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Sample records for biophysics laboratory sbl

  1. Biophysics

    Directory of Open Access Journals (Sweden)

    Mojtaba Amani

    2008-01-01

    Full Text Available There is an idiom that “biophysicist is who discusses about biology when meets physicist, talks about physics when meets biologist and says joke when meets another biophysicist”. This idiom points to multidisciplinary nature of biophysics but what really is the biophysics? And who is the biophysicist? Biophysics was defined as: "that branch of knowledge that applies the principles of physics and chemistry and the methods of mathematical analysis and computer modeling to understand how the mechanisms of biological systems work” in homepage of Biophysical Society . Biophysics may be thought of as the central circle in a two-dimensional array of overlapping circles, which include physics, chemistry, physiology, and general biology. Two wings of Biophysics are Biology and physics. Organisms are made of biomaterials, which can be studied by physical laws, since physical principles and laws hold from microscopic level to macroscopic level. Biophysicist selects a part of biological problems that are pliable to interpret by physical principles and then formulate hypotheses that can be tested by experiment2. Historically, bioluminescence can be considered among the earliest biophysical phenomena. The modern biophysics appeared by discovering of molecular structure of myoglobin and deoxyribonucleic acid (DNA. There is no doubt that Biophysics as a multidisciplinary science covers wide spectrum of subjects as follows: Instrumental biophysics, Radiation Biophysics and radiobiology, Structural biology, Physiological biophysics, bio-cybernetics, Membrane Biophysics, Molecular biophysics, Bioenergetics, Mathematical and theoretical biophysics and Biophysical Chemistry. And the final question, do you still believe the above idiom about the biophysicist?

  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. Clinical biophysics

    Energy Technology Data Exchange (ETDEWEB)

    Anbar, M.; Spangler, R.A.; Scott, P.

    1985-01-01

    Chapters are included on clinical decision making, principles of biomedical engineering, computers and their medical uses, clinical radiobiology, diagnostic x-ray radiology, clinical applications of ultrasonics, nuclear medicine, NMR imaging, diagnostic imaging, bioelectric techniques in diagnosis and therapy, biophysical aspects of the clinical laboratory, and biophysical aspects of modern surgery.

  4. An Inexpensive Biophysics Laboratory Apparatus for Acquiring Pulmonary Function Data with Clinical Applications

    Science.gov (United States)

    Harkay, Gregory

    2001-11-01

    Interest on the part of the Physics Department at KSC in developing a computer interfaced lab with appeal to biology majors and a need to perform a clinical pulmonological study to fulfill a biology requirement led to the author's undergraduate research project in which a recording spirometer (typical cost: $15K) was constructed from readily available materials and a typical undergraduate lab computer interface. Simple components, including a basic photogate circuit, CPU fan, and PVC couplings were used to construct an instrument for measuring flow rates as a function of time. Pasco software was used to build an experiment in which data was collected and integration performed such that one could obtain accurate values for FEV1 (forced expiratory volume for one second) and FVC (forced vital capacity) and their ratio for a large sample of subjects. Results were compared to published norms and subjects with impaired respiratory mechanisms identified. This laboratory exercise is one with which biology students can clearly identify and would be a robust addition to the repertoire for a HS or college physics or biology teaching laboratory.

  5. Modulation of gamma ray induced chromosome aberrations in human peripheral blood lymphocytes by Hippophae rhammnoides leaf extract, SBL-1

    International Nuclear Information System (INIS)

    Hippophae rhammnoides L. commonly known as seabuckthorn is a temperate shrub and native of Asia and Europe. It has high antioxidant potential and is known to the traditional Indian, Chinese and Tibetan medicinal system for treatment of multiple disorders viz., circulatory and digestive disorders, hepatic injuries, neoplasia etc. One time treatment with the standardized leaf extract from H. rhammnoides (SBL-1) before whole body irradiation with 60Co (10 Gy), rendered more than 90% survival in non SBL-1 treated irradiated animals (J herbs, spices medi plants, 2009). Present study investigated the effects of SBL-1 treatment on chromosomal damage in human peripheral blood lymphocytes (PBL), with or without 60Co-gamma-radiation. The lymphocytes were isolated from the blood drawn from different donors. The isolated lymphocytes were divided into several groups: Group 1-untreated control, Group 2-irradiated (2 Gy), Group 3, 4 and 5 were treated with different concentration of SBL-1, 30 min. after irradiation with 60Co-gamma-rays (2 Gy). Group 6 was treated with the maximum concentration of SBL-1 used in the study. The metaphase spreading technique was used as per standard procedure to record chromosome breaks, dicentrics, acentrics and rings. The results were also recorded in terms of total aberrant metaphase and frequency of aberrant metaphase per 100 cells. In comparison to the untreated control, in the irradiated PBL culture, there was 8-fold increase in breaks, 211-folds in dicentrics, 75-folds in acentrics and 3-folds in rings (average data). SBL-1 alone at the highest concentration did not cause any significant change in number of breaks, dicentrics, acentrics and rings. The radiation induced aberrations decreased significantly by treatment with SBL-1 and the maximum decrease was observed when the cells were treated with 22μg/ml of SBL-1. These results demonstrated the anti-clastogenic activity of SBL-1 against gamma radiation induced damage. (author)

  6. 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.

  7. Activities in the SBL-FPL loops for LMFBR safety studies, (2)

    International Nuclear Information System (INIS)

    As the first step for the safety study of liquid metal-cooled fast breeder reactors, it is necessary to understand the initial events of potential accidents in LMFBRs. Local faults and sodium boiling are conceivable. The sodium boiling test loop (SBL) and the fuel failure propagation test loop (FPL) were constructed to investigate such phenomena experimentally. The two loops share one sodium dump tank and the purification system, and the whole facility is called ''Sodium installation for experiment of nuclear reactor safety analysis (SIENA)''. In almost all experiments, electrically heated fuel pin simulators were used in the form of pin bundles. The experimental studies using SBL-FPL have been carried out by the ''Core safety sodium behavior experiment group (CSSBEG)''. In addition, the group has operated two water test rigs for the experiments on large bubble behavior during hypothetical core disruptive accidents. A local event may successively cause the failure of adjacent fuel pins by the local worsening of cooling capability. The studies on fuel pin contact, FP gas release, local blockage and anomaly detection were carried out. The cooling of pin bundles by boiling in low heat flux and low flow rate conditions was tested. The behavior of bubbles in HCDA and the behavior of melted claddings were also investigated. (Kako, I.)

