are important tools for the biophysicists studying these topics. We will review some recently published studies that are advancing our understanding of how cholesterol, vitamin E, and aspirin all work at the molecular level, inside the membrane of our cells. These insights could not have been learned without access to research reactor neutron beams such as those at the Canadian Neutron Beam Centre, and how this new knowledge has really engaged the broader health science community into new ways of thinking about these molecules. (author)

  10. Biophysics at the intersection of health science and nuclear technology

    Energy Technology Data Exchange (ETDEWEB)

    Marquardt, D., E-mail: thad.harroun@brocku.ca [Brock Univ., Dept. of Physics, St. Catherines, Ontario (Canada); Alsop, R.J.; Rheinstadter, M.C. [McMaster Univ., Dept. of Physics and Astronomy, Hamilton, Ontario (Canada); Harroun, T.A. [Brock University, Dept. of Physics, St. Catherines, Ontario (Canada)

    2014-07-01

    We're all on a quest for improved heart health, but what do we really know about it? A daily regimen of aspirin can help some people with heart disease. We need to lower our cholesterol, and increase our intake of omega fatty acids. There is simply no health bene t to taking extra vitamin E, and it's not known why. Apart from cardiac tests with radiopharmaceuticals, what role does nuclear technology play in this story? It turns out that cold and thermal neutrons are important tools for the biophysicists studying these topics. We will review some recently published studies that are advancing our understanding of how cholesterol, vitamin E, and aspirin all work at the molecular level, inside the membrane of our cells. These insights could not have been learned without access to research reactor neutron beams such as those at the Canadian Neutron Beam Centre, and how this new knowledge has really engaged the broader health science community into new ways of thinking about these molecules. (author)

  11. Biophysical properties of the normal-sized aorta in patients with Marfan syndrome: evaluation with MR flow mapping

    NARCIS (Netherlands)

    Groenink, M.; de Roos, A.; Mulder, B. J.; Verbeeten, B.; Timmermans, J.; Zwinderman, A. H.; Spaan, J. A.; van der Wall, E. E.

    2001-01-01

    PURPOSE: To investigate the feasibility of magnetic resonance (MR) flow mapping in the assessment of aortic biophysical properties in patients with Marfan syndrome and to detect differences in biophysical properties in the normal-sized aorta distal to the aortic root between these patients and

  12. Chemoenzymatic Preparation and Biophysical Properties of Sulfated Quercetin Metabolites

    Directory of Open Access Journals (Sweden)

    Kateřina Valentová

    2017-10-01

    Full Text Available Sulfated quercetin derivatives are important authentic standards for metabolic studies. Quercetin-3′-O-sulfate, quercetin-4′-O-sulfate, and quercetin-3-O-sulfate as well as quercetin-di-O-sulfate mixture (quercetin-7,3′-di-O-sulfate, quercetin-7,4′-di-O-sulfate, and quercetin-3′,4′-di-O-sulfate were synthetized by arylsulfotransferase from Desulfitobacterium hafniense. Purified monosulfates and disulfates were fully characterized using MS and NMR and tested for their 1,1-diphenyl-2-picrylhydrazyl (DPPH, 2,2′-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid (ABTS+ and N,N-dimethyl-p-phenylenediamine (DMPD radical scavenging, Folin-Ciocalteau reduction (FCR, ferric reducing antioxidant power (FRAP, and anti-lipoperoxidant activities in rat liver microsomes damaged by tert-butylhydroperoxide. Although, as expected, the sulfated metabolites were usually less active than quercetin, they remained still effective antiradical and reducing agents. Quercetin-3′-O-sulfate was more efficient than quercetin-4′-O-sulfate in DPPH and FCR assays. In contrast, quercetin-4′-O-sulfate was the best ferric reductant and lipoperoxidation inhibitor. The capacity to scavenge ABTS+• and DMPD was comparable for all substances, except for disulfates, which were the most efficient. Quantum calculations and molecular dynamics simulations on membrane models supported rationalization of free radical scavenging and lipid peroxidation inhibition. These results clearly showed that individual metabolites of food bioactives can markedly differ in their biological activity. Therefore, a systematic and thorough investigation of all bioavailable metabolites with respect to native compounds is needed when evaluating food health benefits.

  13. Coupling the biophysical and social dimensions of wildfire risk to improve wildfire mitigation planning

    Science.gov (United States)

    Alan A. Ager; Jeffrey D. Kline; A. Paige Fisher

    2015-01-01

    We describe recent advances in biophysical and social aspects of risk and their potential combined contribution to improve mitigation planning on fire-prone landscapes. The methods and tools provide an improved method for defining the spatial extent of wildfire risk to communities compared to current planning processes. They also propose an expanded role for social...

  14. A dataset mapping the potential biophysical effects of vegetation cover change

    Science.gov (United States)

    Duveiller, Gregory; Hooker, Josh; Cescatti, Alessandro

    2018-02-01

    Changing the vegetation cover of the Earth has impacts on the biophysical properties of the surface and ultimately on the local climate. Depending on the specific type of vegetation change and on the background climate, the resulting competing biophysical processes can have a net warming or cooling effect, which can further vary both spatially and seasonally. Due to uncertain climate impacts and the lack of robust observations, biophysical effects are not yet considered in land-based climate policies. Here we present a dataset based on satellite remote sensing observations that provides the potential changes i) of the full surface energy balance, ii) at global scale, and iii) for multiple vegetation transitions, as would now be required for the comprehensive evaluation of land based mitigation plans. We anticipate that this dataset will provide valuable information to benchmark Earth system models, to assess future scenarios of land cover change and to develop the monitoring, reporting and verification guidelines required for the implementation of mitigation plans that account for biophysical land processes.

  15. Biophysical and human factors determine the distribution of poached elephants in Tsavo East National Park, Kenya

    NARCIS (Netherlands)

    Kyale, D.M.; Ngene, S.M.; Maingi, J.

    2011-01-01

    This study investigates the distribution of poached elephants as well as the biophysical and anthropogenic factors that determine the distribution of the poached elephants in Tsavo East National Park (TENP), Kenya. Data on the distribution of poached elephants, from 1990 to 2005, were acquired from

  16. Canopy-scale biophysical controls of transpiration and evaporation in the Amazon Basin

    NARCIS (Netherlands)

    Mallick, Kaniska; Trebs, Ivonne; Boegh, Eva; Giustarini, Laura; Schlerf, Martin; Drewry, Darren T.; Hoffmann, Lucien; Randow, Von Celso; Kruijt, Bart; Araùjo, Alessandro; Saleska, Scott; Ehleringer, James R.; Domingues, Tomas F.; Ometto, Jean Pierre H.B.; Nobre, Antonio D.; Luiz Leal De Moraes, Osvaldo; Hayek, Matthew; William Munger, J.; Wofsy, Steven C.

    2016-01-01

    Canopy and aerodynamic conductances (gC and gA) are two of the key land surface biophysical variables that control the land surface response of land surface schemes in climate models. Their representation is crucial for predicting transpiration (λET) and

  17. A biophysical index for predicting hydration-mediated microbial diversity in soils

    Science.gov (United States)

    Wang, G.; Or, D.

    2012-04-01

    Exploring the origins of soil microbial diversity represents an immense and uncharted scientific frontier. Progress in resolving mechanisms that promote and sustain the unparalleled soil microbial diversity found in soil requires development of process-based predictive tools that consider dynamic biophysical interactions at highly resolved spatial and temporal scales. We report a novel biophysical metric for hydration-mediated microbial coexistence in soils by integrating key biophysical variables, such as aquatic habitat size and connectivity, nutrient diffusion affecting microbial growth, and aqueous films controlling motility and dispersal, into a predictive index. Results show a surprisingly narrow range of hydration conditions (a few kPa) that mark a sharp transition from suppression (wet) to promotion (dry) of microbial diversity in unsaturated soils in agreement with limited observations and with simulation results based on individual-based models of competing populations. The framework enables systematic hypothesis testing for key factors that regulate microbial populations and affect soil bio-geochemical functions, and represents a step towards deciphering key mechanisms that support soil microbial diversity. New insights into the different roles of biophysical mechanisms in promoting soil microbial diversity enable predictions concerning microbial consortia function and bioremediation activities in soils, and may shape how we quantify microbial diversity within the context of land resources and biogeochemical cycling.

  18. Biochemical and Biophysical Cues in Matrix Design for Chronic and Diabetic Wound Treatment.

    Science.gov (United States)

    Xiao, Yun; Ahadian, Samad; Radisic, Milica

    2017-02-01

    Progress in biomaterial science and engineering and increasing knowledge in cell biology have enabled us to develop functional biomaterials providing appropriate biochemical and biophysical cues for tissue regeneration applications. Tissue regeneration is particularly important to treat chronic wounds of people with diabetes. Understanding and controlling the cellular microenvironment of the wound tissue are important to improve the wound healing process. In this study, we review different biochemical (e.g., growth factors, peptides, DNA, and RNA) and biophysical (e.g., topographical guidance, pressure, electrical stimulation, and pulsed electromagnetic field) cues providing a functional and instructive acellular matrix to heal diabetic chronic wounds. The biochemical and biophysical signals generally regulate cell-matrix interactions and cell behavior and function inducing the tissue regeneration for chronic wounds. Some technologies and devices have already been developed and used in the clinic employing biochemical and biophysical cues for wound healing applications. These technologies can be integrated with smart biomaterials to deliver therapeutic agents to the wound tissue in a precise and controllable manner. This review provides useful guidance in understanding molecular mechanisms and signals in the healing of diabetic chronic wounds and in designing instructive biomaterials to treat them.

  19. Quenching of Tryptophan Fluorescence in Unfolded Cytochrome "c": A Biophysics Experiment for Physical Chemistry Students

    Science.gov (United States)

    Schlamadinger, Diana E.; Kats, Dina I.; Kim, Judy E.

    2010-01-01

    Laboratory experiments that focus on protein folding provide excellent opportunities for undergraduate students to learn important topics in the expanding interdisciplinary field of biophysics. Here, we describe the use of Stern-Volmer plots to determine the extent of solvent accessibility of the single tryptophan residue (trp-59) in unfolded and…

  20. A multivariate decision tree analysis of biophysical factors in tropical forest fire occurrence

    Science.gov (United States)

    Rey S. Ofren; Edward Harvey

    2000-01-01

    A multivariate decision tree model was used to quantify the relative importance of complex hierarchical relationships between biophysical variables and the occurrence of tropical forest fires. The study site is the Huai Kha Kbaeng wildlife sanctuary, a World Heritage Site in northwestern Thailand where annual fires are common and particularly destructive. Thematic...

  1. Biophysical properties and functional significance of stem water storage tissues in Neotropical savanna trees.

    Science.gov (United States)

    F.G. Scholz; S.J. Bucci; G. Goldstein; F.C. Meinzer; A.C. Franco; F. Miralles-Wilhelm

    2007-01-01

    Biophysical characteristics of sapwood and outer parenchyma water storage compartments were studied in stems of eight dominant Brazilian Cerrado tree species to assess the impact of differences in tissue capacitance on whole-plant water relations. Both the sapwood and outer parenchyma tissues played an important role in regulation of internal water deficits of Cerrado...

  2. Summaries of fiscal year 1994 projects in medical applications and biophysical research

    International Nuclear Information System (INIS)

    1995-04-01

    This report provides information on the research supported in Fiscal Year 1994 by the Medical Applications and Biophysical Research Division of the Office of Health and Environmental Research. A brief statement of the scope of the following areas is presented: dosimetry; measurement science; radiological and chemical physics; structural biology; human genome; and medical applications. Summaries of the research projects in these categories are presented

  3. Canopy-scale biophysical controls on transpiration and evaporation in the Amazon Basin

    DEFF Research Database (Denmark)

    Mallick, Kaniska; Trebs, Ivonne; Bøgh, Eva

    2016-01-01

    to directly quantify the canopy-scale biophysical controls on λET and λEE over multiple plant functional types (PFTs) in the Amazon Basin. Combining data from six LBA (Large-scale Biosphere-Atmosphere Experiment in Amazonia) eddy covariance tower sites and a TR-driven physically based modeling approach, we...

  4. 6th international conference on biophysics and synchrotron radiation. Program/Abstracts

    International Nuclear Information System (INIS)

    Pittroff, Connie; Strasser, Susan Barr

    1999-01-01

    This STI product consists of the Program/Abstracts book that was prepared for the participants in the Sixth International Conference on Biophysics and Synchrotron Radiation that was held August 4-8, 1998, at the Advanced Photon Source, Argonne National Laboratory. This book contains the full conference program and abstracts of the scientific presentations

  5. Adjusting policy to institutional, cultural and biophysical context conditions: The case of conservation banking in California

    Science.gov (United States)

    Carsten Mann; James D. Absher

    2013-01-01

    This paper examines the political construction of a policy instrument for matching particular institutional, biophysical and cultural context conditions in a social–ecological system, using the case of conservation banking in California as an example. The guiding research question is: How is policy design negotiated between various actors on its way from early...

  6. 6th international conference on biophysics and synchrotron radiation. Program/Abstracts

    Energy Technology Data Exchange (ETDEWEB)

    Pittroff, Connie; Strasser, Susan Barr [lead editors

    1999-08-03

    This STI product consists of the Program/Abstracts book that was prepared for the participants in the Sixth International Conference on Biophysics and Synchrotron Radiation that was held August 4-8, 1998, at the Advanced Photon Source, Argonne National Laboratory. This book contains the full conference program and abstracts of the scientific presentations.

  7. Riparian influences on the biophysical characteristics of seston in headwater streams.

    Science.gov (United States)

    Scott R. Elliott; Robert J. Naiman; Peter A. Bisson

    2004-01-01

    Suspended particles (seston) in streams are an important source of nutrition for many invertebrates, forming a strong trophic link between plant and animal production. In forested regions the management of riparian corridors may alter alloehthonous and autochthonous contributions to streams, ultimately changing the biophysical characteristics of seston. This article...

  8. Biophysical inhibition of synthetic vs. naturally-derived pulmonary surfactant preparations by polymeric nanoparticles.

    Science.gov (United States)

    Beck-Broichsitter, Moritz; Ruppert, Clemens; Schmehl, Thomas; Günther, Andreas; Seeger, Werner

    2014-01-01

    Reasonable suspicion has accumulated that inhaled nano-scale particulate matter influences the biophysical function of the pulmonary surfactant system. Hence, it is evident to provide novel insights into the extent and mechanisms of nanoparticle-surfactant interactions in order to facilitate the fabrication of safe nanomedicines suitable for pulmonary applications. Negatively- and positively-charged poly(styrene) nanoparticles (diameters of ~100nm) served as model carriers. Nanoparticles were incubated with several synthetic and naturally-derived pulmonary surfactants to characterize the sensitivity of each preparation to biophysical inactivation. Changes in surface properties (i.e. adsorption and dynamic surface tension behavior) were monitored in a pulsating bubble surfactometer. Both nanoparticle formulations revealed a dose-dependent influence on the biophysical behavior of all investigated pulmonary surfactants. However, the surfactant sensitivity towards inhibition depended on both the carrier type, where negatively-charged nanoparticles showed increased inactivation potency compared to their positively-charged counterparts, and surfactant composition. Among the surfactants tested, synthetic mixtures (i.e. phospholipids, phospholipids supplemented with surfactant protein B, and Venticute®) were more susceptible to surface-activity inhibition as the more complex naturally-derived preparations (i.e. Alveofact® and large surfactant aggregates isolated from rabbit bronchoalveolar lavage fluid). Overall, nanoparticle characteristics and surfactant constitution both influence the extent of biophysical inhibition of pulmonary surfactants. © 2013.