  8. Hippophae leaf extract (SBL-1) countered radiation induced dysbiosis in jejunum of total body 60Cobalt gamma - irradiated mice

    International Nuclear Information System (INIS)

    Single dose of SBL-1 administered at the rate 30 mg/kg body weight (b.w.) 30 min prior to whole body 60Co-gamma-irradiation at lethal dose (10 Gy), rendered >90% survival in comparison to zero survival in the non-SBL-1 treated 60Co-gamma-irradiated (10 Gy) mice population (J Herbs Spices Med Plants, 2009; 15(2): 203-215). Present study investigated the effect of SBL-1 on jejunal microbiota in lethally irradiated mice. Study was performed with inbred Swiss albino Strain 'A' male mice (age 9 weeks) weighing 28±2 g. The animals were maintained under controlled environment at 26±2℃; 12 h light/dark cycle and offered standard animal food (Golden feed, Delhi) as well as tap water ad libitum. Metagenomic DNA was extracted, purified and quantified from jejunum of the mice. Universal primers (27f and 1492r) were used to amplify the 16S rRNA DNA from the metagenomic DNA. Amplicons were sequenced, vector contamination and chimeras were removed. The sequences (GenBank Accession No: KF681283 to KF681351) were taxonomically classified by using Sequence Match program, Ribosomal Database Project as well as by nucleotide-BLAST (E-value: 10, database: 16S rRNA gene sequences, Bacteria and Archea). Phylogenetic Tree was prepared using MEGA 5.2 package, using maximum likelihood algorithm after sequence alignment by MUSCLE. Thermus aquaticus was used as out-group to construct rooted tree. Branch stability was assessed by bootstrap analysis. Untreated animals and the animals treated with SBL-1 had 100% Lactobacillus; 60Co gamma-irradiated animals had 55% Cohaesibacter (Alphaproteobacteria); 27% Mycoplasma (Tenericutes) and only 18% Lactobacillus; animals treated with SBL-1 prior to irradiation had 89% Lactobacillus and 11% Clostridium. This study demonstrated that treatment with SBL-1 at radioprotective doses before total body irradiation with lethal dose (10 Gy) countered the jejunal dysbiosis. (author)

  9. 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...

  10. Children's Social Behaviour for Learning (SBL): Reported and Observed Social Behaviours in Contexts of School and Home

    Science.gov (United States)

    Fisher, Laurel; Spencer, Fiona

    2015-01-01

    The aim is to understand the diversity in children's social behaviours that are vital to learning. It is proposed that a model of Social Behaviours for Learning (SBL) relies on the positions of the observers in relevant contexts. In this case, children are observed at school and at home. The alternatives are sociability as a personal trait or…

  11. Structural biophysics

    International Nuclear Information System (INIS)

    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

  12. Small Bioactive Lipoplex (SBL) Nanoparticles Self-Assembled at Elevated Temperature and Pressure

    Science.gov (United States)

    Huang, Leaf

    2009-03-01

    Conventional lipoplex (cationic liposome/DNA complex) serves well for gene transfer in cultured cells. However, their in vivo gene delivery activity is limited due to its relatively large size (>100 nm). This is due to incomplete charge neutralization as a result of the steric hindrance during the complexation between DNA and liposomes. Behr et al hypothesized that monomolecular DNA condensate can be prepared if the DNA sees the cationic lipid as monomers. Indeed, small nanoparticles (˜30 nm) were prepared by using a single-chain cationic amphiphile which has a high solubility at the physiological condition. To stabilize the monomolecular condensate, Behr has included a SH group in the cationic amphiphile which could be oxidized to form a dimer. Unfortunately, the stabilized nanoparticles showed no transfection activity when delivered into cells. We hypothesized that similar small lipoplex can be prepared by using a double-chain cationic amphiphile if both DNA and the amphiphile can be soluble in the same solvent. A hydrofluorocarbon HFC-152a is an excellent solvent for the cationic lipid DOTAP at an elevated temperature (˜35 ^oC) and pressure (˜300 atm). Since the solvent can accommodate small amounts of water, DNA or siRNA could be introduced into the system to allow lipoplex formation. The resulting Small Bioactive Lipoplex (SBL) is 30-50 nm in diameter and can transfect cultured cells. Freeze-fracture electron microscopy showed that SBL are solid nanoparticles without any lipid bilayer structure. Since plasmid DNA is fragile at elevated temperature and pressure, we have concentrated our effort in siRNA which is stable under the same conditions. The new formulation shows great promise as an in vivo delivery vector when small particles are required for efficient penetration into the tissues.

  13. Radiation biophysics

    International Nuclear Information System (INIS)

    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

  14. Biophysics: Concepts and Fields

    Directory of Open Access Journals (Sweden)

    Mojtaba Amani

    2013-01-01

    Full Text Available There is an idiom that “biophysicist is who discusses about biology when meets physicist, talks about physics when meets biologist and says joke when meets another biophysicist”. This idiom points to multidisciplinary nature of biophysics but what really is the biophysics? And who is the biophysicist? Biophysics was defined as: "that branch of knowledge that applies the principles of physics and chemistry and the methods of mathematical analysis and computer modeling to understand how the mechanisms of biological systems work” in homepage of Biophysical Society . Biophysics may be thought of as the central circle in a two-dimensional array of overlapping circles, which include physics, chemistry, physiology, and general biology. Two wings of Biophysics are Biology and physics. Organisms are made of biomaterials, which can be studied by physical laws, since physical principles and laws hold from microscopic level to macroscopic level. Biophysicist selects a part of biological problems that are pliable to interpret by physical principles and then formulate hypotheses that can be tested by experiment2. Historically, bioluminescence can be considered among the earliest biophysical phenomena. The modern biophysics appeared by discovering of molecular structure of myoglobin and deoxyribonucleic acid (DNA. There is no doubt that Biophysics as a multidisciplinary science covers wide spectrum of subjects as follows: Instrumental biophysics, Radiation Biophysics and radiobiology, Structural biology, Physiological biophysics, bio-cybernetics, Membrane Biophysics, Molecular biophysics, Bioenergetics, Mathematical and theoretical biophysics and Biophysical Chemistry. And the final question, do you still believe the above idiom about the biophysicist?

  15. Biophysical chemistry

    International Nuclear Information System (INIS)

    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

  16. 2. biophysical work meeting

    International Nuclear Information System (INIS)

    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.)

  17. Biophysics conference 1978

    International Nuclear Information System (INIS)

    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)

  18. 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...

  19. 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...

  20. 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.

  1. New horizons in Biophysics

    Directory of Open Access Journals (Sweden)

    Moylan Elizabeth C

    2011-03-01

    Full Text Available Abstract This editorial celebrates the re-launch of PMC Biophysics previously published by PhysMath Central, in its new format as BMC Biophysics published by BioMed Central with an expanded scope and Editorial Board. BMC Biophysics will fill its own niche in the BMC series alongside complementary companion journals including BMC Bioinformatics, BMC Medical Physics, BMC Structural Biology and BMC Systems Biology.

  2. Quantification of the antioxidant 3, 4, 5,-Trihydroxybenzoic acid in radioprotective drug SBL-1 and its modifying effects on radiation induced changes in renal oxidative stress

    International Nuclear Information System (INIS)

    Development of radioprotective drug is international challenge and till date no radioprotective agent has been approved for human use. Leaf extract of Hippophae rhamnoides, code name SBL-1, was demonstrated to have significant radioprotective properties. Antioxidant properties have contributed significantly to radiation protection potential of many herbs. In this study we have developed simple, sensitive, reliable, rapid and validated HPTLC protocol, for quantification of a major antioxidant 3, 4, 5,-Trihydroxybenzoic acid (Gallic acid ethyl ester) in SBL-1 and also studied the effect of treatment of mice with SBL-1 before total body irradiation (10 Gy, lethal dose) on renal anti-oxidant enzymes. Separation was carried out on silica gel 60F254 pre-coated TLC aluminum plates, while allowing linear ascending development in twin trough glass chamber, saturated with suitably designed mobile phase. Densitometric detection of Gallic acid was at 280 nm. The protocol produced a discrete band where retention factor was 0.58; correlation coefficient for linear relationship between concentrations and peak areas was 0.9999; detection limits was 25 ng; limits of quantification was 50 ng and percentage recovery was 98.76. Administration of SBL-1 to mice before total body irradiation with lethal dose of low LET 60Co-gamma rays (10 Gy), resulted in significant countering of the radiation induced disturbances in the levels of Glutathione S-Transferase (GST), Catalase and Superoxide dismutase (SOD) in kidney. This study elucidated an important mechanism of protection to kidney in total body lethally irradiated mice. (author)

  3. SBL-1 treatment before total body irradiation countered radiation induced oxidative stress, DNA damage and histological changes in jejunum of conditioned rats

    International Nuclear Information System (INIS)

    Conditioned taste aversion (CTA) in experimental rats is considered to be parallel to behavioural changes (nausea and vomiting) in humans. There is a need to develop medical countermeasures which can counter the radiation induced nausea and vomiting. The standardized radioprotective preparation from leaves of Hippophae rhamnoides (Seabuckthorn, SBL-1) was also demonstrated to counter 60Co γ-irradiation (2 Gy) induced CTA in experimental Sprague-Dawley rats. This study investigated the time dependent changes in oxidative stress, DNA damage (γH2AX assay) and histology of rats jejunum in SBL-1 (12 mg/kg b.w., i.p, ∼ 30 min) treated irradiated rats and compared it with the non SBL-1 treated irradiated rats. In comparison to untreated controls (DC), the irradiated animals showed significant increase (p<0.05) in levels of nitric oxide (NOx), lactate dehydrogenase (LDH) and γH2AX foci at 5 h and malondialdehyde (MDA) at 24 h; but decrease in total thiols (GSH), superoxide dismutase (SOD) and catalase (CAT); villi and crypt numbers per circumference as well as villi and crypt lengths at 5 h. The treatment with SBL-1 prior to irradiation countered the radiation induced increase in levels of MDA, NOx, LDH and γH2AX foci; decrease in GSH, SOD and CAT; villi and crypt numbers per circumference and villi and crypt lengths at 5 h. In irradiated group, on day 5 the levels of MDA, NOx, LDH, GSH, SOD and γH2AX foci were not different than UC but significant decrease persisted in levels of CAT, number of villi and crypts, and also villi length. In SBL-1 treated irradiated group, on day 5, there was significant reduction in MDA levels (p<0.05); increase of SOD levels to match the UC; the increase of villi and crypt numbers/circumference by 15-20%, in comparison to irradiated animals. The observations indicated that SBL-1 could counter the radiation induced oxidative stress, DNA damage and changes in tissue histology within 5 h. This may have been an important reason for

  4. An Evaluation Quality Framework for Analysing School-Based Learning (SBL) to Work-Based Learning (WBL) Transition Module

    Science.gov (United States)

    Alseddiqi, M.; Mishra, R.; Pislaru, C.

    2012-05-01

    The paper presents the results from a quality framework to measure the effectiveness of a new engineering course entitled 'school-based learning (SBL) to work-based learning (WBL) transition module' in the Technical and Vocational Education (TVE) system in Bahrain. The framework is an extended version of existing information quality frameworks with respect to pedagogical and technological contexts. It incorporates specific pedagogical and technological dimensions as per the Bahrain modern industry requirements. Users' views questionnaire on the effectiveness of the new transition module was distributed to various stakeholders including TVE teachers and students. The aim was to receive critical information in diagnosing, monitoring and evaluating different views and perceptions about the effectiveness of the new module. The analysis categorised the quality dimensions by their relative importance. This was carried out using the principal component analysis available in SPSS. The analysis clearly identified the most important quality dimensions integrated in the new module for SBL-to-WBL transition. It was also apparent that the new module contains workplace proficiencies, prepares TVE students for work placement, provides effective teaching and learning methodologies, integrates innovative technology in the process of learning, meets modern industrial needs, and presents a cooperative learning environment for TVE students. From the principal component analysis finding, to calculate the percentage of relative importance of each factor and its quality dimensions, was significant. The percentage comparison would justify the most important factor as well as the most important quality dimensions. Also, the new, re-arranged quality dimensions from the finding with an extended number of factors tended to improve the extended version of the quality information framework to a revised quality framework.

  5. An Evaluation Quality Framework for Analysing School-Based Learning (SBL) to Work-Based Learning (WBL) Transition Module

    International Nuclear Information System (INIS)

    The paper presents the results from a quality framework to measure the effectiveness of a new engineering course entitled 'school-based learning (SBL) to work-based learning (WBL) transition module' in the Technical and Vocational Education (TVE) system in Bahrain. The framework is an extended version of existing information quality frameworks with respect to pedagogical and technological contexts. It incorporates specific pedagogical and technological dimensions as per the Bahrain modern industry requirements. Users' views questionnaire on the effectiveness of the new transition module was distributed to various stakeholders including TVE teachers and students. The aim was to receive critical information in diagnosing, monitoring and evaluating different views and perceptions about the effectiveness of the new module. The analysis categorised the quality dimensions by their relative importance. This was carried out using the principal component analysis available in SPSS. The analysis clearly identified the most important quality dimensions integrated in the new module for SBL-to-WBL transition. It was also apparent that the new module contains workplace proficiencies, prepares TVE students for work placement, provides effective teaching and learning methodologies, integrates innovative technology in the process of learning, meets modern industrial needs, and presents a cooperative learning environment for TVE students. From the principal component analysis finding, to calculate the percentage of relative importance of each factor and its quality dimensions, was significant. The percentage comparison would justify the most important factor as well as the most important quality dimensions. Also, the new, re-arranged quality dimensions from the finding with an extended number of factors tended to improve the extended version of the quality information framework to a revised quality framework.