  9. Simulated Local and Remote Biophysical Effects of Afforestation over the Southeast United States in Boreal Summer

    Science.gov (United States)

    Guang-Shan Chen; Michael Notaro; Zhengyu Liu; Yongqiang Liu

    2012-01-01

    Afforestation has been proposed as a climate change mitigation strategy by sequestrating atmospheric carbon dioxide. With the goal of increasing carbon sequestration, a Congressional project has been planned to afforest about 18 million acres by 2020 in the Southeast United States (SEUS), the Great Lake states, and the Corn Belt states. However, biophysical feedbacks...

  10. Microporous silica membranes

    DEFF Research Database (Denmark)

    Boffa, Vittorio; Yue, Yuanzheng

    2012-01-01

    Hydrothermal stability is a crucial factor for the application of microporous silica-based membranes in industrial processes. Indeed, it is well established that steam exposure may cause densification and defect formation in microporous silica membranes, which are detrimental to both membrane...... permeability and selectivity. Numerous previous studies show that microporous transition metal doped-silica membranes are hydrothermally more stable than pure silica membranes, but less permeable. Here we present a quantitative study on the impact of type and concentration of transition metal ions...... on the microporous structure, stability and permeability of amorphous silica-based membranes, providing information on how to design chemical compositions and synthetic paths for the fabrication of silica-based membranes with a well accessible and highly stabile microporous structure....

  11. Clustering on Membranes

    DEFF Research Database (Denmark)

    Johannes, Ludger; Pezeshkian, Weria; Ipsen, John H

    2018-01-01

    Clustering of extracellular ligands and proteins on the plasma membrane is required to perform specific cellular functions, such as signaling and endocytosis. Attractive forces that originate in perturbations of the membrane's physical properties contribute to this clustering, in addition to direct...... protein-protein interactions. However, these membrane-mediated forces have not all been equally considered, despite their importance. In this review, we describe how line tension, lipid depletion, and membrane curvature contribute to membrane-mediated clustering. Additional attractive forces that arise...... from protein-induced perturbation of a membrane's fluctuations are also described. This review aims to provide a survey of the current understanding of membrane-mediated clustering and how this supports precise biological functions....

  12. Biophysical effects on temperature and precipitation due to land cover change

    Science.gov (United States)

    Perugini, Lucia; Caporaso, Luca; Marconi, Sergio; Cescatti, Alessandro; Quesada, Benjamin; de Noblet-Ducoudré, Nathalie; House, Johanna I.; Arneth, Almut

    2017-05-01

    Anthropogenic land cover changes (LCC) affect regional and global climate through biophysical variations of the surface energy budget mediated by albedo, evapotranspiration, and roughness. This change in surface energy budget may exacerbate or counteract biogeochemical greenhouse gas effects of LCC, with a large body of emerging assessments being produced, sometimes apparently contradictory. We reviewed the existing scientific literature with the objective to provide an overview of the state-of-the-knowledge of the biophysical LCC climate effects, in support of the assessment of mitigation/adaptation land policies. Out of the published studies that were analyzed, 28 papers fulfilled the eligibility criteria, providing surface air temperature and/or precipitation change with respect to LCC regionally and/or globally. We provide a synthesis of the signal, magnitude and uncertainty of temperature and precipitation changes in response to LCC biophysical effects by climate region (boreal/temperate/tropical) and by key land cover transitions. Model results indicate that a modification of biophysical processes at the land surface has a strong regional climate effect, and non-negligible global impact on temperature. Simulations experiments of large-scale (i.e. complete) regional deforestation lead to a mean reduction in precipitation in all regions, while air surface temperature increases in the tropics and decreases in boreal regions. The net global climate effects of regional deforestation are less certain. There is an overall consensus in the model experiments that the average global biophysical climate response to complete global deforestation is atmospheric cooling and drying. Observed estimates of temperature change following deforestation indicate a smaller effect than model-based regional estimates in boreal regions, comparable results in the tropics, and contrasting results in temperate regions. Regional/local biophysical effects following LCC are important for

  13. Application of dynamic membranes in anaerobic membranes in anaerobic membrane bioreactor systems

    NARCIS (Netherlands)

    Erşahin, M.E.

    2015-01-01

    Anaerobic membrane bioreactors (AnMBRs) physically ensure biomass retention by the application of a membrane filtration process. With growing application experiences from aerobic membrane bioreactors (MBRs), the combination of membrane and anaerobic processes has received much attention and become

  14. Past and Present Biophysical Redundancy of Countries as a Buffer to Changes in Food Supply

    Science.gov (United States)

    Fader, Marianela; Rulli, Maria Cristina; Carr, Joel; Dell' Angelo, Jampel; D' Odorico, Paolo; Gephart, Jessica A.; Kummu, Matti; Magliocca, Nicholas; Porkka, Miina; Prell, Christina; hide

    2016-01-01

    Spatially diverse trends in population growth, climate change, industrialization, urbanization and economic development are expected to change future food supply and demand. These changes may affect the suitability of land for food production, implying elevated risks especially for resource constrained, food-importing countries. We present the evolution of biophysical redundancy for agricultural production at country level, from 1992 to 2012. Biophysical redundancy, defined as unused biotic and abiotic environmental resources, is represented by the potential food production of 'spare land', available water resources (i.e., not already used for human activities), as well as production increases through yield gap closure on cultivated areas and potential agricultural areas. In 2012, the biophysical redundancy of 75 (48) countries, mainly in North Africa, Western Europe, the Middle East and Asia, was insufficient to produce the caloric nutritional needs for at least 50% (25%) of their population during a year. Biophysical redundancy has decreased in the last two decades in 102 out of 155 countries, 11 of these went from high to limited redundancy, and nine of these from limited to very low redundancy. Although the variability of the drivers of change across different countries is high, improvements in yield and population growth have a clear impact on the decreases of redundancy towards the very low redundancy category. We took a more detailed look at countries classified as 'Low Income Economies (LIEs)' since they are particularly vulnerable to domestic or external food supply changes, due to their limited capacity to offset for food supply decreases with higher purchasing power on the international market. Currently, nine LIEs have limited or very low biophysical redundancy. Many of these showed a decrease in redundancy over the last two decades, which is not always linked with improvements in per capita food availability.

  15. Past and present biophysical redundancy of countries as a buffer to changes in food supply

    Science.gov (United States)

    Fader, Marianela; Rulli, Maria Cristina; Carr, Joel; Dell'Angelo, Jampel; D'Odorico, Paolo; Gephart, Jessica A.; Kummu, Matti; Magliocca, Nicholas; Porkka, Miina; Prell, Christina; Puma, Michael J.; Ratajczak, Zak; Seekell, David A.; Suweis, Samir; Tavoni, Alessandro

    2016-05-01

    Spatially diverse trends in population growth, climate change, industrialization, urbanization and economic development are expected to change future food supply and demand. These changes may affect the suitability of land for food production, implying elevated risks especially for resource-constrained, food-importing countries. We present the evolution of biophysical redundancy for agricultural production at country level, from 1992 to 2012. Biophysical redundancy, defined as unused biotic and abiotic environmental resources, is represented by the potential food production of ‘spare land’, available water resources (i.e., not already used for human activities), as well as production increases through yield gap closure on cultivated areas and potential agricultural areas. In 2012, the biophysical redundancy of 75 (48) countries, mainly in North Africa, Western Europe, the Middle East and Asia, was insufficient to produce the caloric nutritional needs for at least 50% (25%) of their population during a year. Biophysical redundancy has decreased in the last two decades in 102 out of 155 countries, 11 of these went from high to limited redundancy, and nine of these from limited to very low redundancy. Although the variability of the drivers of change across different countries is high, improvements in yield and population growth have a clear impact on the decreases of redundancy towards the very low redundancy category. We took a more detailed look at countries classified as ‘Low Income Economies (LIEs)’ since they are particularly vulnerable to domestic or external food supply changes, due to their limited capacity to offset for food supply decreases with higher purchasing power on the international market. Currently, nine LIEs have limited or very low biophysical redundancy. Many of these showed a decrease in redundancy over the last two decades, which is not always linked with improvements in per capita food availability.

  16. Estimating biophysical properties of eucalyptus plantations using optical remote sensing techniques

    Science.gov (United States)

    Soares, Joao V.; Xavier, Alexandre C.; de Almeida, Auro C.; da Costa Freitas, Corina

    1998-12-01

    The feasibility of the inversion of optical remote sensing products to measure critical biophysical properties of Eucalyptus Forests at regional scales is investigated here. The biophysical variables used were leaf area Index, LAI, Diameter at Breast Height, DBH, Height and Age of Eucalyptus stands pertaining to a combination of different genetic materials (E. urophylla x E. grandis hybrids) and propagating systems (seeds or cuttings) and management system (planting and coppicing). The field sampling was done daily during 3 months, from April to June 1997, and covered 130 stands of minimum sizes of 9 hectares, within an Eucalyptus farming area of about 800 km2, centered at 19 degrees South, 42 degrees West, Brazil. The stands ranged from 12 to 84 months old. The measurements of LAI were done using two pairs of LAI-2000 (LICOR) under conditions of diffuse light. The Normalized Difference Vegetation Index, NDVI, and the Soil Adjusted Vegetation Index, SAVI, were derived from a LANDSAT-TM image acquired on June 5, 1997. Furthermore, a mixture model technique was applied to derive three new parameters: fraction of green vegetation, FGV, fraction of shadow, FSH, and fraction of soil, FS. Regression analysis were done between biophysical variables and remote sensing products. Linear correlation with coefficients of determination, R2, as high as 0.8 were found between LAI versus FGV and LAI versus SAVI, on all genetic materials. In general, SAVI was shown to give better estimates of LAI than NDVI, which is explained by the openings in the canopy as the Eucalyptus grow older. The correlation with the other biophysical variables (Height and DBH) were also shown to be significant, although the R2 ranged from 0.4 to 0.6. The correlation between FGV and SAVI was higher than 90% such that they can be used to estimate Eucalyptus biophysical parameters with the same statistical significance.

  17. Supported ionic liquid membrane in membrane reactor

    Science.gov (United States)

    Makertihartha, I. G. B. N.; Zunita, M.; Dharmawijaya, P. T.; Wenten, I. G.

    2017-01-01

    Membrane reactor is a device that integrates membrane based separation and (catalytic) chemical reaction vessel in a single device. Ionic liquids, considered to be a relatively recent magical chemical due to their unique properties, have a large variety of applications in all areas of chemical industries. Moreover, the ionic liquid can be used as membrane separation layer and/or catalytically active site. This paper will review utilization of ionic liquid in membrane reactor related applications especially Fischer-Tropsch, hydrogenation, and dehydrogenation reaction. This paper also reviews about the capability of ionic liquid in equilibrium reaction that produces CO2 product so that the reaction will move towards the product. Water gas shift reaction in ammonia production also direct Dimethyl Ether (DME) synthesis that produces CO2 product will be discussed. Based on a review of numerous articles on supported ionic liquid membrane (SILM) indicate that ionic liquids have the potential to support the process of chemical reaction and separation in a membrane reactor.

  18. Remodeling of the postsynaptic plasma membrane during neural development.

    Science.gov (United States)

    Tulodziecka, Karolina; Diaz-Rohrer, Barbara B; Farley, Madeline M; Chan, Robin B; Di Paolo, Gilbert; Levental, Kandice R; Waxham, M Neal; Levental, Ilya

    2016-11-07

    Neuronal synapses are the fundamental units of neural signal transduction and must maintain exquisite signal fidelity while also accommodating the plasticity that underlies learning and development. To achieve these goals, the molecular composition and spatial organization of synaptic terminals must be tightly regulated; however, little is known about the regulation of lipid composition and organization in synaptic membranes. Here we quantify the comprehensive lipidome of rat synaptic membranes during postnatal development and observe dramatic developmental lipidomic remodeling during the first 60 postnatal days, including progressive accumulation of cholesterol, plasmalogens, and sphingolipids. Further analysis of membranes associated with isolated postsynaptic densities (PSDs) suggests the PSD-associated postsynaptic plasma membrane (PSD-PM) as one specific location of synaptic remodeling. We analyze the biophysical consequences of developmental remodeling in reconstituted synaptic membranes and observe remarkably stable microdomains, with the stability of domains increasing with developmental age. We rationalize the developmental accumulation of microdomain-forming lipids in synapses by proposing a mechanism by which palmitoylation of the immobilized scaffold protein PSD-95 nucleates domains at the postsynaptic plasma membrane. These results reveal developmental changes in lipid composition and palmitoylation that facilitate the formation of postsynaptic membrane microdomains, which may serve key roles in the function of the neuronal synapse. © 2016 Tulodziecka et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  19. Interaction of a synthetic peptide corresponding to the N-terminus of canine distemper virus fusion protein with phospholipid vesicles: a biophysical study.

    Science.gov (United States)

    Aranda, Francisco J; Teruel, José A; Ortiz, Antonio

    2003-12-03

    The F protein of canine distemper virus (CDV) is a classic type I glycoprotein formed by two polypeptides, F1 and F2. The N-terminal regions of the F1 polypeptides of CDV, measles virus and other paramyxoviruses present moderate to high homology, supporting the existence of a high conservation within these structures, which emphasises its role in viral-host cell membrane fusion. This N-terminal polypeptide is usually termed the fusion peptide. The fusion peptides of most viral fusion-mediating glycoproteins contain a high proportion of hydrophobic amino acids, which facilitates its insertion into target membranes during fusion. In this work we report on the interaction of a 31-residue synthetic peptide (FP31) corresponding to the N terminus of CDV F1 protein with phospholipid membranes composed of various phospholipids, as studied by means of various biophysical techniques. FTIR investigation of FP31 secondary structure in aqueous medium and in membranes resulted in a major proportion of alpha-helical structure which increased upon membrane insertion. Differential scanning calorimetry (DSC) showed that the presence of concentrations of FP31 as low as 0.1 mol%, in mixtures with L-alpha-dimyristoylphosphatidylcholine (DMPC), L-alpha-dipalmitoylphosphatidylcholine (DPPC) and L-alpha-distearoylphosphatidylcholine (DSPC), already affected the thermotropic properties of the gel to liquid-crystalline phase transition. In mixtures with the three lipids, increasing the concentration of peptide made the pretransition to disappear, and lowered and broadened the main transition. This effect was slightly stronger as the acyl chain length of the phospholipid grew larger. In the corresponding partial phase diagrams, no immiscibilities or critical points were observed. FTIR showed that incorporation of 1 mol% of peptide in DPPC shifted the antisymmetric and symmetric CH2 stretching bands to higher values, indicating the existence of an additional disordering of the acyl chain

  20. Emulsification using microporous membranes

    Directory of Open Access Journals (Sweden)

    Goran T. Vladisavljević

    2011-10-01

    Full Text Available Membrane emulsification is a process of injecting a pure dispersed phase or pre-emulsion through a microporous membrane into the continuous phase. As a result of the immiscibility of the two phases, droplets of the dispersed phase are formed at the outlets of membrane pores. The droplets formed in the process are removed from the membrane surface by applying cross-flow or stirring of the continuous phase or using a dynamic (rotating or vibrating membrane. The most commonly used membrane for emulsification is the Shirasu Porous Glass (SPG membrane, fabricated through spinodal decomposition in a melt consisting of Japanese volcanic ash (Shirasu, boric acid and calcium carbonate. Microsieve membranes are increasingly popular as an alternative to highly tortuous glass and ceramic membranes. Microsieves are usually fabricated from nickel by photolithography and electroplating or they can be manufactured from silicon nitride via Reactive Ion Etching (RIE. An advantage of microsieves compared to the SPG membrane is in much higher transmembrane fluxes and higher tolerance to fouling by the emulsion ingredients due to the existence of short, straight through pores. Unlike conventional emulsification devices such as high-pressure valve homogenisers and rotor-stator devices, membrane emulsification devices permit a precise control over the mean pore size over a wide range and during the process insignificant amount of energy is dissipated as heat. The drop size is primarily determined by the pore size, but it depends also on other parameters, such as membrane wettability, emulsion formulation, shear stress on the membrane surface, transmembrane pressure, etc.