  6. 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.

  7. Seabuckthorn leaf extract (SBL-1) counters radiation damage by regulating time kinetics of apoptosis in jejunal crypts in total body 60Co-gamma-irradiated mice

    International Nuclear Information System (INIS)

    The radioprotective properties of plant Hippophae rhamnoides L. (common name Seabuckthorn, family Eleagnaceae) were reported and treatment with SBL-1 (herbal preparation from Seabuckthorn leaves), before whole body exposure to 60Co-gamma-rays (10 Gy), rendered >90% survivors in mice population, while 100% mortality was observed in non-SBL-1 treated, 60Co-gamma-irradiated (10 Gy) controls. Purpose of this study was to investigate the early as well as late modifying effects of SBL-1 on radiation induced apoptosis in jejunal crypts and m-RNA levels and protein levels of Bcl2 and Bax. A 30 day study was performed with 8-9 weeks old inbred male Swiss albino Strain 'A mice. Histology study was performed with jejunum to record the time dependent changes in the number of apoptotic cells in Crypts of Lieberkuhn; quantitative reverse polymerase chain reaction was performed to record the time kinetic of changes in m-RNA levels of BcI-2 and Bax genes. The changes in BcI-2 and Bax proteins were also recorded by western blotting. One time administration of SBL-1, prior to lethal whole body irradiation (10 Gy), significantly (p< 0.05) countered the radiation induced increases in cryptal apoptotic cells, Bax levels, and decrease in BcI-2 in a time dependent manner from 24 h till day 30. This study demonstrated that one of the underlying mechanisms of SBL-1 for countering radiation induced GI syndrome was by altering the time kinetics of apoptosis in cryptal cells; besides reducing the early damage. (author)

  8. The New School-Based Learning (SBL) to Work-Based Learning (WBL) Transition Module: A Practical Implementation in the Technical and Vocational Education (TVE) System in Bahrain

    OpenAIRE

    Alseddiqi, Mohamed; Mishra, Rakesh; Pislaru, Crinela

    2012-01-01

    This paper diagnoses the implementation of a new engineering course entitled „school-based learning (SBL) to work-based learning (WBL) transition module‟ in the Bahrain Technical and Vocational Education (TVE) learning environment. The module was designed to incorporate an innovative education and training approach with a variety of learning activities that are included in various learning case studies. Each case study was based on with learning objectives coupled with desired learning outcom...

  9. A standardized seabuckthorn leaf extract (SBL-1) counters radiation induced renal histopathology, oxidative stress as well as changes in mRNA levels

    International Nuclear Information System (INIS)

    Hippophae rhamnoides L., (common name Seabuckthorn; Family: Elaeagnaceae) is a plant growing naturally as well as cultivated in North-West Himalayas at 7000-15,000 feet. It is known for antioxidant and medicinal properties. Our earlier studies showed that administration of SBL-1 (30 mg/kg body weight), 30 minutes before 60Co-γ-radiation (10 Gy, lethal dose) rendered > 90% survival in mice population. The present study was planned to investigate the effects of radioprotective dose (30 mg/kg body weight) dose of SBL-1 treatment in kidneys of irradiated and control animals. Strain 'A' male mice (weighing 28±2 g) were irradiated without or 30 minutes after administration of SBL-1. Animals were sacrificed at different days (1, 2, 3, 5, 7 and 15) after the treatment. Histopathology and biochemical assays were performed using standardized procedures. Gene expression study was performed by PCR of mRNA. The 60Co γ-irradiated animals showed a significant reduction in total thiol (T-SH) content till day 5 (p< 0.05), activity of catalase, superoxide dismutase (SOD) (p<0.01) and glutathione-s-transferase (GST) (p<0.05) and significant increase in LPx, ALP and free iron content (p<0.05) on all study days. Histopathology showed Glomeruli shrinkage, nuclear degeneration, tubular dilations, widening of tubular lumen and collapsing of cellular architecture which increased from day 2 till day 7. Significant alterations in mRNA levels of some of the key genes involved in acute renal failure were observed. In animals treated with SBL-1 before irradiation the T-SH increased significantly at day 2, 3 and 5, activity of catalase, SOD and GST decreased significantly (p<0.05) only at day 2 and 3 respectively. Significant increase in (p<0.05) LPx was observed till day 3, ALP levels only at day 3 while free iron content till day 5. Only mild changes in the tissues histology were observed at day 2, 5 and 7. By day 10 no significant difference was observed in comparison to control

  10. 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...

  11. Project support of practical training in biophysics.

    Science.gov (United States)

    Mornstein, V; Vlk, D; Forytkova, L

    2006-01-01

    The Department of Biophysics ensures practical training in biophysics and related subjects for students of medical and health study programmes. Demonstrations of medical technology are an important part of this training. Teaching for Faculty of Sciences in biophysical study programmes becomes also very important. Some lectures and demonstrations of technology are involved, but the practical trainig is missing. About 1 mil. CZK for additional laboratory equipment was obtained from the HEIDF project No. 1866/ 2005 "The demonstration and measuring technology for education in medical biophysics and radiological physics" for measuring system DEWETRON for high frequency signal analysis, Fluke Ti30 IR camera, PM 9000B patient monitor, ARSENAL AF 1 fluorescence microscope, and Nikon Coolpix 4500 digital camera with accessories for microphotography. At the present time, further financial resources are being provided by a development project of Ministry of Education "Inter-university co-operation in biomedical technology and engineering using top technologies" in total amount of almost 5 mil CZK, whereas over 2 mil CZK from this project are reserved for student laboratory equipment. The main goal of this project is to ensure the participation of Medical Faculty in educational co-operation in the biomedical technology and engineering, namely with the Faculty of Electrical Engineering and Communication (FEEC), Brno University of Technology. There will be taught those areas of biophysics which are not covered by FEEC, thus forming a separate subject "General Biophysics". The following instruments will be installed: UV-VIS spectrophotometers, rotation viscometers, tensiometers, microscopes with digital image processing, cooled centrifuge, optical benches, and some smaller instruments for practical measurements. PMID:17125070

  12. 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. PMID:25815978

  13. Recent progress in Biophysics

    International Nuclear Information System (INIS)

    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)

  14. What Is the True Color of Fresh Meat? A Biophysical Undergraduate Laboratory Experiment Investigating the Effects of Ligand Binding on Myoglobin Using Optical, EPR, and NMR Spectroscopy

    Science.gov (United States)

    Linenberger, Kimberly; Bretz, Stacey Lowery; Crowder, Michael W.; McCarrick, Robert; Lorigan, Gary A.; Tierney, David L.

    2011-01-01

    With an increased focus on integrated upper-level laboratories, we present an experiment integrating concepts from inorganic, biological, and physical chemistry content areas. Students investigate the effects of ligand strength on the spectroscopic properties of the heme center in myoglobin using UV-vis, [superscript 1]H NMR, and EPR…

  15. Fetal Biophysical Profile Scoring

    Directory of Open Access Journals (Sweden)

    H.R. HaghighatKhah

    2009-01-01

    Full Text Available   "nFetal biophysical profile scoring is a sonographic-based method of fetal assessment first described by Manning and Platt in 1980. "nThe biophysical profile score was developed as a method to integrate real-time observations of the fetus and his/her intrauterine environment in order to more comprehensively assess the fetal condition. These findings must be evaluated in the context of maternal/fetal history (i.e., chronic hypertension, post-dates, intrauterine growth restriction, etc, fetal structural integrity (presence or absence of congenital anomalies, and the functionality of fetal support structures (placental and umbilical cord. For example, acute asphyxia due to placental abruption may result in an absence of the acute variables of the biophysical profile score (fetal breathing movements, fetal movement, fetal tone, and fetal heart rate reactivity with a normal amniotic fluid volume. With post maturity the asphyxial event may be intermittent and chronic resulting in a decrease in amniotic fluid volume, but with the acute variables remaining normal. "nWhile the 5 components of the biophysical profile score have remained unchanged since 1980 (Manning, 1980, the definitions of a normal and abnormal parameter have evolved with increasing experience. "nIn 1984 the definition of oligohydramnios was increased from < 1cm pocket of fluid to < 2.0 x 1.0 cm pocket. Oligohydramnios is now defined as a pocket of amniotic fluid < 2.0 x 2.0 cm (Manning, 1995a "nIf the four ultrasound variables are normal, the accuracy of the biophysical profile score was not found to be significantly improved by adding the non-stress test. As a result, in 1987 the profile score was modified to incorporate the non-stress test only when one of the ultrasound variables was abnormal (Manning 1987. Table 1 outlines the current definitions for quantifying a variable as present or absent. "nEach of the 5 components of the biophysical profile score does not have equal

  16. 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.

  17. 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.

  18. 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...

  19. 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.

  20. 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

  1. 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...

  2. 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.

  3. Post test calculation of the experiment `small break loss-of- coolant test` SBL-22 at the Finnish integral test facility PACTEL with the thermohydraulic code ATHLET

    Energy Technology Data Exchange (ETDEWEB)

    Lischke, W.; Vandreier, B. [Univ. for Applied Sciences, Zittau/Goerlitz (Germany). Dept. of Nuclear Technology

    1997-12-31

    At the University for Applied Sciences Zittau/Goerlitz (FH) calculations for the verification of the ATHLET-code for reactors of type VVER are carried out since 1991, sponsored by the German Ministry for Education, Science and Technology (BMBF). The special features of these reactors in comparison to reactors of western countries are characterized by the duct route of reactor coolant pipes and the horizontal steam generators. Because of these special features, a check of validity of the ATHLET-models is necessary. For further verification of the ATHLET-code the post test calculation of the experiment SBL-22 (Small break loss-of-coolant test) realized at the finnish facility PACTEL was carried out. The experiment served for the examination of the natural circulation behaviour of the loop over a continuous range of primary side water inventory. 5 refs.

  4. Biophysics of protein evolution and evolutionary protein biophysics

    OpenAIRE

    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 ...

  5. [Biophysics of nerve excitation].

    Science.gov (United States)

    Kol'e, O R; Maksimov, G V

    2010-01-01

    The studies testifying to the presence of the interrelation between the physiological functions of the organism and physical and chemical processes in nerves are discussed. Changes in some physical and chemical parameters observed both upon elicited rhythmic exaltation of nerves and during the spontaneous rhythmic activity of neurons are analyzed. Upon rhythmic exaltation, a complex of physical and chemical processes is triggered, and reversible structural and metabolic rearrangements at the subcellular and molecular levels occur that do not take place during the generation of a single action potential. Thus, only in conditions of rhythmic exaltation of a nerve, it is possible to reveal those processes that provide exaltation of nerves in the organism. The future possibilities of the investigations combining the biophysical and physiological approaches are substantiated. Characteristic changes in physicochemical parameters are observed in nerves during the generation of a series of action potentials of different frequency and duration ("frequency dependence") under normal physiological conditions, as well as in extreme situations and in nerve pathology. The structural and metabolic rearrangements are directly related to the mode of rhythmic exaltation and proceed both in the course of rhythmic exaltation and after its termination. Participation and the basic components of the nervous fulcrum (an axon, Shwan cell, myelin, subcellular organelles) in the realization of rhythmic exaltation is shown. In the coordination of all processes involved in rhythmic exaltation, the main role is played by the systems of redistribution and transport of intercellular and endocellular calcium. The idea is put forward that myelin of nerve fibers is not only an isolator, but also an "intercellular depot" of calcium and participates in the redistribution of different ions. Thus, the rhythmic excitation is of great importance in the realization of some physiological functions, the

  6. Biophysical measurements of cells, microtubules, and DNA with an atomic force microscope

    Science.gov (United States)

    Devenica, Luka M.; Contee, Clay; Cabrejo, Raysa; Kurek, Matthew; Deveney, Edward F.; Carter, Ashley R.

    2016-04-01

    Atomic force microscopes (AFMs) are ubiquitous in research laboratories and have recently been priced for use in teaching laboratories. Here, we review several AFM platforms and describe various biophysical experiments that could be done in the teaching laboratory using these instruments. In particular, we focus on experiments that image biological materials (cells, microtubules, and DNA) and quantify biophysical parameters including membrane tension, persistence length, contour length, and the drag force.

  7. 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...

  8. Radiation dosimetry and radiation biophysics

    International Nuclear Information System (INIS)

    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

  9. Radiation dosimetry and radiation biophysics

    International Nuclear Information System (INIS)

    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

  10. The biophysics of neuronal growth

    Science.gov (United States)

    Franze, Kristian; Guck, Jochen

    2010-09-01

    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.

  11. 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...

  12. 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...