  1. PTEN interaction with tethered bilayer lipid membranes containing PI(4,5)P2

    Science.gov (United States)

    Moldovan, R.; Shenoy, S.; Shekhar, P.; Kalinowski, A.; Gericke, A.; Heinrich, F.; Loesche, M.

    2009-03-01

    Synthetic lipid membrane models are frequently used for the study of biophysical processes at cell membranes. We use a robust membrane model, the tethered bilayer lipid membrane (tBLM), based on a (C14)2-(PEO)6-thiol anchor, WC14 [1]. Such membranes can be prepared to contain single phospholipids or complex lipid mixtures [2], including functional lipids involved in cell signaling, such as the highly charged phosphatidylinositol phosphates (PIPs). To study the interaction between the tumor suppressor PTEN (phosphatase and tensin homologue deleted on chromosome 10) and model membranes we have incorporated phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) in tBLMs and use fluorescence correlation spectroscopy (FCS), neutron reflectometry (NR) and surface plasmon resonance (SPR) for their characterization. NR shows that tBLMs formed with PI(4,5)P2 are complete. FCS of labeled PI(4,5)P2 shows that diffusion occurs at the time scale characteristic of membrane-incorporated lipid. Finally, SPR shows specific binding of PTEN to the model membrane thus confirming the incorporation of PI(4,5)P2 into the tBLM. [1] McGillivray et al, Biointerphases 2, 21-33 (2007) [2] Heinrich et al, Langmuir, submitted

  2. New tools to study biophysical properties of single molecules and single cells

    Directory of Open Access Journals (Sweden)

    Márcio S. Rocha

    2007-03-01

    Full Text Available We present a review on two new tools to study biophysical properties of single molecules and single cells. A laser incident through a high numerical aperture microscope objective can trap small dielectric particles near the focus. This arrangement is named optical tweezers. This technique has the advantage to permit manipulation of a single individual object. We use optical tweezers to measure the entropic elasticity of a single DNA molecule and its interaction with the drug Psoralen. Optical tweezers are also used to hold a kidney cell MDCK away from the substrate to allow precise volume measurements of this single cell during an osmotic shock. This procedure allows us to obtain information about membrane water permeability and regulatory volume increase. Defocusing microscopy is a recent technique invented in our laboratory, which allows the observation of transparent objects, by simply defocusing the microscope in a controlled way. Our physical model of a defocused microscope shows that the image contrast observed in this case is proportional to the defocus distance and to the curvature of the transparent object. Defocusing microscopy is very useful to study motility and mechanical properties of cells. We show here the application of defocusing microscopy to measurements of macrophage surface fluctuations and their influence on phagocytosis.Apresentamos uma revisão de duas novas técnicas para estudar propriedades biofísicas de moléculas únicas e células únicas. Um laser incidindo em uma objetiva de microscópio de grande abertura numérica é capaz de aprisionar pequenas partículas dielétricas na região próxima ao foco. Este aparato é chamado de pinça óptica. Esta técnica tem a grande vantagem de permitir a manipulação de um objeto individual. Usamos a pinça óptica para medir a elasticidade entrópica de uma molécula única de DNA em sua interação com o fármaco Psoralen. A pinça óptica também é usada para segurar

  3. Effects of seaweed sterols fucosterol and desmosterol on lipid membranes.

    Science.gov (United States)

    Mouritsen, Ole G; Bagatolli, Luis A; Duelund, Lars; Garvik, Olav; Ipsen, John H; Simonsen, Adam Cohen

    2017-06-01

    Higher sterols are universally present in large amounts (20-30%) in the plasma membranes of all eukaryotes whereas they are universally absent in prokaryotes. It is remarkable that each kingdom of the eukaryotes has chosen, during the course of evolution, its preferred sterol: cholesterol in animals, ergosterol in fungi and yeast, phytosterols in higher plants, and e.g., fucosterol and desmosterol in algae. The question arises as to which specific properties do sterols impart to membranes and to which extent do these properties differ among the different sterols. Using a range of biophysical techniques, including calorimetry, fluorescence microscopy, vesicle-fluctuation analysis, and atomic force microscopy, we have found that fucosterol and desmosterol, found in red and brown macroalgae (seaweeds), similar to cholesterol support liquid-ordered membrane phases and induce coexistence between liquid-ordered and liquid-disordered domains in lipid bilayers. Fucosterol and desmosterol induce acyl-chain order in liquid membranes, but less effectively than cholesterol and ergosterol in the order: cholesterol>ergosterol>desmosterol>fucosterol, possibly reflecting the different molecular structure of the sterols at the hydrocarbon tail. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Reduction of anion reversal potential subverts the inhibitory control of firing rate in spinal lamina I neurons: towards a biophysical basis for neuropathic pain

    Directory of Open Access Journals (Sweden)

    Sejnowski Terrence J

    2006-10-01

    Full Text Available Abstract Background Reduction of the transmembrane chloride gradient in spinal lamina I neurons contributes to the cellular hyperexcitability producing allodynia and hyperalgesia after peripheral nerve injury. The resultant decrease in anion reversal potential (i.e. shift in Eanion to less negative potentials reduces glycine/GABAA receptor-mediated hyperpolarization, but the large increase in membrane conductance caused by inhibitory input can nonetheless shunt concurrent excitatory input. Without knowing the relative contribution of hyperpolarization and shunting to inhibition's modulation of firing rate, it is difficult to predict how much net disinhibition results from reduction of Eanion. We therefore used a biophysically accurate lamina I neuron model to investigate quantitatively how changes in Eanion affect firing rate modulation. Results Simulations reveal that even a small reduction of Eanion compromises inhibitory control of firing rate because reduction of Eanion not only decreases glycine/GABAA receptor-mediated hyperpolarization, but can also indirectly compromise the capacity of shunting to reduce spiking. The latter effect occurs because shunting-mediated modulation of firing rate depends on a competition between two biophysical phenomena: shunting reduces depolarization, which translates into reduced spiking, but shunting also shortens the membrane time constant, which translates into faster membrane charging and increased spiking; the latter effect predominates when average depolarization is suprathreshold. Disinhibition therefore occurs as both hyperpolarization- and shunting-mediated modulation of firing rate are subverted by reduction of Eanion. Small reductions may be compensated for by increased glycine/GABAA receptor-mediated input, but the system decompensates (i.e. compensation fails as reduction of Eanion exceeds a critical value. Hyperexcitability necessarily develops once disinhibition becomes incompensable

  5. Effects of Single Amino Acid Substitution on the Biophysical Properties and Biological Activities of an Amphipathic α-Helical Antibacterial Peptide Against Gram-Negative Bacteria

    Directory of Open Access Journals (Sweden)

    Juanjuan Tan

    2014-07-01

    Full Text Available An antimicrobial peptide, known as V13K, was utilized as the framework to study the effects of charge, hydrophobicity and helicity on the biophysical properties and biological activities of α-helical peptides. Six amino acids (Lys, Glu, Gly, Ser, Ala, and Leu were individually used to substitute the original hydrophobic valine at the selected sixteenth location on the non-polar face of V13K. The results showed that the single amino acid substitutions changed the hydrophobicity of peptide analogs as monitored by RP-HPLC, but did not cause significant changes on peptide secondary structures both in a benign buffer and in a hydrophobic environment. The biological activities of the analogs exhibited a hydrophobicity-dependent behavior. The mechanism of peptide interaction with the outer membrane and cytoplasmic membrane of Gram-negative bacteria was investigated. We demonstrated that this single amino acid substitution method has valuable potential for the rational design of antimicrobial peptides with enhanced activities.

  6. Ion-conducting membranes

    Energy Technology Data Exchange (ETDEWEB)

    Masel, Richard I.; Sajjad, Syed Dawar; Gao, Yan; Liu, Zengcai; Chen, Qingmei

    2017-12-26

    An anion-conducting polymeric membrane comprises a terpolymer of styrene, vinylbenzyl-R.sub.s and vinylbenzyl-R.sub.x. R.sub.s is a positively charged cyclic amine group. R.sub.x is at least one constituent selected from the group consisting Cl, OH and a reaction product between an OH or Cl and a species other than a simple amine or a cyclic amine. The total weight of the vinylbenzyl-R.sub.x groups is greater than 0.3% of the total weight of the membrane. In a preferred embodiment, the membrane is a Helper Membrane that increases the faradaic efficiency of an electrochemical cell into which the membrane is incorporated, and also allows product formation at lower voltages than in cells without the Helper Membrane.

  7. Gas separation with membranes

    International Nuclear Information System (INIS)

    Schulz, G.; Michele, H.; Werner, U.

    1982-01-01

    Gas separation with membranes has already been tested in numerous fields of application, e.g. uranium enrichment of H 2 separation. In many of these processes the mass transfer units, so-called permeators, have to be connected in tandem in order to achieve high concentrations. A most economical operating method provides for each case an optimization of the cascades with regard to the membrane materials, construction and design of module. By utilization of the concentration gradient along the membrane a new process development has been accomplished - the continuously operating membrane rectification unit. Investment and operating costs can be reduced considerably for a number of separating processes by combining a membrane rectification unit with a conventional recycling cascade. However, the new procedure requires that the specifications for the module construction, flow design, and membrane properties be reconsidered. (orig.) [de

  8. Mechanism of coupling drug transport reactions located in two different membranes

    Directory of Open Access Journals (Sweden)

    Helen I. Zgurskaya

    2015-02-01

    Full Text Available Gram- negative bacteria utilize a diverse array of multidrug transporters to pump toxic compounds out of cells. Some transporters together with periplasmic membrane fusion proteins (MFPs and outer membrane channels assemble trans-envelope complexes that expel multiple antibiotics across outer membranes of Gram-negative bacteria and into the external medium. Others further potentiate this efflux by pumping drugs across the inner membrane into the periplasm. Together these transporters create a powerful network of efflux that protect bacteria against a broad range of antimicrobial agents. This review is focused on the mechanism of coupling transport reactions located in two different membranes of Gram-negative bacteria. Using a combination of biochemical, genetic and biophysical approaches we have reconstructed the sequence of events leading to the assembly of trans-envelope drug efflux complexes and characterized the roles of periplasmic and outer membrane proteins in this process. Our recent data suggest a critical step in the activation of intermembrane efflux pumps, which is controlled by MFPs. We propose that the reaction cycles of transporters are tightly coupled to the assembly of the trans-envelope complexes. Transporters and MFPs exist in the inner membrane as dormant complexes. The activation of complexes is triggered by MFP binding to the outer membrane channel, which leads to a conformational change in the membrane proximal domain of MFP needed for stimulation of transporters. The activated MFP-transporter complex engages the outer membrane channel to expel substrates across the outer membrane. The recruitment of the channel is likely triggered by binding of effectors (substrates to MFP or MFP-transporter complexes. This model together with recent structural and functional advances in the field of drug efflux provides a fairly detailed understanding of the mechanism of drug efflux across the two membranes.

  9. Biomechanics and Thermodynamics of Nanoparticle Interactions with Plasma and Endosomal Membrane Lipids in Cellular Uptake and Endosomal Escape

    Science.gov (United States)

    2015-01-01

    To be effective for cytoplasmic delivery of therapeutics, nanoparticles (NPs) taken up via endocytic pathways must efficiently transport across the cell membrane and subsequently escape from the secondary endosomes. We hypothesized that the biomechanical and thermodynamic interactions of NPs with plasma and endosomal membrane lipids are involved in these processes. Using model plasma and endosomal lipid membranes, we compared the interactions of cationic NPs composed of poly(d,l-lactide-co-glycolide) modified with the dichain surfactant didodecyldimethylammonium bromide (DMAB) or the single-chain surfactant cetyltrimethylammonium bromide (CTAB) vs anionic unmodified NPs of similar size. We validated our hypothesis in doxorubicin-sensitive (MCF-7, with relatively fluid membranes) and resistant breast cancer cells (MCF-7/ADR, with rigid membranes). Despite their cationic surface charges, DMAB- and CTAB-modified NPs showed different patterns of biophysical interaction: DMAB-modified NPs induced bending of the model plasma membrane, whereas CTAB-modified NPs condensed the membrane, thereby resisted bending. Unmodified NPs showed no effects on bending. DMAB-modified NPs also induced thermodynamic instability of the model endosomal membrane, whereas CTAB-modified and unmodified NPs had no effect. Since bending of the plasma membrane and destabilization of the endosomal membrane are critical biophysical processes in NP cellular uptake and endosomal escape, respectively, we tested these NPs for cellular uptake and drug efficacy. Confocal imaging showed that in both sensitive and resistant cells DMAB-modified NPs exhibited greater cellular uptake and escape from endosomes than CTAB-modified or unmodified NPs. Further, paclitaxel-loaded DMAB-modified NPs induced greater cytotoxicity even in resistant cells than CTAB-modified or unmodified NPs or drug in solution, demonstrating the potential of DMAB-modified NPs to overcome the transport barrier in resistant cells. In

  10. Chelating polymeric membranes

    KAUST Repository

    Peinemann, Klaus-Viktor

    2015-01-22

    The present application offers a solution to the current problems associated with recovery and recycling of precious metals from scrap material, discard articles, and other items comprising one or more precious metals. The solution is premised on a microporous chelating polymeric membrane. Embodiments include, but are not limited to, microporous chelating polymeric membranes, device comprising the membranes, and methods of using and making the same.

  11. Polyarylether composition and membrane

    Science.gov (United States)

    Hung, Joyce; Brunelle, Daniel Joseph; Harmon, Marianne Elisabeth; Moore, David Roger; Stone, Joshua James; Zhou, Hongyi; Suriano, Joseph Anthony

    2010-11-09

    A composition including a polyarylether copolymer is provided. The copolymer includes a polyarylether backbone; and a sulfonated oligomeric group bonded to the polyarylether suitable for use as a cation conducting membrane. Method of bonding a sulfonated oligomeric group to the polyarylether backbone to form a polyarylether copolymer. The membrane may be formed from the polyarylether copolymer composition. The chain length of the sulfonated oligomeric group may be controlled to affect or control the ion conductivity of the membrane.

  12. Satellite mapping of surface biophysical parameters at the biome scale over the North American grasslands: A case study

    Science.gov (United States)

    Wylie, B.K.; Meyer, D.J.; Tieszen, L.L.; Mannel, S.

    2002-01-01

    Quantification of biophysical parameters is needed by terrestrial process modeling and other applications. A study testing the role of multispectral data for monitoring biophysical parameters was conducted over a network of grassland field sites in the Great Plains of North America. Grassland biophysical parameters [leaf area index (LAI), fraction of absorbed photosynthetically active radiation (fPAR), and biomass] and their relationships with ground radiometer normalized difference vegetation index (NDVI) were established in this study (r2=.66–.85) from data collected across the central and northern Great Plains in 1995. These spectral/biophysical relationships were compared to 1996 field data from the Tallgrass Prairie Preserve in northeastern Oklahoma and showed no consistent biases, with most regression estimates falling within the respective 95% confidence intervals. Biophysical parameters were estimated for 21 “ground pixels” (grids) at the Tallgrass Prairie Preserve in 1996, representing three grazing/burning treatments. Each grid was 30×30 m in size and was systematically sampled with ground radiometer readings. The radiometric measurements were then converted to biophysical parameters and spatially interpolated using geostatistical kriging. Grid-based biophysical parameters were monitored through the growing season and regressed against Landsat Thematic Mapper (TM) NDVI (r2=.92–.94). These regression equations were used to estimate biophysical parameters for grassland TM pixels over the Tallgrass Prairie Preserve in 1996. This method maintained consistent regression development and prediction scales and attempted to minimize scaling problems associated with mixed land cover pixels. A method for scaling Landsat biophysical parameters to coarser resolution satellite data sets (1 km2) was also investigated.

  13. Photoresponsive nanostructured membranes

    KAUST Repository

    Madhavan, Poornima

    2016-07-26

    The perspective of adding stimuli-response to isoporous membranes stimulates the development of separation devices with pores, which would open or close under control of environment chemical composition, temperature or exposure to light. Changes in pH and temperature have been previously investigated. In this work, we demonstrate for the first time the preparation of photoresponsive isoporous membranes, applying self-assembly non-solvent induced phase separation to a new light responsive block copolymer. First, we optimized the membrane formation by using poly(styrene-b-anthracene methyl methacrylate-b-methylmethacrylate) (PS-b-PAnMMA-b-PMMA) copolymer, identifying the most suitable solvent, copolymer block length, and other parameters. The obtained final triblock copolymer membrane morphologies were characterized using atomic force and electron microscopy. The microscopic analysis reveals that the PS-b-PAnMMA-b-PMMA copolymer can form both lamellar and ordered hexagonal nanoporous structures on the membrane top layer in appropriate solvent compositions. The nanostructured membrane emits fluorescence due to the presence of the anthracene mid-block. On irradiation of light the PS-b-PAnMMA-b-PMMA copolymer membranes has an additional stimuli response. The anthracene group undergoes conformational changes by forming [4 + 4] cycloadducts and this alters the membrane\\'s water flux and solute retention. © 2016 The Royal Society of Chemistry.

  14. Gas separation membranes

    Science.gov (United States)

    Schell, William J.

    1979-01-01

    A dry, fabric supported, polymeric gas separation membrane, such as cellulose acetate, is prepared by casting a solution of the polymer onto a shrinkable fabric preferably formed of synthetic polymers such as polyester or polyamide filaments before washing, stretching or calendering (so called griege goods). The supported membrane is then subjected to gelling, annealing, and drying by solvent exchange. During the processing steps, both the fabric support and the membrane shrink a preselected, controlled amount which prevents curling, wrinkling or cracking of the membrane in flat form or when spirally wound into a gas separation element.

  15. Comparison of Modified Biophysical Profile with Doppler Ultrasonographic Analysis in Determining Fetal well Being in the Third Trimester

    Directory of Open Access Journals (Sweden)

    Kadir Bakay

    2016-05-01

    CONCLUSION: Modified biophysical profile was found to be a more reliable tool than Doppler analysis in determining perinatal outcome and in prediction of acute fetal distress. But combining modified biophysical profile with Doppler analysis has yielded a higher sensitivity aiding in the diagnosis of perinatal outcome and acute fetal distress. In conclusion, in order to effectively predict acute fetal distress and to maintain a reliable screening method, combined use of these tests, namely modified biophysical profile and umbilical artery Doppler analysis, has proven to be the most valuable and effective method as shown in our study.

  16. On Biophysical Properties and Sensitivity to Gap Junction Blockers of Connexin 39 Hemichannels Expressed in HeLa Cells

    Science.gov (United States)

    Vargas, Anibal A.; Cisterna, Bruno A.; Saavedra-Leiva, Fujiko; Urrutia, Carolina; Cea, Luis A.; Vielma, Alex H.; Gutierrez-Maldonado, Sebastian E.; Martin, Alberto J. M.; Pareja-Barrueto, Claudia; Escalona, Yerko; Schmachtenberg, Oliver; Lagos, Carlos F.; Perez-Acle, Tomas; Sáez, Juan C.

    2017-01-01

    Although connexins (Cxs) are broadly expressed by cells of mammalian organisms, Cx39 has a very restricted pattern of expression and the biophysical properties of Cx39-based channels [hemichannels (HCs) and gap junction channels (GJCs)] remain largely unknown. Here, we used HeLa cells transfected with Cx39 (HeLa-Cx39 cells) in which intercellular electrical coupling was not detected, indicating the absence of GJCs. However, functional HCs were found on the surface of cells exposed to conditions known to increase the open probability of other Cx HCs (e.g., extracellular divalent cationic-free solution (DCFS), extracellular alkaline pH, mechanical stimulus and depolarization to positive membrane potentials). Cx39 HCs were blocked by some traditional Cx HC blockers, but not by others or a pannexin1 channel blocker. HeLa-Cx39 cells showed similar resting membrane potentials (RMPs) to those of parental cells, and exposure to DCFS reduced RMPs in Cx39 transfectants, but not in parental cells. Under these conditions, unitary events of ~75 pS were frequent in HeLa-Cx39 cells and absent in parental cells. Real-time cellular uptake experiments of dyes with different physicochemical features, as well as the application of a machine-learning approach revealed that Cx39 HCs are preferentially permeable to molecules characterized by six categories of descriptors, namely: (1) electronegativity, (2) ionization potential, (3) polarizability, (4) size and geometry, (5) topological flexibility and (6) valence. However, Cx39 HCs opened by mechanical stimulation or alkaline pH were impermeable to Ca2+. Molecular modeling of Cx39-based channels suggest that a constriction present at the intracellular portion of the para helix region co-localizes with an electronegative patch, imposing an energetic and steric barrier, which in the case of GJCs may hinder channel function. Results reported here demonstrate that Cx39 form HCs and add to our understanding of the functional roles of Cx39 HCs

  17. Membrane remodeling by amyloidogenic and non-amyloidogenic proteins studied by EPR

    Science.gov (United States)

    Varkey, Jobin; Langen, Ralf

    2017-07-01

    The advancement in site-directed spin labeling of proteins has enabled EPR studies to expand into newer research areas within the umbrella of protein-membrane interactions. Recently, membrane remodeling by amyloidogenic and non-amyloidogenic proteins has gained a substantial interest in relation to driving and controlling vital cellular processes such as endocytosis, exocytosis, shaping of organelles like endoplasmic reticulum, Golgi and mitochondria, intracellular vesicular trafficking, formation of filopedia and multivesicular bodies, mitochondrial fusion and fission, and synaptic vesicle fusion and recycling in neurotransmission. Misregulation in any of these processes due to an aberrant protein (mutation or misfolding) or alteration of lipid metabolism can be detrimental to the cell and cause disease. Dissection of the structural basis of membrane remodeling by proteins is thus quite necessary for an understanding of the underlying mechanisms, but it remains a formidable task due to the difficulties of various common biophysical tools in monitoring the dynamic process of membrane binding and bending by proteins. This is largely since membranes generally complicate protein structure analysis and this problem is amplified for structural analysis in the presence of different types of membrane curvatures. Recent EPR studies on membrane remodeling by proteins show that a significant structural information can be generated to delineate the role of different protein modules, domains and individual amino acids in the generation of membrane curvature. These studies also show how EPR can complement the data obtained by high resolution techniques such as X-ray and NMR. This perspective covers the application of EPR in recent studies for understanding membrane remodeling by amyloidogenic and non-amyloidogenic proteins that is useful for researchers interested in using or complimenting EPR to gain better understanding of membrane remodeling. We also discuss how a single

  18. Combined influence of biophysical and biochemical cues on maintenance and proliferation of hematopoietic stem cells.

    Science.gov (United States)

    Gvaramia, David; Müller, Eike; Müller, Katrin; Atallah, Passant; Tsurkan, Mikhail; Freudenberg, Uwe; Bornhäuser, Martin; Werner, Carsten

    2017-09-01

    Homeostasis of hematopoietic stem and progenitor cells (HSPC) is controlled by a combination of biochemical and biophysical environmental cues in the bone marrow (BM) niche, where a tight balance of quiescence and proliferation of HSPC is maintained. Specifically, alongside soluble factors and extracellular matrix (ECM) proteins, spatial confinement and ECM stiffness have been recognized to be critical for regulation of HSPC fate. Here we employ a modular, glycosaminoglycan (GAG)-based biohybrid hydrogel system to balance proliferation of human HSPC and maintenance of quiescent hematopoietic stem cells (HSC) through simultaneous regulation of exogenous biochemical and biophysical cues. Our results demonstrate that HSPC respond to increased spatial confinement with lowered proliferation and cell cycling, which results in higher frequency of quiescent LTC-IC (long-term culture initiating cells), while GAG-rich 3D environments further support maintenance of the cells. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Chiropractic biophysics technique: a linear algebra approach to posture in chiropractic.

    Science.gov (United States)

    Harrison, D D; Janik, T J; Harrison, G R; Troyanovich, S; Harrison, D E; Harrison, S O

    1996-10-01

    This paper discusses linear algebra as applied to human posture in chiropractic, specifically chiropractic biophysics technique (CBP). Rotations, reflections and translations are geometric functions studied in vector spaces in linear algebra. These mathematical functions are termed rigid body transformations and are applied to segmental spinal movement in the literature. Review of the literature indicates that these linear algebra concepts have been used to describe vertebral motion. However, these rigid body movers are presented here as applying to the global postural movements of the head, thoracic cage and pelvis. The unique inverse functions of rotations, reflections and translations provide a theoretical basis for making postural corrections in neutral static resting posture. Chiropractic biophysics technique (CBP) uses these concepts in examination procedures, manual spinal manipulation, instrument assisted spinal manipulation, postural exercises, extension traction and clinical outcome measures.

  20. Principles and applications of selective biophysical methods for characterization and comparability assessment of a monoclonal antibody.

    Science.gov (United States)

    Maity, Haripada; Lai, Yin; Srivastava, Arvind; Goldstein, Joel

    2012-08-01

    The strategy for a comparability assessment is developed on a hierarchical risk-based approach. Critical analysis of physicochemical and biological characterization assays is essential for the development of a good comparability protocol. Therefore, selection and sensitivity of these assays is very important. This article discusses a case study to evaluate the sensitivity of various methods in a comparability assessment of three lots of an IgG1 monoclonal antibody (mAb). Analysis with eighteen methods demonstrated that only six of the methods were sensitive enough to show a measurable difference of comparability under accelerated conditions (40°C). Samples stored at 4°C were found to be comparable by all methods. A brief comparison of the results of biochemical and functional assays with biophysical analysis is discussed. Basic principles, applications, strength, and limitations of different biophysical methods are also discussed here.

  1. Ground-and satellite-based evidence of the biophysical mechanisms behind the greening Sahel

    DEFF Research Database (Denmark)

    Brandt, Martin Stefan; Mbow, Cheikh; Diouf, Abdoul A.

    2015-01-01

    After a dry period with prolonged droughts in the 1970s and 1980s, recent scientific outcome suggests that the decades of abnormally dry conditions in the Sahel have been reversed by positive anomalies in rainfall. Various remote sensing studies observed a positive trend in vegetation greenness...... over the last decades which is known as the re-greening of the Sahel. However, little investment has been made in including long-term ground-based data collections to evaluate and better understand the biophysical mechanisms behind these findings. Thus, deductions on a possible increment in biomass...... remain speculative. Our aim is to bridge these gaps and give specifics on the biophysical background factors of the re-greening Sahel. Therefore, a trend analysis was applied on long time series (1987-2013) of satellite-based vegetation and rainfall data, as well as on ground-observations of leaf biomass...

  2. Biophysical characteristics of the Meibomian lipid layer under in vitro conditions.

    Science.gov (United States)

    Kaercher, T; Möbius, D; Welt, R

    1992-05-01

    The biophysical behaviour of the Meibomian gland secretion was tested under in vitro conditions. Thereby, simultaneous recording of surface pressure and surface potential was performed. The Meibomian lipid layer was compared with other surface-active components like polyvinylalcohol and polyvinylpyrrolidone. On the other hand, Eledoisin was tested as an example for a surface-inactive substance. An attempt was made to describe the biophysical interaction between a given artificial tear substitute and the Meibomian lipid layer. With respect to the surface potential Dipalmitoyl-phosphatidyl-choline was established as an analogue for Meibomian gland secretion. Fluorescence measurements in the presence of a cyanine dye (1 N,N'dioctadecyloxacarbocyanine) were used as a method to localize the site of the characteristic potential change. From the fluorescence spectra under compression we conclude that the molecular change takes place at the lipid-subphase interface of the Meibomian lipid layer.

  3. Biophysics of skin and its treatments structural, nanotribological, and nanomechanical studies

    CERN Document Server

    Bhushan, Bharat

    2017-01-01

    This book provides a comprehensive overview of the structural, nanotribological and nanomechanical properties of skin with and without cream treatment as a function of operating environment. The biophysics of skin as the outer layer covering human or animal body is discussed as a complex biological structure. Skin cream is used to improve skin health and create a smooth, soft, and flexible surface with moist perception by altering the surface roughness, friction, adhesion, elastic modulus, and surface charge of the skin surface. .

  4. Assessment of bio-physical drought hazards. A case study of Karkheh River basin in Iran

    Science.gov (United States)

    Kamali, Bahareh; Abbaspour, Karim; Houshmand Kouchi, Delaram; Yang, Hong

    2016-04-01

    Iran has been affected by frequent droughts. Climate change is expected to intensify the situation in the future. Extreme drought events have had serious impacts on hydrological and agricultural sector. Thus, identification of bio-physical drought hazard is critically important for formulating effective adaptive measures to improve water and food security. This study aims to investigate temporal and spatial pattern of drought hazards in meteorological, hydrological, and agricultural (inclusively biophysical) sectors in the Karkheh River Basin of Iran in the historical and future climate change context. To do so, drought hazard indices were built based on the severity and frequency of standardized precipitation index (SPI), standardized runoff index (SRI), and standardized soil moisture index (SSMI), which represent the three aspects of drought hazards. Variables required for calculating these indices were obtained from SWAT (Soil and Water Assessment Tool) model constructed for the basin. The model was calibrated based on monthly runoff using the Sequential Uncertainty Fitting (SUFI-2) algorithm in SWAT-CUP. Based on the climate variability and drought analysis, three drought hazard classes, namely low, medium and high, were defined. This help identify how agricultural and hydrological sectors are related to meteorological droughts. Additionally, the bio-physical drivers of drought hazards were identified for each class. Comparing the results during historic and future scenarios revealed that the frequency of high- severity hazards will increase, whereas the same is not predicted for the area with medium hazard intensity. Inferred from findings of this study, the combined application of the SWAT model with bio-physical drought hazard concept helps better understanding of climate risks to water and food security. The developed approach is replicable at different scales to provide a robust planning tool for policy makers.