  13. Surface-Enhanced Raman Scattering and Biophysics

    Science.gov (United States)

    Kneipp, Katrin

    2001-03-01

    Surface-enhanced Raman scattering (SERS) is a phenomenon resulting in strongly increased Raman signals from molecules which have been attached to metallic nanostructures such as colloidal silver or gold particles. The effect combines the structural information content of a vibrational spectroscopy with extremely high sensitivity and in some cases, it showes promise in overcoming the low-sensitivity problems inherent in Raman spectroscopy. Cross sections effective in SERS can reach 10 16 to 10 15 cm2 per molecule corresponding to enhancement factors of about fourteen orders of magnitude compared with “normal” non-resonant Raman scattering. Such extremely large cross sections are sufficient for single molecule Raman spectroscopy. The high sensitivity and particularly the single molecule capabilities open up exciting perspectives for SERS as tool for basic research in biophysics, biochemistry and in laboratory medicine, where it allows to study extremely small amounts of biolomedically relevant molecules in order to understand development of diseases, treatment and therapy control based on molecular structural information at the single molecule level. The most spectacular applications might appear in rapidly spectroscopic characterization of specific DNA fragments down to structurally sensitive detection of single bases in order to elucidate the human genome sequence without any labeling technology. I will briefly introduce the SERS effect and report experiments with Raman scattering of single molecules. Potential and limitations of surface-enhanced Raman techniques as a tool in biophysics and biomedical spectroscopy will be considered.

  14. Deep sea biophysics

    International Nuclear Information System (INIS)

    A collection of deep-sea bacterial cultures was completed. Procedures were instituted to shelter the culture collection from accidential warming. A substantial data base on the rates of reproduction of more than 100 strains of bacteria from that collection was obtained from experiments and the analysis of that data was begun. The data on the rates of reproduction were obtained under conditions of temperature and pressure found in the deep sea. The experiments were facilitated by inexpensively fabricated pressure vessels, by the streamlining of the methods for the study of kinetics at high pressures, and by computer-assisted methods. A polybarothermostat was used to study the growth of bacteria along temperature gradients at eight distinct pressures. This device should allow for the study of microbial processes in the temperature field simulating the environment around buried HLW. It is small enough to allow placement in a radiation field in future studies. A flow fluorocytometer was fabricated. This device will be used to determine the DNA content per cell in bacteria grown in laboratory culture and in microorganisms in samples from the ocean. The technique will be tested for its rapidity in determining the concentration of cells (standing stock of microorganisms) in samples from the ocean

  15. Leukocyte biophysics. An invited review.

    Science.gov (United States)

    Schmid-Schönbein, G W

    1990-10-01

    The biophysical properties of leukocytes in the passive and active state are discussed. In the passive unstressed state, leukocytes are spherical with numerous membrane folds. Passive leukocytes exhibit viscoelastic properties, and the stress is carried largely by the cell cytoplasm and the nucleus. The membrane is highly deformable in shearing and bending, but resists area expansion. Membrane tension can usually be neglected but plays a role in cases of large deformation when the membrane becomes unfolded. The constant membrane area constraint is a determinant of phagocytic capacity, spreading of cells, and passage through narrow pores. In the active state, leukocytes undergo large internal cytoplasmic deformation, pseudopod projection, and granule redistribution. Several different measurements for assessment of biophysical properties and the internal cytoplasmic deformation in form of strain and strain rate tensors are presented. The current theoretical models for active cytoplasmic motion in leukocytes are discussed in terms of specific macromolecular reactions. PMID:1705479

  16. Biophysical modelling in radiation protection

    International Nuclear Information System (INIS)

    Biophysical models have historically provided essential concepts by which risk estimates have been extrapolated from observations in humans and animals to the low radiation levels of prime relevance in radiation protection. But there remain major uncertainties, and modelling has an essential continuing role to reduce these and seek alternative approaches in the light of advancing knowledge. Particularly important are the capabilities of single radiation tracks in cells, and the great differences between radiations, in perturbing biological processes. (author)

  17. The New School-Based Learning (SBL) to Work-Based Learning (WBL) Transition Module: A Practical Implementation in the Technical and Vocational Education (TVE) System in Bahrain

    Science.gov (United States)

    Alseddiqi, M.; Mishra, R.; Pislaru, C.

    2012-05-01

    This paper diagnoses the implementation of a new engineering course entitled 'school-based learning (SBL) to work-based learning (WBL) transition module' in the Bahrain Technical and Vocational Education (TVE) learning environment. The module was designed to incorporate an innovative education and training approach with a variety of learning activities that are included in various learning case studies. Each case study was based on with learning objectives coupled with desired learning outcomes. The TVE students should meet the desired outcomes after the completion of the learning activities and assessments. To help with the implementation phase of the new module, the authors developed guidelines for each case study. The guidelines incorporated learning activities to be delivered in an integrated learning environment. The skills to be transferred were related to cognitive, affective, and technical proficiencies. The guidelines included structured instructions to help students during the learning process. In addition, technology was introduced to improve learning effectiveness and flexibility. The guidelines include learning indicators for each learning activity and were based on their interrelation with competencies to be achieved with respect to modern industrial requirements. Each learning indicator was then correlated against the type of learning environment, teaching and learning styles, examples of mode of delivery, and assessment strategy. Also, the learning activities were supported by technological features such as discussion forums for social perception and engagement and immediate feedback exercises for self-motivation. Through the developed module, TVE teachers can effectively manage the teaching and learning process as well as the assessment strategy to satisfy students' individual requirements and enable them to meet workplace requirements.

  18. 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

  19. 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...

  20. Biophysics

    International Nuclear Information System (INIS)

    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

  1. Biophysics of BK Channel Gating.

    Science.gov (United States)

    Pantazis, A; Olcese, R

    2016-01-01

    BK channels are universal regulators of cell excitability, given their exceptional unitary conductance selective for K(+), joint activation mechanism by membrane depolarization and intracellular [Ca(2+)] elevation, and broad expression pattern. In this chapter, we discuss the structural basis and operational principles of their activation, or gating, by membrane potential and calcium. We also discuss how the two activation mechanisms interact to culminate in channel opening. As members of the voltage-gated potassium channel superfamily, BK channels are discussed in the context of archetypal family members, in terms of similarities that help us understand their function, but also seminal structural and biophysical differences that confer unique functional properties. PMID:27238260

  2. Molecular Biophysics Symposium, November 6, 2014

    OpenAIRE

    Capelluto, Daniel

    2014-01-01

    Virginia Tech hosted the first Molecular Biophysics Symposium focusing on structural biology studies of proteins. The event pursued two goals. First, it was designed to enrich the interaction among biophysical research groups located in southwest Virginia. Second, the symposium offered undergraduate students, interested in continuing their graduate studies in biophysics, the opportunity to meet with local and invited biophysicists and structural biologists. Four speakers were selected from su...

  3. 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.

  4. Future aims of biophysical models

    International Nuclear Information System (INIS)

    The present workshop has demonstrated, that it is easy to produce models, but frequently difficult to define their purposes and aims. A reliable prediction of future aims of biophysical modelling may be nearly impossible. It is less difficult to outline those uses of modelling that are unavailable for the pragmatic uses in radiation therapy and in radiation protection. The applications will also determine the general direction of development of the less empirical models that may facilitate the understanding of the mechanisms of radiation action and that may ultimately lead back to applications in radiation therapy and radiation protection. This paper addresses likely aims for modelling in the three areas of radiation therapy, radiation protection and cellular radiation effects. (author)

  5. Relating Biophysical Properties Across Scales

    CERN Document Server

    Flenner, Elijah; Neagu, Adrian; Kosztin, Ioan; Forgacs, Gabor

    2007-01-01

    A distinguishing feature of a multicellular living system is that it operates at various scales, from the intracellular to organismal. Very little is known at present on how tissue level properties are related to cell and subcellular properties. Modern measurement techniques provide quantitative results at both the intracellular and tissue level, but not on the connection between these. In the present work we outline a framework to address this connection. We specifically concentrate on the morphogenetic process of tissue fusion, by following the coalescence of two contiguous multicellular aggregates. The time evolution of this process can accurately be described by the theory of viscous liquids. We also study fusion by Monte Carlo simulations and a novel Cellular Particle Dynamics (CPD) model, which is similar to the earlier introduced Subcellular Element Model (Newman, 2005). Using the combination of experiments, theory and modeling we are able to relate the measured tissue level biophysical quantities to s...

  6. 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.

  7. 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...

  8. Applications of synchrotron radiation in Biophysics

    International Nuclear Information System (INIS)

    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.)

  9. Biophysics software for interdisciplinary education and research

    OpenAIRE

    Deutsch, J. M.

    2013-01-01

    Biophysics is a subject that is spread over many disciplines and transcends the skills and knowledge of the individual student. This makes it challenging both to teach and to learn. Educational materials are described to aid in teaching undergraduates biophysics in an interdisciplinary manner. Projects have been devised on topics that range from x-ray diffraction to the Hodgkin Huxley equations. They are team-based and encourage collaboration. The projects make extensive use of software writt...

  10. 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

  11. 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.

  12. 6th international conference on biophysics and synchrotron radiation. Program/Abstracts

    International Nuclear Information System (INIS)

    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

  13. 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…

  14. Stochastic biophysical modeling of irradiated cells

    CERN Document Server

    Fornalski, Krzysztof Wojciech

    2014-01-01

    The paper presents a computational stochastic model of virtual cells irradiation, based on Quasi-Markov Chain Monte Carlo method and using biophysical input. The model is based on a stochastic tree of probabilities for each cell of the entire colony. Biophysics of the cells is described by probabilities and probability distributions provided as the input. The adaptation of nucleation and catastrophe theories, well known in physics, yields sigmoidal relationships for carcinogenic risk as a function of the irradiation. Adaptive response and bystander effect, incorporated into the model, improves its application. The results show that behavior of virtual cells can be successfully modeled, e.g. cancer transformation, creation of mutations, radioadaptation or radiotherapy. The used methodology makes the model universal and practical for simulations of general processes. Potential biophysical curves and relationships are also widely discussed in the paper. However, the presented theoretical model does not describe ...

  15. 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.

  16. The numerical modelling studies performed at the Gazi Biophysics Laboratory

    OpenAIRE

    TUYSUZ, Mehmet; CANSEVEN, Ayse; SEYHAN, Nesrin

    2013-01-01

    In recent years humans are more exposed to human-made electromagnetic (EM) fields than natural fields with developing technologies. Especially, widespread use of wireless communication technologies in all areas of daily life and getting closer to sensitive organs like brain caused an increase in possible risks and worries about human health. For this reason, the potential health effects from the use of mobile phones has been studied intensively in scientific field. Specific Absorption Rate (S...

  17. Incorporating Modeling and Simulations in Undergraduate Biophysical Chemistry Course to Promote Understanding of Structure-Dynamics-Function Relationships in Proteins

    Science.gov (United States)

    Hati, Sanchita; Bhattacharyya, Sudeep

    2016-01-01

    A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and…

  18. Biophysical characterization of GPCR oligomerization in viro

    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...

  19. Biophysical Measurements of Cells, Microtubules, and DNA with an Atomic Force Microscope

    CERN Document Server

    Devenica, Luka M; Cabrejo, Raysa; Kurek, Matthew; Deveney, Edward F; Carter, Ashley R

    2015-01-01

    Atomic force microscopes (AFMs) are ubiquitous in research laboratories and have recently been priced for use in teaching laboratories. Here we review several AFM platforms (Dimension 3000 by Digital Instruments, EasyScan2 by Nanosurf, ezAFM by Nanomagnetics, and TKAFM by Thorlabs) and describe various biophysical experiments that could be done in the teaching laboratory using these instruments. In particular, we focus on experiments that image biological materials and quantify biophysical parameters: 1) imaging cells to determine membrane tension, 2) imaging microtubules to determine their persistence length, 3) imaging the random walk of DNA molecules to determine their contour length, and 4) imaging stretched DNA molecules to measure the tensional force.

  20. The role of biophysical cohesion on subaqueous bed form size

    Science.gov (United States)

    Parsons, Daniel R.; Schindler, Robert J.; Hope, Julie A.; Malarkey, Jonathan; Baas, Jaco H.; Peakall, Jeffrey; Manning, Andrew J.; Ye, Leiping; Simmons, Steve; Paterson, David M.; Aspden, Rebecca J.; Bass, Sarah J.; Davies, Alan G.; Lichtman, Ian D.; Thorne, Peter D.

    2016-02-01

    Biologically active, fine-grained sediment forms abundant sedimentary deposits on Earth's surface, and mixed mud-sand dominates many coasts, deltas, and estuaries. Our predictions of sediment transport and bed roughness in these environments presently rely on empirically based bed form predictors that are based exclusively on biologically inactive cohesionless silt, sand, and gravel. This approach underpins many paleoenvironmental reconstructions of sedimentary successions, which rely on analysis of cross-stratification and bounding surfaces produced by migrating bed forms. Here we present controlled laboratory experiments that identify and quantify the influence of physical and biological cohesion on equilibrium bed form morphology. The results show the profound influence of biological cohesion on bed form size and identify how cohesive bonding mechanisms in different sediment mixtures govern the relationships. The findings highlight that existing bed form predictors require reformulation for combined biophysical cohesive effects in order to improve morphodynamic model predictions and to enhance the interpretations of these environments in the geological record.

  1. Commentary on “Biophysical Economics” and Evolving Areas

    Science.gov (United States)

    Flomenbom, Ophir; Coban, Gul Unal; Adigüzel, Yekbun

    2016-07-01

    In this Issue, papers in the area of socio-econo-physics and biophysical economics are presented. We have recently introduced socio-econo-physics and biophysical economics in Biophysical Reviews and Letters (BRL), yet saw 3 to 4 relevant papers just in these most recent three quarters. In this commentary, we therefore would like to elaborate on the topics of socio-econo-physics and biophysical economics and to introduce these concepts to the readers of BRL and the biophysical community of science, with the purpose of supporting many more publications here in BRL, in this evolving area.