  5. Replacing natural wetlands with stormwater management facilities: biophysical and perceived social values

    OpenAIRE

    Rooney, R.C.; Foote, L.; Krogman, N.; Pattison, J.K.; Wilson, M.J.; Bayley, S.E.

    2015-01-01

    Urban expansion replaces wetlands of natural origin with artificial stormwater management facilities. The literature suggests that efforts to mimic natural wetlands in the design of stormwater facilities can expand the provision of ecosystem services. Policy developments seek to capitalize on these improvements, encouraging developers to build stormwater wetlands in place of stormwater ponds; however, few have compared the biophysical values and social perceptions of these created wetlands to...

  6. Estimation efficiency of usage satellite derived and modelled biophysical products for yield forecasting

    Science.gov (United States)

    Kolotii, Andrii; Kussul, Nataliia; Skakun, Sergii; Shelestov, Andrii; Ostapenko, Vadim; Oliinyk, Tamara

    2015-04-01

    Efficient and timely crop monitoring and yield forecasting are important tasks for ensuring of stability and sustainable economic development [1]. As winter crops pay prominent role in agriculture of Ukraine - the main focus of this study is concentrated on winter wheat. In our previous research [2, 3] it was shown that usage of biophysical parameters of crops such as FAPAR (derived from Geoland-2 portal as for SPOT Vegetation data) is far more efficient for crop yield forecasting to NDVI derived from MODIS data - for available data. In our current work efficiency of usage such biophysical parameters as LAI, FAPAR, FCOVER (derived from SPOT Vegetation and PROBA-V data at resolution of 1 km and simulated within WOFOST model) and NDVI product (derived from MODIS) for winter wheat monitoring and yield forecasting is estimated. As the part of crop monitoring workflow (vegetation anomaly detection, vegetation indexes and products analysis) and yield forecasting SPIRITS tool developed by JRC is used. Statistics extraction is done for landcover maps created in SRI within FP-7 SIGMA project. Efficiency of usage satellite based and modelled with WOFOST model biophysical products is estimated. [1] N. Kussul, S. Skakun, A. Shelestov, O. Kussul, "Sensor Web approach to Flood Monitoring and Risk Assessment", in: IGARSS 2013, 21-26 July 2013, Melbourne, Australia, pp. 815-818. [2] F. Kogan, N. Kussul, T. Adamenko, S. Skakun, O. Kravchenko, O. Kryvobok, A. Shelestov, A. Kolotii, O. Kussul, and A. Lavrenyuk, "Winter wheat yield forecasting in Ukraine based on Earth observation, meteorological data and biophysical models," International Journal of Applied Earth Observation and Geoinformation, vol. 23, pp. 192-203, 2013. [3] Kussul O., Kussul N., Skakun S., Kravchenko O., Shelestov A., Kolotii A, "Assessment of relative efficiency of using MODIS data to winter wheat yield forecasting in Ukraine", in: IGARSS 2013, 21-26 July 2013, Melbourne, Australia, pp. 3235 - 3238.

  7. Biophysical Assessment of Single Cell Cytotoxicity: Diesel Exhaust Particle-Treated Human Aortic Endothelial Cells

    OpenAIRE

    Wu, Yangzhe; Yu, Tian; Gilbertson, Timothy A.; Zhou, Anhong; Xu, Hao; Nguyen, Kytai Truong

    2012-01-01

    Exposure to diesel exhaust particles (DEPs), a major source of traffic-related air pollution, has become a serious health concern due to its adverse influences on human health including cardiovascular and respiratory disorders. To elucidate the relationship between biophysical properties (cell topography, cytoskeleton organizations, and cell mechanics) and functions of endothelial cells exposed to DEPs, atomic force microscope (AFM) was applied to analyze the toxic effects of DEPs on a model ...

  8. Biochemical and Biophysical Cues in Matrix Design for Chronic and Diabetic Wound Treatment

    OpenAIRE

    Xiao, Yun; Ahadian, Samad; Radisic, Milica

    2017-01-01

    Progress in biomaterial science and engineering and increasing knowledge in cell biology have enabled us to develop functional biomaterials providing appropriate biochemical and biophysical cues for tissue regeneration applications. Tissue regeneration is particularly important to treat chronic wounds of people with diabetes. Understanding and controlling the cellular microenvironment of the wound tissue are important to improve the wound healing process. In this study, we review different bi...

  9. A biophysical model for identifying splicing regulatory elements and their interactions.

    Directory of Open Access Journals (Sweden)

    Ji Wen

    Full Text Available Alternative splicing (AS of precursor mRNA (pre-mRNA is a crucial step in the expression of most eukaryotic genes. Splicing factors (SFs play an important role in AS regulation by binding to the cis-regulatory elements on the pre-mRNA. Although many splicing factors (SFs and their binding sites have been identified, their combinatorial regulatory effects remain to be elucidated. In this paper, we derive a biophysical model for AS regulation that integrates combinatorial signals of cis-acting splicing regulatory elements (SREs and their interactions. We also develop a systematic framework for model inference. Applying the biophysical model to a human RNA-Seq data set, we demonstrate that our model can explain 49.1%-66.5% variance of the data, which is comparable to the best result achieved by biophysical models for transcription. In total, we identified 119 SRE pairs between different regions of cassette exons that may regulate exon or intron definition in splicing, and 77 SRE pairs from the same region that may arise from a long motif or two different SREs bound by different SFs. Particularly, putative binding sites of polypyrimidine tract-binding protein (PTB, heterogeneous nuclear ribonucleoprotein (hnRNP F/H and E/K are identified as interacting SRE pairs, and have been shown to be consistent with the interaction models proposed in previous experimental results. These results show that our biophysical model and inference method provide a means of quantitative modeling of splicing regulation and is a useful tool for identifying SREs and their interactions. The software package for model inference is available under an open source license.

  10. Chemistry and Biophysics. Conversation with Jesús Jiménez-Barbero

    OpenAIRE

    Salgado Benito, Jesús

    2015-01-01

    Chemistry and Biophysics need, and embrace, multidisciplinarity. They both look at problems from many different perspectives. However, while we should not hide behind the walls of disciplines, we cannot ambition to be experts on everything. "We are not in Leonardo's times. Collaboration is essential, as the way to reach far outside our own background knowledge". From his intense career dedicated biomolecular interactions, Jiménez-Barbero knows well how important it is for a chemist working cl...

  11. Polish Academy of Sciences. Institute of Biochemistry and Biophysics. Research Report 1998-1999

    International Nuclear Information System (INIS)

    2000-01-01

    The report presented research activities of the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, in 1998-1999. Research interests focus on: replication, mutagenesis and repair of DNA, regulation of gene expression, biosynthesis and post-translational modifications of proteins, gene sequencing and functional gene analysis, structure and function of enzymes, conformation of proteins and peptides, modeling of structures and prediction of function of proteins

  12. Biophysical and sociocultural factors underlying spatial trade-offs of ecosystem services in semiarid watersheds

    Directory of Open Access Journals (Sweden)

    Marina García-Llorente

    2015-09-01

    Full Text Available Biophysical and social systems are linked to form social-ecological systems whose sustainability depends on their capacity to absorb uncertainty and cope with disturbances. In this study, we explored the key biophysical and socio-cultural factors underlying ecosystem service supply in two semiarid watersheds of southern Spain. These included variables associated with the role that freshwater flows and biodiversity play in securing the system's capacity to sustain essential ecosystem services and their relationship with social demand for services, local water governance, and land-use intensification. Our results reveal the importance of considering the invisible dimensions of water and biodiversity, i.e. green freshwater flows and trait-based indicators, because of their relevance to the supply of ecosystem services. Furthermore, they uncover the importance of traditional irrigation canals, a local water governance system, in maintaining the ecosystems' capacity to supply services. The study also highlights the complex trade-offs that occur because of the spatial mismatch between ecosystem service supply (upstream and ecosystem service demand (downstream in watersheds. Finally, we found that land-use intensification generally resulted in losses of the biophysical factors that underpin the supply of some ecosystem services, increases in social demand for less diversified services, and the abandonment of local governance practices. Attempts to manage social-ecological systems toward sustainability at the local scale should identify the key biophysical and socio-cultural factors that are essential for maintaining ecosystem services and should recognize existing interrelationships between them. Land-use management should also take into account ecosystem service trade-offs and the consequences resulting from land-use intensification.

  13. Biophysical and Economic Uncertainty in the Analysis of Poverty Impacts of Climate Change

    Science.gov (United States)

    Hertel, T. W.; Lobell, D. B.; Verma, M.

    2011-12-01

    This paper seeks to understand the main sources of uncertainty in assessing the impacts of climate change on agricultural output, international trade, and poverty. We incorporate biophysical uncertainty by sampling from a distribution of global climate model predictions for temperature and precipitation for 2050. The implications of these realizations for crop yields around the globe are estimated using the recently published statistical crop yield functions provided by Lobell, Schlenker and Costa-Roberts (2011). By comparing these yields to those predicted under current climate, we obtain the likely change in crop yields owing to climate change. The economic uncertainty in our analysis relates to the response of the global economic system to these biophysical shocks. We use a modified version of the GTAP model to elicit the impact of the biophysical shocks on global patterns of production, consumption, trade and poverty. Uncertainty in these responses is reflected in the econometrically estimated parameters governing the responsiveness of international trade, consumption, production (and hence the intensive margin of supply response), and factor supplies (which govern the extensive margin of supply response). We sample from the distributions of these parameters as specified by Hertel et al. (2007) and Keeney and Hertel (2009). We find that, even though it is difficult to predict where in the world agricultural crops will be favorably affected by climate change, the responses of economic variables, including output and exports can be far more robust (Table 1). This is due to the fact that supply and demand decisions depend on relative prices, and relative prices depend on productivity changes relative to other crops in a given region, or relative to similar crops in other parts of the world. We also find that uncertainty in poverty impacts of climate change appears to be almost entirely driven by biophysical uncertainty.

  14. Enantioseparation with liquid membranes

    NARCIS (Netherlands)

    Gössi, Angelo; Riedl, Wolfgang; Schuur, Boelo

    Chiral resolution of racemic products is a challenging and important task in the pharmaceutical, agrochemical, flavor, polymer and fragrances industries. One of the options for these challenging separations is to use liquid membranes. Although liquid membranes have been known for almost four decades

  15. Porous ceramic membranes

    NARCIS (Netherlands)

    Biesheuvel, P.M.; Biesheuvel, Pieter Maarten

    2000-01-01

    Synthetic membranes are increasingly used for energy-efficient separation of liquid and gaseous mixtures in household applications, environmental technology and the chemical and energy industry. Besides, membranes are used in component-specific sensors in gas and liquid streams, preferably combined

  16. Polymide gas separation membranes

    Science.gov (United States)

    Ding, Yong; Bikson, Benjamin; Nelson, Joyce Katz

    2004-09-14

    Soluble polyamic acid salt (PAAS) precursors comprised of tertiary and quaternary amines, ammonium cations, sulfonium cations, or phosphonium cations, are prepared and fabricated into membranes that are subsequently imidized and converted into rigid-rod polyimide articles, such as membranes with desirable gas separation properties. A method of enhancing solubility of PAAS polymers in alcohols is also disclosed.

  17. Membrane module assembly

    Science.gov (United States)

    Kaschemekat, Jurgen

    1994-01-01

    A membrane module assembly adapted to provide a flow path for the incoming feed stream that forces it into prolonged heat-exchanging contact with a heating or cooling mechanism. Membrane separation processes employing the module assembly are also disclosed. The assembly is particularly useful for gas separation or pervaporation.

  18. Progress and challenges of engineering a biophysical CO2-concentrating mechanism into higher plants.

    Science.gov (United States)

    Rae, Benjamin D; Long, Benedict M; Förster, Britta; Nguyen, Nghiem D; Velanis, Christos N; Atkinson, Nicky; Hee, Wei Yih; Mukherjee, Bratati; Price, G Dean; McCormick, Alistair J

    2017-06-01

    Growth and productivity in important crop plants is limited by the inefficiencies of the C3 photosynthetic pathway. Introducing CO2-concentrating mechanisms (CCMs) into C3 plants could overcome these limitations and lead to increased yields. Many unicellular microautotrophs, such as cyanobacteria and green algae, possess highly efficient biophysical CCMs that increase CO2 concentrations around the primary carboxylase enzyme, Rubisco, to enhance CO2 assimilation rates. Algal and cyanobacterial CCMs utilize distinct molecular components, but share several functional commonalities. Here we outline the recent progress and current challenges of engineering biophysical CCMs into C3 plants. We review the predicted requirements for a functional biophysical CCM based on current knowledge of cyanobacterial and algal CCMs, the molecular engineering tools and research pipelines required to translate our theoretical knowledge into practice, and the current challenges to achieving these goals. © 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.

  19. Biophysically-based modelling of the interstitial cells of Cajal: Current status and future perspectives

    Directory of Open Access Journals (Sweden)

    Rachel eLees-Green

    2011-07-01

    Full Text Available Gastrointestinal motility research is progressing rapidly, leading to significant advances in the last 15 years in understanding the cellular mechanisms underlying motility, following the discovery of the central role played by the interstitial cells of Cajal (ICC. As experimental knowledge of ICC physiology has expanded, biophysically-based modelling has become a valuable tool for integrating experimental data, for testing hypotheses on ICC pacemaker mechanisms, and for applications in in silico studies including in multiscale models. This review is focused on the cellular electrophysiology of ICC. Recent evidence from both experimental and modelling domains have called aspects of the existing pacemaker theories into question. Therefore, current experimental knowledge of ICC pacemaker mechanisms is examined in depth, and current theories of ICC pacemaking are evaluated and further developed. Existing biophysically-based ICC models and their physiological foundations are then critiqued in light of the recent advances in experimental knowledge, and opportunities to improve these models are identified. The review concludes by examining several potential clinical applications of biophysically-based ICC modelling from the subcellular through to the organ level, including ion channelopathies and ICC network degradation.

  20. Final report for Conference Support Grant "From Computational Biophysics to Systems Biology - CBSB12"

    Energy Technology Data Exchange (ETDEWEB)

    Hansmann, Ulrich H.E.

    2012-07-02

    This report summarizes the outcome of the international workshop From Computational Biophysics to Systems Biology (CBSB12) which was held June 3-5, 2012, at the University of Tennessee Conference Center in Knoxville, TN, and supported by DOE through the Conference Support Grant 120174. The purpose of CBSB12 was to provide a forum for the interaction between a data-mining interested systems biology community and a simulation and first-principle oriented computational biophysics/biochemistry community. CBSB12 was the sixth in a series of workshops of the same name organized in recent years, and the second that has been held in the USA. As in previous years, it gave researchers from physics, biology, and computer science an opportunity to acquaint each other with current trends in computational biophysics and systems biology, to explore venues of cooperation, and to establish together a detailed understanding of cells at a molecular level. The conference grant of $10,000 was used to cover registration fees and provide travel fellowships to selected students and postdoctoral scientists. By educating graduate students and providing a forum for young scientists to perform research into the working of cells at a molecular level, the workshop adds to DOE's mission of paving the way to exploit the abilities of living systems to capture, store and utilize energy.

  1. Morphological, structural and biophysical properties of French and Brazilian photoaged skin.

    Science.gov (United States)

    Mercurio, D G; Jdid, R; Morizot, F; Masson, P; Maia Campos, P M B G

    2016-03-01

    Knowledge of skin biology and its alterations in different populations is very important for the development of appropriate skincare strategies. To evaluate and compare morphological, structural and biophysical properties of photoaged skin in French and Brazilian populations, using biophysical and skin-imaging techniques. Forty-one French and 41 Brazilian healthy, female volunteers aged between 40 and 65 years were enrolled. Each participant completed a questionnaire concerning habits related to cosmetic use, sun exposure and sun protection during different life periods. Skin on the face and volar forearm was evaluated using noninvasive techniques, to determine skin colour, transepidermal water loss (TEWL), stratum corneum water content, skin microrelief, skin viscoelasticity and dermis structure. Reflectance confocal microscopy was used to measure epidermal layer thickness and epidermal morphological and structural characteristics. Compared with Brazilian skin, French skin was more hydrated, had a lower TEWL and presented a distinct viscoelastic profile on the forearms and face. Brazilian facial skin was more wrinkled, and the dermis was less echogenic on the forearms and face. The French participants had thicker stratum corneum. Brazilian facial skin presented a higher prevalence of rete ridge effacement, low interkeratinocyte reflectance, huddled collagen and solar elastosis. Morphological, structural and biophysical differences were found when assessing the skin of the Brazilian and French participants, who were exposed to different environmental factors. © 2015 British Association of Dermatologists.

  2. Biophysical Approach to Mechanisms of Cancer Prevention and Treatment with Green Tea Catechins.

    Science.gov (United States)

    Suganuma, Masami; Takahashi, Atsushi; Watanabe, Tatsuro; Iida, Keisuke; Matsuzaki, Takahisa; Yoshikawa, Hiroshi Y; Fujiki, Hirota

    2016-11-18

    Green tea catechin and green tea extract are now recognized as non-toxic cancer preventives for humans. We first review our brief historical development of green tea cancer prevention. Based on exciting evidence that green tea catechin, (-)-epigallocatechin gallate (EGCG) in drinking water inhibited lung metastasis of B16 melanoma cells, we and other researchers have studied the inhibitory mechanisms of metastasis with green tea catechins using biomechanical tools, atomic force microscopy (AFM) and microfluidic optical stretcher. Specifically, determination of biophysical properties of cancer cells, low cell stiffness, and high deformability in relation to migration, along with biophysical effects, were studied by treatment with green tea catechins. The study with AFM revealed that low average values of Young's moduli, indicating low cell stiffness, are closely associated with strong potential of cell migration and metastasis for various cancer cells. It is important to note that treatments with EGCG and green tea extract elevated the average values of Young's moduli resulting in increased stiffness (large elasticity) of melanomas and various cancer cells. We discuss here the biophysical basis of multifunctions of green tea catechins and green tea extract leading to beneficial effects for cancer prevention and treatment.

  3. Biophysical Approach to Mechanisms of Cancer Prevention and Treatment with Green Tea Catechins

    Directory of Open Access Journals (Sweden)

    Masami Suganuma

    2016-11-01

    Full Text Available Green tea catechin and green tea extract are now recognized as non-toxic cancer preventives for humans. We first review our brief historical development of green tea cancer prevention. Based on exciting evidence that green tea catechin, (−-epigallocatechin gallate (EGCG in drinking water inhibited lung metastasis of B16 melanoma cells, we and other researchers have studied the inhibitory mechanisms of metastasis with green tea catechins using biomechanical tools, atomic force microscopy (AFM and microfluidic optical stretcher. Specifically, determination of biophysical properties of cancer cells, low cell stiffness, and high deformability in relation to migration, along with biophysical effects, were studied by treatment with green tea catechins. The study with AFM revealed that low average values of Young’s moduli, indicating low cell stiffness, are closely associated with strong potential of cell migration and metastasis for various cancer cells. It is important to note that treatments with EGCG and green tea extract elevated the average values of Young’s moduli resulting in increased stiffness (large elasticity of melanomas and various cancer cells. We discuss here the biophysical basis of multifunctions of green tea catechins and green tea extract leading to beneficial effects for cancer prevention and treatment.

  4. Assessment of the biophysical impacts of utility-scale photovoltaics through observations and modelling

    Science.gov (United States)

    Broadbent, A. M.; Georgescu, M.; Krayenhoff, E. S.; Sailor, D.

    2017-12-01

    Utility-scale solar power plants are a rapidly growing component of the solar energy sector. Utility-scale photovoltaic (PV) solar power generation in the United States has increased by 867% since 2012 (EIA, 2016). This expansion is likely to continue as the cost PV technologies decrease. While most agree that solar power can decrease greenhouse gas emissions, the biophysical effects of PV systems on surface energy balance (SEB), and implications for surface climate, are not well understood. To our knowledge, there has never been a detailed observational study of SEB at a utility-scale solar array. This study presents data from an eddy covariance observational tower, temporarily placed above a utility-scale PV array in Southern Arizona. Comparison of PV SEB with a reference (unmodified) site, shows that solar panels can alter the SEB and near surface climate. SEB observations are used to develop and validate a new and more complete SEB PV model. In addition, the PV model is compared to simpler PV modelling methods. The simpler PV models produce differing results to our newly developed model and cannot capture the more complex processes that influence PV SEB. Finally, hypothetical scenarios of PV expansion across the continental United States (CONUS) were developed using various spatial mapping criteria. CONUS simulations of PV expansion reveal regional variability in biophysical effects of PV expansion. The study presents the first rigorous and validated simulations of the biophysical effects of utility-scale PV arrays.

  5. A biotic video game smart phone kit for formal and informal biophysics education

    Science.gov (United States)

    Kim, Honesty; Lee, Seung Ah; Riedel-Kruse, Ingmar

    2015-03-01

    Novel ways for formal and informal biophysics education are important. We present a low-cost biotic game design kit that incorporates microbial organisms into an interactive gaming experience: A 3D-printable microscope containing four LEDs controlled by a joystick enable human players to provide directional light stimuli to the motile single-celled organism Euglena gracilis. These cellular behaviors are displayed on the integrated smart phone. Real time cell-tracking couples these cells into interactive biotic video game play, i.e., the human player steers Euglena to play soccer with virtual balls and goals. The player's learning curve in mastering this fun game is intrinsically coupled to develop a deeper knowledge about Euglena's cell morphology and the biophysics of its phototactic behavior. This kit is dual educational - via construction and via play - and it provides an engaging theme for a formal biophysics devices class as well as to be presented in informal outreach activities; its low cost and open soft- and hardware should enable wide adoption.

  6. BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE

    Science.gov (United States)

    Rao, Archana N.; Grainger, David W.

    2014-01-01

    Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA’s persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools. PMID:24765522

  7. Human Pluripotent Stem Cell Mechanobiology: Manipulating the Biophysical Microenvironment for Regenerative Medicine and Tissue Engineering Applications.

    Science.gov (United States)

    Ireland, Ronald G; Simmons, Craig A

    2015-11-01

    A stem cell in its microenvironment is subjected to a myriad of soluble chemical cues and mechanical forces that act in concert to orchestrate cell fate. Intuitively, many of these soluble and biophysical factors have been the focus of intense study to successfully influence and direct cell differentiation in vitro. Human pluripotent stem cells (hPSCs) have been of considerable interest in these studies due to their great promise for regenerative medicine. Culturing and directing differentiation of hPSCs, however, is currently extremely labor-intensive and lacks the efficiency required to generate large populations of clinical-grade cells. Improved efficiency may come from efforts to understand how the cell biophysical signals can complement biochemical signals to regulate cell pluripotency and direct differentiation. In this concise review, we explore hPSC mechanobiology and how the hPSC biophysical microenvironment can be manipulated to maintain and differentiate hPSCs into functional cell types for regenerative medicine and tissue engineering applications. © 2015 AlphaMed Press.

  8. Variation of Biophysical Parameters of the Skin with Age, Gender, and Body Region

    Directory of Open Access Journals (Sweden)

    Alireza Firooz

    2012-01-01

    Full Text Available Background. Understanding the physiological, chemical, and biophysical characteristics of the skin helps us to arrange a proper approach to the management of skin diseases. Objective. The aim of this study was to measure 6 biophysical characteristics of normal skin (sebum content, hydration, transepidermal water loss (TEWL, erythema index, melanin index, and elasticity in a normal population and assess the effect of sex, age, and body location on them. Methods. Fifty healthy volunteers in 5 age groups (5 males and females in each were enrolled in this study. A multifunctional skin physiology monitor (Courage & Khazaka electronic GmbH, Germany was used to measure skin sebum content, hydration, TEWL, erythema index, melanin index, and elasticity in 8 different locations of the body. Results. There were significant differences between the hydration, melanin index, and elasticity of different age groups. Regarding the locations, forehead had the highest melanin index, where as palm had the lowest value. The mean values of erythema index and melanin index and TEWL were significantly higher in males and anatomic location was a significant independent factor for all of 6 measured parameters. Conclusion. Several biophysical properties of the skin vary among different gender, age groups, and body locations.

  9. Time-resolved methods in biophysics. 9. Laser temperature-jump methods for investigating biomolecular dynamics.

    Science.gov (United States)

    Kubelka, Jan

    2009-04-01

    Many important biochemical processes occur on the time-scales of nanoseconds and microseconds. The introduction of the laser temperature-jump (T-jump) to biophysics more than a decade ago opened these previously inaccessible time regimes up to direct experimental observation. Since then, laser T-jump methodology has evolved into one of the most versatile and generally applicable methods for studying fast biomolecular kinetics. This perspective is a review of the principles and applications of the laser T-jump technique in biophysics. A brief overview of the T-jump relaxation kinetics and the historical development of laser T-jump methodology is presented. The physical principles and practical experimental considerations that are important for the design of the laser T-jump experiments are summarized. These include the Raman conversion for generating heating pulses, considerations of size, duration and uniformity of the temperature jump, as well as potential adverse effects due to photo-acoustic waves, cavitation and thermal lensing, and their elimination. The laser T-jump apparatus developed at the NIH Laboratory of Chemical Physics is described in detail along with a brief survey of other laser T-jump designs in use today. Finally, applications of the laser T-jump in biophysics are reviewed, with an emphasis on the broad range of problems where the laser T-jump methodology has provided important new results and insights into the dynamics of the biomolecular processes.

  10. Age of oil palm plantations causes a strong change in surface biophysical variables

    Science.gov (United States)

    Sabajo, Clifton; le Maire, Guerric; Knohl, Alexander

    2016-04-01

    Over the last decades, Indonesia has experienced dramatic land transformations with an expansion of oil palm plantations at the expense of tropical forests. As vegetation is a modifier of the climate near the ground these large-scale land transformations are expected to have major impacts on the surface biophysical variables i.e. surface temperature, albedo, and vegetation indices, e.g. the NDVI. Remote sensing data are needed to assess such changes at regional scale. We used 2 Landsat images from Jambi Province in Sumatra/Indonesia covering a chronosequence of oil palm plantations to study the 20 - 25 years life cycle of oil palm plantations and its relation with biophysical variables. Our results show large differences between the surface temperature of young oil palm plantations and forest (up to 9.5 ± 1.5 °C) indicating that the surface temperature is raised substantially after the establishment of oil palm plantations following the removal of forests. During the oil palm plantation lifecycle the surface temperature differences gradually decreases and approaches zero around an oil palm plantation age of 10 years. Similarly, NDVI increases and the albedo decreases approaching typical values of forests. Our results show that in order to assess the full climate effects of oil palm expansion biophysical processes play an important role and the full life cycle of oil palm plantations need to be considered.

  11. Elastic membranes in confinement.

    Science.gov (United States)

    Bostwick, J B; Miksis, M J; Davis, S H

    2016-07-01

    An elastic membrane stretched between two walls takes a shape defined by its length and the volume of fluid it encloses. Many biological structures, such as cells, mitochondria and coiled DNA, have fine internal structure in which a membrane (or elastic member) is geometrically 'confined' by another object. Here, the two-dimensional shape of an elastic membrane in a 'confining' box is studied by introducing a repulsive confinement pressure that prevents the membrane from intersecting the wall. The stage is set by contrasting confined and unconfined solutions. Continuation methods are then used to compute response diagrams, from which we identify the particular membrane mechanics that generate mitochondria-like shapes. Large confinement pressures yield complex response diagrams with secondary bifurcations and multiple turning points where modal identities may change. Regions in parameter space where such behaviour occurs are then mapped. © 2016 The Author(s).

  12. Membrane projection lithography

    Energy Technology Data Exchange (ETDEWEB)

    Burckel, David Bruce; Davids, Paul S; Resnick, Paul J; Draper, Bruce L

    2015-03-17

    The various technologies presented herein relate to a three dimensional manufacturing technique for application with semiconductor technologies. A membrane layer can be formed over a cavity. An opening can be formed in the membrane such that the membrane can act as a mask layer to the underlying wall surfaces and bottom surface of the cavity. A beam to facilitate an operation comprising any of implantation, etching or deposition can be directed through the opening onto the underlying surface, with the opening acting as a mask to control the area of the underlying surfaces on which any of implantation occurs, material is removed, and/or material is deposited. The membrane can be removed, a new membrane placed over the cavity and a new opening formed to facilitate another implantation, etching, or deposition operation. By changing the direction of the beam different wall/bottom surfaces can be utilized to form a plurality of structures.

  13. Membrane technology and applications

    International Nuclear Information System (INIS)

    Khalil, F.H.

    1997-01-01

    The main purpose of this dissertation is to prepare and characterize some synthetic membranes obtained by radiation-induced graft copolymerization of and A Am unitary and binary system onto nylon-6 films. The optimum conditions at which the grafting process proceeded homogeneously were determined. Some selected properties of the prepared membranes were studied. Differential scanning calorimetry (DSC), thermal gravimetric analysis (TGA), x-ray diffraction (XRD), mechanical properties and U.V./vis, instruments and techniques were used to characterize the prepared membranes. The use of such membranes for the decontamination of radioactive waste and some heavy metal ions as water pollutants were investigated. These grafted membranes showed good cation exchange properties and may be of practical interest in waste water treatment whether this water was radioactive or not. 4 tabs., 68 figs., 146 refs

  14. A subsequent closed-form description of propagated signaling phenomena in the membrane of an axon

    Science.gov (United States)

    Melendy, Robert. F.

    2016-05-01

    I recently introduced a closed-form description of propagated signaling phenomena in the membrane of an axon [R.F. Melendy, Journal of Applied Physics 118, 244701 (2015)]. Those results demonstrate how intracellular conductance, the thermodynamics of magnetization, and current modulation, function together in generating an action potential in a unified, closed-form description. At present, I report on a subsequent closed-form model that unifies intracellular conductance and the thermodynamics of magnetization, with the membrane electric field, Em. It's anticipated this work will compel researchers in biophysics, physical biology, and the computational neurosciences, to probe deeper into the classical and quantum features of membrane magnetization and signaling, informed by the computational features of this subsequent model.

  15. A subsequent closed-form description of propagated signaling phenomena in the membrane of an axon

    Energy Technology Data Exchange (ETDEWEB)

    Melendy, Robert F., E-mail: rfmelendy@liberty.edu [School of Engineering and Computational Science, Liberty University, Lynchburg, Virginia, 24515 (United States)

    2016-05-15

    I recently introduced a closed-form description of propagated signaling phenomena in the membrane of an axon [R.F. Melendy, Journal of Applied Physics 118, 244701 (2015)]. Those results demonstrate how intracellular conductance, the thermodynamics of magnetization, and current modulation, function together in generating an action potential in a unified, closed-form description. At present, I report on a subsequent closed-form model that unifies intracellular conductance and the thermodynamics of magnetization, with the membrane electric field, E{sub m}. It’s anticipated this work will compel researchers in biophysics, physical biology, and the computational neurosciences, to probe deeper into the classical and quantum features of membrane magnetization and signaling, informed by the computational features of this subsequent model.

  16. A New Strain Collection for Improved Expression of Outer Membrane Proteins

    Directory of Open Access Journals (Sweden)

    Ina Meuskens

    2017-11-01

    Full Text Available Almost all integral membrane proteins found in the outer membranes of Gram-negative bacteria belong to the transmembrane β-barrel family. These proteins are not only important for nutrient uptake and homeostasis, but are also involved in such processes as adhesion, protein secretion, biofilm formation, and virulence. As surface exposed molecules, outer membrane β-barrel proteins are also potential drug and vaccine targets. High production levels of heterologously expressed proteins are desirable for biochemical and especially structural studies, but over-expression and subsequent purification of membrane proteins, including outer membrane proteins, can be challenging. Here, we present a set of deletion mutants derived from E. coli BL21(DE3 designed for the over-expression of recombinant outer membrane proteins. These strains harbor deletions of four genes encoding abundant β-barrel proteins in the outer membrane (OmpA, OmpC, OmpF, and LamB, both single and in all combinations of double, triple, and quadruple knock-outs. The sequences encoding these outer membrane proteins were deleted completely, leaving only a minimal scar sequence, thus preventing the possibility of genetic reversion. Expression tests in the quadruple mutant strain with four test proteins, including a small outer membrane β-barrel protein and variants thereof as well as two virulence-related autotransporters, showed significantly improved expression and better quality of the produced proteins over the parent strain. Differences in growth behavior and aggregation in the presence of high salt were observed, but these phenomena did not negatively influence the expression in the quadruple mutant strain when handled as we recommend. The strains produced in this study can be used for outer membrane protein production and purification, but are also uniquely useful for labeling experiments for biophysical measurements in the native membrane environment.

  17. The Acinar Cage: Basement Membranes Determine Molecule Exchange and Mechanical Stability of Human Breast Cell Acini.

    Directory of Open Access Journals (Sweden)

    Aljona Gaiko-Shcherbak

    Full Text Available The biophysical properties of the basement membrane that surrounds human breast glands are poorly understood, but are thought to be decisive for normal organ function and malignancy. Here, we characterize the breast gland basement membrane with a focus on molecule permeation and mechanical stability, both crucial for organ function. We used well-established and nature-mimicking MCF10A acini as 3D cell model for human breast glands, with ether low- or highly-developed basement membrane scaffolds. Semi-quantitative dextran tracer (3 to 40 kDa experiments allowed us to investigate the basement membrane scaffold as a molecule diffusion barrier in human breast acini in vitro. We demonstrated that molecule permeation correlated positively with macromolecule size and intriguingly also with basement membrane development state, revealing a pore size of at least 9 nm. Notably, an intact collagen IV mesh proved to be essential for this permeation function. Furthermore, we performed ultra-sensitive atomic force microscopy to quantify the response of native breast acini and of decellularized basement membrane shells against mechanical indentation. We found a clear correlation between increasing acinar force resistance and basement membrane formation stage. Most important native acini with highly-developed basement membranes as well as cell-free basement membrane shells could both withstand physiologically relevant loads (≤ 20 nN without loss of structural integrity. In contrast, low-developed basement membranes were significantly softer and more fragile. In conclusion, our study emphasizes the key role of the basement membrane as conductor of acinar molecule influx and mechanical stability of human breast glands, which are fundamental for normal organ function.

  18. HIV gp41 fusion peptide increases membrane ordering in a cholesterol-dependent fashion.

    Science.gov (United States)

    Lai, Alex L; Freed, Jack H

    2014-01-07

    Fusion between viral envelopes and host cell membranes, which is mediated by special glycoproteins anchored on the viral membrane, is required for HIV viral entry and infection. The HIV gp41 fusion peptide (FP), which initiates membrane fusion, adopts either an α-helical or β-sheeted structure depending on the cholesterol concentration. We used phosphocholine spin labels on the lipid headgroup and different positions on the acyl chain to detect its perturbation on lipid bilayers containing different cholesterol concentrations by electron-spin resonance. Our findings were as follows. 1), gp41 FP affects the lipid order in the same manner as previously shown for influenza hemagglutinin FP, i.e., it has a cooperative effect versus the peptide/lipid ratio, supporting our hypothesis that membrane ordering is a common prerequisite for viral membrane fusion. 2), gp41 FP induces membrane ordering in all lipid compositions studied, whereas a nonfusion mutant FP perturbs lipid order to a significantly smaller extent. 3), In high-cholesterol-containing lipid bilayers, where gp41 FP is in the β-aggregation conformation, its effect on the lipid ordering reaches deeper into the bilayer. The different extent to which the two conformers perturb is correlated with their fusogenicity. The possible role of the two conformers in membrane fusion is discussed. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  19. Epigenetic Modulation of the Biophysical Properties of Drug-Resistant Cell Lipids to Restore Drug Transport and Endocytic Functions

    OpenAIRE

    Vijayaraghavalu, Sivakumar; Peetla, Chiranjeevi; Lu, Shan; Labhasetwar, Vinod

    2012-01-01

    In our recent studies exploring the biophysical characteristics of resistant cell lipids, and the role they play in drug transport, we demonstrated the difference of drug-resistant breast cancer cells from drug-sensitive cells in lipid composition and biophysical properties, suggesting that cancer cells acquire a drug-resistant phenotype through the alteration of lipid synthesis to inhibit intracellular drug transport to protect from cytotoxic effect. In cancer cells, epigenetic changes (e.g....

  20. Population size dependence of fitness effect distribution and substitution rate probed by biophysical model of protein thermostability

    OpenAIRE

    Goldstein, R. A.

    2013-01-01

    The predicted effect of effective population size on the distribution of fitness effects and substitution rate is critically dependent on the relationship between sequence and fitness. This highlights the importance of using models that are informed by the molecular biology, biochemistry, and biophysics of the evolving systems. We describe a computational model based on fundamental aspects of biophysics, the requirement for (most) proteins to be thermodynamically stable. Using this model, we ...

  1. Application of virus-like particles (VLP) to NMR characterization of viral membrane protein interactions

    Energy Technology Data Exchange (ETDEWEB)

    Antanasijevic, Aleksandar; Kingsley, Carolyn [University of Illinois at Chicago, Department of Biochemistry and Molecular Genetics (United States); Basu, Arnab; Bowlin, Terry L. [Microbiotix Inc. (United States); Rong, Lijun [University of Illinois at Chicago, Department of Microbiology and Immunology (United States); Caffrey, Michael, E-mail: caffrey@uic.edu [University of Illinois at Chicago, Department of Biochemistry and Molecular Genetics (United States)

    2016-03-15

    The membrane proteins of viruses play critical roles in the virus life cycle and are attractive targets for therapeutic intervention. Virus-like particles (VLP) present the possibility to study the biochemical and biophysical properties of viral membrane proteins in their native environment. Specifically, the VLP constructs contain the entire protein sequence and are comprised of native membrane components including lipids, cholesterol, carbohydrates and cellular proteins. In this study we prepare VLP containing full-length hemagglutinin (HA) or neuraminidase (NA) from influenza and characterize their interactions with small molecule inhibitors. Using HA-VLP, we first show that VLP samples prepared using the standard sucrose gradient purification scheme contain significant amounts of serum proteins, which exhibit high potential for non-specific interactions, thereby complicating NMR studies of ligand-target interactions. We then show that the serum contaminants may be largely removed with the addition of a gel filtration chromatography step. Next, using HA-VLP we demonstrate that WaterLOGSY NMR is significantly more sensitive than Saturation Transfer Difference (STD) NMR for the study of ligand interactions with membrane bound targets. In addition, we compare the ligand orientation to HA embedded in VLP with that of recombinant HA by STD NMR. In a subsequent step, using NA-VLP we characterize the kinetic and binding properties of substrate analogs and inhibitors of NA, including study of the H274Y-NA mutant, which leads to wide spread resistance to current influenza antivirals. In summary, our work suggests that VLP have high potential to become standard tools in biochemical and biophysical studies of viral membrane proteins, particularly when VLP are highly purified and combined with control VLP containing native membrane proteins.

  2. Representing biophysical landscape interactions in soil models by bridging disciplines and scales.

    Science.gov (United States)

    van der Ploeg, M. J.; Carranza, C.; Teixeira da Silva, R.; te Brake, B.; Baartman, J.; Robinson, D.

    2017-12-01

    The combination of climate change, population growth and soil threats including carbon loss, biodiversity decline and erosion, increasingly confront the global community (Schwilch et al., 2016). One major challenge in studying processes involved in soil threats, landscape resilience, ecosystem stability, sustainable land management and resulting economic consequences, is that it is an interdisciplinary field (Pelletier et al., 2012). Less stringent scientific disciplinary boundaries are therefore important (Liu et al., 2007), because as a result of disciplinary focus, ambiguity may arise on the understanding of landscape interactions. This is especially true in the interaction between a landscape's physical and biological processes (van der Ploeg et al. 2012). Biophysical landscape interactions are those biotic and abiotic processes in a landscape that have an influence on the developments within and evolution of a landscape. An important aspect in biophysical landscape interactions is the differences in scale related to the various processes that play a role in these systems. Moreover, the interplay between the physical landscape and the occurring vegetation, which often co-evolve, and the resulting heterogeneity and emerging patterns are the reason why it is so challenging to establish a theoretical basis to describe biophysical processes in landscapes (e.g. te Brake et al. 2013, Robinson et al. 2016). Another complicating factor is the response of vegetation to changing environmental conditions, including a possible, and often unknown, time-lag (e.g. Metzger et al., 2009). An integrative description for modelling biophysical interactions has been a long standing goal in soil science (Vereecken et al., 2016). We need the development of soil models that are more focused on networks, connectivity and feedbacks incorporating the most important aspects of our detailed mechanistic modelling (Paola & Leeder, 2011). Additionally, remote sensing measurement techniques

  3. Biophysical and Socioeconomic Factors Associated with Forest Transitions at Multiple Spatial and Temporal Scales

    Directory of Open Access Journals (Sweden)

    Charles B. Yackulic

    2011-09-01

    Full Text Available Forest transitions (FT occur when socioeconomic development leads to a shift from net deforestation to reforestation; these dynamics have been observed in multiple countries across the globe, including the island of Puerto Rico in the Caribbean. Starting in the 1950s, Puerto Rico transitioned from an agrarian to a manufacturing and service economy reliant on food imports, leading to extensive reforestation. In recent years, however, net reforestation has leveled off. Here we examine the drivers of forest transition in Puerto Rico from 1977 to 2000 at two subnational, nested spatial scales (municipality and barrio and over two time periods (1977-1991 and 1991-2000. This study builds on previous work by considering the social and biophysical factors that influence both reforestation and deforestation at multiple spatial and temporal scales. By doing so within one analysis, this study offers a comprehensive understanding of the relative importance of various social and biophysical factors for forest transitions and the scales at which they are manifest. Biophysical factors considered in these analyses included slope, soil quality, and land-cover in the surrounding landscape. We also considered per capita income, population density, and the extent of protected areas as potential factors associated with forest change. Our results show that, in the 1977-1991 period, biophysical factors that exhibit variation at municipality scales (~100 km² were more important predictors of forest change than socioeconomic factors. In this period, forest dynamics were driven primarily by abandonment of less productive, steep agricultural land in the western, central part of the island. These factors had less predictive power at the smaller barrio scale (~10 km² relative to the larger municipality scale during this time period. The relative importance of socioeconomic variables for deforestation, however, increased over time as development pressures on available land

  4. Hierarchy and Interactions in Environmental Interfaces Regarded as Biophysical Complex Systems

    Science.gov (United States)

    Mihailovic, Dragutin T.; Balaz, Igor

    The field of environmental sciences is abundant with various interfaces and is the right place for the application of new fundamental approaches leading towards a better understanding of environmental phenomena. For example, following the definition of environmental interface by Mihailovic and Balaž [23], such interface can be placed between: human or animal bodies and surrounding air, aquatic species and water and air around them, and natural or artificially built surfaces (vegetation, ice, snow, barren soil, water, urban communities) and the atmosphere. Complex environmental interface systems are open and hierarchically organised, interactions between their constituent parts are nonlinear, and the interaction with the surrounding environment is noisy. These systems are therefore very sensitive to initial conditions, deterministic external perturbations and random fluctuations always present in nature. The study of noisy non-equilibrium processes is fundamental for modelling the dynamics of environmental interface systems and for understanding the mechanisms of spatio-temporal pattern formation in contemporary environmental sciences, particularly in environmental fluid mechanics. In modelling complex biophysical systems one of the main tasks is to successfully create an operative interface with the external environment. It should provide a robust and prompt translation of the vast diversity of external physical and/or chemical changes into a set of signals, which are "understandable" for an organism. Although the establishment of organisation in any system is of crucial importance for its functioning, it should not be forgotten that in biophysical systems we deal with real-life problems where a number of other conditions should be reached in order to put the system to work. One of them is the proper supply of the system by the energy. Therefore, we will investigate an aspect of dynamics of energy flow based on the energy balance equation. The energy as well as

  5. Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating.

    Science.gov (United States)

    Yoo, Jejoong; Aksimentiev, Aleksei

    2015-12-03

    DNA self-assembly has emerged as a new paradigm for design of biomimetic membrane channels. Several experimental groups have already demonstrated assembly and insertion of DNA channels into lipid bilayer membranes; however, the structure of the channels and their conductance mechanism have remained undetermined. Here, we report the results of molecular dynamics simulations that characterized the biophysical properties of the DNA membrane channels with atomic precision. We show that, while overall remaining stable, the local structure of the channels undergoes considerable fluctuations, departing from the idealized design. The transmembrane ionic current flows both through the central pore of the channel as well as along the DNA walls and through the gaps in the DNA structure. Surprisingly, we find that the conductance of DNA channels depend on the membrane tension, making them potentially suitable for force-sensing applications. Finally, we show that electro-osmosis governs the transport of druglike molecules through the DNA channels.

  6. Fluorine NMR-based screening on cell membrane extracts.

    Science.gov (United States)

    Veronesi, Marina; Romeo, Elisa; Lambruschini, Chiara; Piomelli, Daniele; Bandiera, Tiziano; Scarpelli, Rita; Garau, Gianpiero; Dalvit, Claudio

    2014-02-01

    The possibility of measuring the action of inhibitors of specific enzymatic reactions in intact cells, cell lysates or membrane preparations represents a major advance in the lead discovery process. Despite the relevance of assaying in physiological conditions, only a small number of biophysical techniques, often requiring complex set-up, are applicable to these sample types. Here, we demonstrate the first application of n-fluorine atoms for biochemical screening (n-FABS), a homogeneous and versatile assay based on (19) F NMR spectroscopy, to the detection of high- and low-affinity inhibitors of a membrane enzyme in cell extracts and determination of their IC50 values. Our approach can allow the discovery of novel binding fragments against targets known to be difficult to purify or where membrane-association is required for activity. These results pave the way for future applications of the methodology to these relevant and complex biological systems. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Variation of the detergent-binding capacity and phospholipid content of membrane proteins when purified in different detergents.

    Science.gov (United States)

    Ilgü, Hüseyin; Jeckelmann, Jean-Marc; Gachet, María Salomé; Boggavarapu, Rajendra; Ucurum, Zöhre; Gertsch, Jürg; Fotiadis, Dimitrios

    2014-04-15

    Purified membrane proteins are ternary complexes consisting of protein, lipid, and detergent. Information about the amounts of detergent and endogenous phospholipid molecules bound to purified membrane proteins is largely lacking. In this systematic study, three model membrane proteins of different oligomeric states were purified in nine different detergents at commonly used concentrations and characterized biochemically and biophysically. Detergent-binding capacities and phospholipid contents of the model proteins were determined and compared. The insights on ternary complexes obtained from the experimental results, when put into a general context, are summarized as follows. 1), The amount of detergent and 2) the amount of endogenous phospholipids bound to purified membrane proteins are dependent on the size of the hydrophobic lipid-accessible protein surface areas and the physicochemical properties of the detergents used. 3), The size of the detergent and lipid belt surrounding the hydrophobic lipid-accessible surface of purified membrane proteins can be tuned by the appropriate choice of detergent. 4), The detergents n-nonyl-β-D-glucopyranoside and Cymal-5 have exceptional delipidating effects on ternary complexes. 5), The types of endogenous phospholipids bound to membrane proteins can vary depending on the detergent used for solubilization and purification. 6), Furthermore, we demonstrate that size-exclusion chromatography can be a suitable method for estimating the molecular mass of ternary complexes. The findings presented suggest a strategy to control and tune the numbers of detergent and endogenous phospholipid molecules bound to membrane proteins. These two parameters are potentially important for the successul crystallization of membrane proteins for structure determination by crystallographic approaches. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  8. PERSISTENT PUPILLARY MEMBRANE OR ACCESSORY IRIS MEMBRANE?.

    Science.gov (United States)

    Gavriş, Monica; Horge, Ioan; Avram, Elena; Belicioiu, Roxana; Olteanu, Ioana Alexandra; Kedves, Hanga

    2015-01-01

    Frequently, in literature and curent practice, accessory iris membrane (AIM) and persistant pupillary membrane (PPM) are confused. Both AIM and PPM are congenital iris anomalies in which fine or thick iris strands arrise form the collarette and obscure the pupil. AIM, which is also called iris duplication, closely resembles the normal iris tissue in color and thickness and presents a virtual second pseudopupil aperture in the centre while PPM even in its extreme forms presents as a translucent or opaque membranous structure that extends across the pupil and has no pseudopupil. Mydriatiscs, laser treatment or surgery is used to clear the visual axis and optimize visual development. Surgical intervention is reserved for large, dense AIMs and PPMs. Our patient, a 29 year old male, has come with bilateral dense AIM, bilateral compound hyperopic astigmatism, BCVA OD = 0.6, BCVA OS = 0.4, IOP OU = 17 mmHg. To improve the visual acuity of the patient we decided to do a bilateral membranectomy, restoring in this way transparency of the visual axis. After surgery, the visual acuity improved to BCVA OD= 0.8, BCVA OS=0.8.

  9. Primate cathelicidin orthologues display different structures and membrane interactions.

    Science.gov (United States)

    Morgera, Francesca; Vaccari, Lisa; Antcheva, Nikolinka; Scaini, Denis; Pacor, Sabrina; Tossi, Alessandro

    2009-02-01

    The human cathelicidin LL-37 displays both direct antibacterial activities and the capacity to modulate host-cell activities. These depend on structural characteristics that are subject to positive selection for variation, as observed in a previous analysis of the CAMP gene (encoding LL-37) in primates. The altered balance between cationic and anionic residues in different primate orthologues affects intramolecular salt-bridging and influences the stability of the helical conformation and tendency to aggregate in solution of the peptide. In the present study, we have analysed the effects of these structural variations on membrane interactions for human LL-37, rhesus RL-37 and orang-utan LL-37, using several complementary biophysical and biochemical methods. CD and ATR (attenuated total reflection)-FTIR (Fourier-transform IR) spectroscopy on model membranes indicate that RL-37, which is monomeric and unstructured in bulk solution [F-form (free form)], and human LL-37, which is partly structured and probably aggregated [A-form (aggregated form)], bind biological membranes in different manners. RL-37 may insert more deeply into the lipid bilayer than LL-37, which remains aggregated. AFM (atomic force microscopy) performed on the same supported bilayer as used for ATR-FTIR measurements suggests a carpet-like mode of permeabilization for RL37 and formation of more defined worm-holes for LL-37. Comparison of data from the biological activity on bacterial cells with permeabilization of model membranes indicates that the structure/aggregation state also affects the trajectory of the peptides from bulk solution through the outer cell-wall layers to the membrane. The results of the present study suggest that F-form cathelicidin orthologues may have evolved to have primarily a direct antimicrobial defensive capacity, whereas the A-forms have somewhat sacrificed this to gain host-cell modulating functions.

  10. Fuel cell membrane humidification

    Science.gov (United States)

    Wilson, Mahlon S.

    1999-01-01

    A polymer electrolyte membrane fuel cell assembly has an anode side and a cathode side separated by the membrane and generating electrical current by electrochemical reactions between a fuel gas and an oxidant. The anode side comprises a hydrophobic gas diffusion backing contacting one side of the membrane and having hydrophilic areas therein for providing liquid water directly to the one side of the membrane through the hydrophilic areas of the gas diffusion backing. In a preferred embodiment, the hydrophilic areas of the gas diffusion backing are formed by sewing a hydrophilic thread through the backing. Liquid water is distributed over the gas diffusion backing in distribution channels that are separate from the fuel distribution channels.

  11. Extracorporeal membrane oxygenation

    Science.gov (United States)

    Extracorporeal membrane oxygenation (ECMO) is a treatment that uses a pump to circulate blood through an artificial lung back into the bloodstream of a very ill baby. This system provides heart-lung bypass support ...

  12. Novel Catalytic Membrane Reactors

    Energy Technology Data Exchange (ETDEWEB)

    None

    2009-02-01

    This factsheet describes a research project that will focus on the development and application of nonporous high gas flux perfluoro membranes with high temperature rating and excellent chemical resistance.

  13. Cellular membrane accommodation of copper-induced oxidative conditions in the coral Seriatopora caliendrum

    International Nuclear Information System (INIS)

    Tang, Chuan-Ho; Lin, Ching-Yu; Lee, Shu-Hui; Wang, Wei-Hsien

    2014-01-01

    -phosphatidylcholines were shown to facilitate membrane fusion. Based on the biochemical and biophysical properties of these lipids, the chronic effects of copper, such as coral resistance and growth, can be logically interpreted to result from long-term perturbations in cellular membrane-related functions. In conclusion, the cells of S. caliendrum alter their lipid metabolism and sacrifice fitness to allow the membrane to accommodate copper-induced oxidative situations

  14. Vesicles mimicking normal and cancer cell membranes exhibit differential responses to the cell-penetrating peptide Pep-1.

    Science.gov (United States)

    Almarwani, Bashiyar; Phambu, Esther Nzuzi; Alexander, Christopher; Nguyen, Ha Aimee T; Phambu, Nsoki; Sunda-Meya, Anderson

    2018-06-01

    The cell-penetrating peptide (CPP) Pep-1 presents a great potential in drug delivery due to its intrinsic property to cross plasma membrane. However, its mechanism of entry into the cell remains unresolved. In this study, we compare the selectivity of Pep-1 towards vesicles mimicking normal and cancer cell membranes. The interaction was performed in a wide range of peptide-to-lipid molar ratios using infrared (IR), fluorescence, scanning electron microscopy (SEM), thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) techniques. At low peptide concentration, fluorescence experiments show that lipid-phosphatidylserine (PS) seems to enable Pep-1 translocation into cancer cell membrane as evidenced by the blue shift of its maximal emission wavelength. DSC data show that Pep-1 induces segregation of lipids. At high peptide concentration, IR data indicate that the interaction of Pep-1 is relatively stronger with normal cell membrane than with cancer cell membrane through the phosphate groups, while the interaction is weaker with normal cell membrane than with cancer cell membrane through the carbonyl groups. TGA and DSC data reveal that vesicles of normal cell membrane are thermally more stable than vesicles of cancer cell membrane. This suggests that the additional lipid PS included in cancer cell membrane has a destabilizing effect on the membrane structure. SEM images reveal that Pep-1 form superstructures including spherical particles and fibrils in the presence of both model membranes. PS seems to enhance peptide transport across cellular membranes. The biophysical techniques in this study provide valuable insights into the properties of CPPs in drug delivery systems. Copyright © 2018 Elsevier B.V. All rights reserved.

  15. Biophysics Education

    Science.gov (United States)

    Panijpan, Bhinyo

    2010-07-01

    Many topics in basic physics are presented to the students based on examples that they find too intangible, uninteresting and unrelated to the real world. We propose here some examples from the biological world that can equally be used to illustrate seemingly arcane physical principles and laws [1] [2]. Energetic aspects of the Krebs Cycle, the Calvin Cycle, and the ion pump can make learning of thermodynamics and electricity much more realistic. The contraction relaxation cycle of a muscle sarcomere can be used to represent that of a machine "photographs" of the sarcomere and large biopolymers such as ordered protein and nucleic acid structures illustrate Bragg's Law about regular submicron distances as well as those from crystals of inorganic salts. Movements of nanostructures of the proton pump subunits and sliding filaments are just as good for calculation of the moment of inertia and mechanical energy involved. Transport of sugars made from photosynthesis in the leaf into the fruit can pose problems about concentration gradient very realistically. Aspect about light such as absorption and fluorescence of biological molecules such as chlorophylls and rhodopsins should make such phenomena more interesting and real. Interference of visible light from feathers and scales should also be used to showchanges of apparent colors and patterns when viewed from different angles. Circular dichroism and streaming birefringence of biological macromolecules should make students appreciate polarization better.

  16. Biophysical chemistry

    International Nuclear Information System (INIS)

    Klein, M.P.

    1987-01-01

    Phosphorus-31 NMR spectroscopy is evolving into an important means for determining the in vivo concentrations of phosphorylated metabolites and is now entering the clinical arena. Our previous contributions to this field demonstrated the feasibility of employing implanted radio frequency coils around organs of laboratory animals to permit eliciting the NMR spectra over long periods to establish normative spectra. Using these devices and techniques we have determined phosphorus exchange reactions in rat hearts and kidney, in situ, and have demonstrated that there are pools of metabolic intermediates that are not directly visible in the conventional high resolution NMR spectra. Comparison of the results from NMR spectroscopy with those obtained from radiolabeling studies on chick embryo fibroblasts also showed that there are significant pools of phosphorus not visible in the P-31 NMR spectrum. Both sets of studies suggest that compartmentation occurs. The invisibility of these pools is assumed to result from the immobilization of the molecules by cellular macromolecules or organelles

  17. Inverse colloidal crystal membranes for hydrophobic interaction membrane chromatography.

    Science.gov (United States)

    Vu, Anh T; Wang, Xinying; Wickramasinghe, S Ranil; Yu, Bing; Yuan, Hua; Cong, Hailin; Luo, Yongli; Tang, Jianguo

    2015-08-01

    Hydrophobic interaction membrane chromatography has gained interest due to its excellent performance in the purification of humanized monoclonal antibodies. The membrane material used in hydrophobic interaction membrane chromatography has typically been commercially available polyvinylidene fluoride. In this contribution, newly developed inverse colloidal crystal membranes that have uniform pores, high porosity and, therefore, high surface area for protein binding are used as hydrophobic interaction membrane chromatography membranes for humanized monoclonal antibody immunoglobulin G purification. The capacity of the inverse colloidal crystal membranes developed here is up to ten times greater than commercially available polyvinylidene fluoride membranes with a similar pore size. This work highlights the importance of developing uniform pore size high porosity membranes in order to maximize the capacity of hydrophobic interaction membrane chromatography. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Fabrication of electrospun nanofibrous membranes for membrane distillation application

    KAUST Repository

    Francis, Lijo

    2013-02-01

    Nanofibrous membranes of Matrimid have been successfully fabricated using an electrospinning technique under optimized conditions. Nanofibrous membranes are found to be highly hydrophobic with a high water contact angle of 130°. Field emission scanning electron microscopy and pore size distribution analysis revealed the big pore size structure of electrospun membranes to be greater than 2 μm and the pore size distribution is found to be narrow. Flat sheet Matrimid membranes were fabricated via casting followed by phase inversion. The morphology, pore size distribution, and water contact angle were measured and compared with the electrospun membranes. Both membranes fabricated by electrospinning and phase inversion techniques were tested in a direct contact membrane distillation process. Electrospun membranes showed high water vapor flux of 56 kg/m2-h, which is very high compared to the casted membrane as well as most of the fabricated and commercially available highly hydrophobic membranes. ©2013 Desalination Publications.

  19. Gamma-irradiation and neutron effect on DNA-membrane complexes of mammalian cells

    International Nuclear Information System (INIS)

    Lapidus, I.L.; Nazarov, V.M.; Ehrtsgreber, G.

    1984-01-01

    The first results of radiobiological investigations in the biophysical channel of the JINR reactor IBR-2 are presented. Sedimentation behaviour of DNA-membrane complexes has been studied at irradiation of the Chinese hamster cells (VT9-4) in a wide dose range of 137 Cs γ-irradiation and neutrons. An earlier assumption of the authors on the role of DNA double-strand breaks in changing the relative sedimentation velocity of complexes at irradiation of cells with doses over 50 Gy has been confirmed

  20. Bacterial membrane proteomics.

    Science.gov (United States)

    Poetsch, Ansgar; Wolters, Dirk

    2008-10-01

    About one quarter to one third of all bacterial genes encode proteins of the inner or outer bacterial membrane. These proteins perform essential physiological functions, such as the import or export of metabolites, the homeostasis of metal ions, the extrusion of toxic substances or antibiotics, and the generation or conversion of energy. The last years have witnessed completion of a plethora of whole-genome sequences of bacteria important for biotechnology or medicine, which is the foundation for proteome and other functional genome analyses. In this review, we discuss the challenges in membrane proteome analysis, starting from sample preparation and leading to MS-data analysis and quantification. The current state of available proteomics technologies as well as their advantages and disadvantages will be described with a focus on shotgun proteomics. Then, we will briefly introduce the most abundant proteins and protein families present in bacterial membranes before bacterial membrane proteomics studies of the last years will be presented. It will be shown how these works enlarged our knowledge about the physiological adaptations that take place in bacteria during fine chemical production, bioremediation, protein overexpression, and during infections. Furthermore, several examples from literature demonstrate the suitability of membrane proteomics for the identification of antigens and different pathogenic strains, as well as the elucidation of membrane protein structure and function.