  2. 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...

  3. 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...

  4. Biophysical limits to global food production

    OpenAIRE

    1995-01-01

    Global food production, so far, has increased continuously because cropped area has expanded and productivity per unit area has increased. In some regions of the world, however, there is little scope for further spatial expansion of agriculture. In other areas, crop yields are stagnating. Does this imply that the world is approaching the biophysical limits of food production? In this research nine food-demand scenarios were analyzed, ranging from minimum population growth combined with a vege...

  5. Recent microwave research studies of Gazi Biophysics & Gazi Non-Ionizing Radiation Protection Center

    OpenAIRE

    SEYHAN, Nesrin

    2013-01-01

    Gazi Biophysics is located in Ankara at the Medical Faculty of Gazi University and has been carrying out in vivo and in vitro research studies on the biological impacts of Static, Extremely Low Frequency (ELF) and Microwave (MW) electromagnetic fields (EMF) since 1989. Our laboratory includes: Physicists, biologists, electrical engineers, all of whom are studying how living systems respond to EMF. Our research team includes physicists, biologists, electrical engineers, physicians, biochemists...

  6. 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

  7. Biophysical Technologies for Management of Wound Bioburden.

    Science.gov (United States)

    Korzendorfer, Holly; Hettrick, Heather

    2014-12-01

    Significance: Chronic wounds commonly have high levels of bioburden and antibiotic-resistant pathogens. This review article focuses on findings from current literature related to four biophysical technologies (ultrasound, electrical stimulation, phototherapy, and negative pressure wound therapy) believed to be beneficial for managing wound bioburden and support healing. Recent Advances and Critical Issues: Recent advances for each modality are provided as a basic synopsis of the technology followed by brief overviews of the most recent literature addressing its effectiveness for managing wound bioburden, and critical issues for each modality are provided as conclusions. Future Directions: This review highlights the need for further clinically relevant studies examining bacterial levels in addition to healing progression for each technology. PMID:25493207

  8. Biophysical Evaluation of SonoSteam®:

    DEFF Research Database (Denmark)

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

    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...... photon fluorescence microscopy and green fluorescence protein expressing Escherichia coli and Campylobacter jejuni. We employ these methods in the investigation of the effects of SonoSteam on both bacteria and broiler skin and compare our results with those obtained by traditional methods of food quality....../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...

  9. Biophysics of NASA radiation quality factors

    International Nuclear Information System (INIS)

    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. (author)

  10. Main: 2SBL [RPSD[Archive

    Lifescience Database Archive (English)

    Full Text Available NAFLGRSVSLQLISATKADAHGKGKVGKDTFLEGINTSLPTLGAGESAFNIHFEWDGSMGIPGAFYIKNYMQVEFFLKSLTLEAISNQGTIRFVCNSWVYNTKLYKSV...PHVVQVSQSAWMTDEEFAREMIAGVNPCVIRGLEEFPPKSNLDPAIYGDQSSKITADSLDLDGYTMDEALGSRRLFMLDYHDIFMPYVRQINQLNSAKTYATRTILFLREDGTLKPVAI...LINANGIIETTFLPSKYSVEMSSAVYKNWVFTDQALPADLIKRGVAIKDPSTPHGVRLLIEDYPYAADGLEIWAAIKTWVQ

  11. 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

  12. Contribution to researches in biophysics and biology

    International Nuclear Information System (INIS)

    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

  13. Biophysical and biomathematical adventures in radiobiology

    International Nuclear Information System (INIS)

    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

  14. Nanodosimetry: Bridging the gap to radiation biophysics

    International Nuclear Information System (INIS)

    Nanodosimetry strives to link phenomenological dosimetric concepts like radiation quality and relative biological effectiveness to measurable physical quantities related to the track structure of ionising radiation. The ultimate goal of nanodosimetry is therefore to determine novel dosimetric quantities that include the initial biological or biophysical action of ionising radiation. As a step towards this, experimental and numerical techniques have been developed to characterise particle track structure based on the formation of ionisation clusters within a target volume comparable in mass per unit area to a DNA segment. Several attempts have been made to connect the nanodosimetric parameters derived from these ionisation cluster size distributions to biological radiation effects. This work gives an overview of the basic aspects of nanodosimetry, including a discussion of two nanodosimetry-based approaches used to derive estimators of biological effectiveness of ionising radiation. It also includes preliminary results from an ongoing Monte Carlo study into the limitations of using the physical properties of liquid water to approximate those of DNA in nanodosimetric modelling. The findings suggest an overestimation of radiobiological effectiveness may occur when the cross section data for liquid water are used as a substitute for those of DNA.

  15. Brain Mapping Center Opens at Institute of Biophysics

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    @@ Agroup of world-class scie, ntists in brain imaging came to China's capital to .witness the inauguration of the Beijing MRI Center for Brain Research, which was officially opened on May 25 at the CAS Institute of Biophysics.

  16. 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: 1.194, year: 2014

  17. Modeling economic, biophysical, and environmental dynamics of potato production system

    OpenAIRE

    Khakbazan, Mohammad; Hamilton, Cliff; Belcher, Kenneth W.

    2006-01-01

    The adoption and use of diversified cropping practices has become widely accepted by producers. However, the profitability of an enterprise is dependent on the biophysical and economic factors. The biophysical factors determine the enterprise relationship among the various crops, their interactions with the ecosystem, and how each of them fits into the overall management plan. The economic factors determine the relative advantage of each crop and service in the farm plan. Although there have ...

  18. 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.

  19. Signatures of protein biophysics in coding sequence evolution

    OpenAIRE

    Wilke, Claus O; Drummond, D Allan

    2010-01-01

    Since the early days of molecular evolution, the conventional wisdom has been that the evolution of protein-coding genes is primarily determined by functional constraints. Yet recent evidence indicates that the evolution of these genes is strongly shaped by the biophysical processes of protein synthesis, protein folding, and specific as well as non-specific protein–protein interactions. Selection pressures related to these biophysical processes affect primarily the amino-acid sequence of gene...

  20. The relationship between fetal biophysical profile and cord blood PH

    Directory of Open Access Journals (Sweden)

    Valadan M

    2009-02-01

    Full Text Available "nBackground: The Biophysical Profile (BPP is a noninvasive test that predicts the presence or absence of fetal asphyxia and, ultimately, the risk of fetal death in the antenatal period. Intervention on the basis of an abnormal biophysical profile result has been reported to yield a significant reduction in prenatal mortality, and an association exists between biophysical profile scoring and a decreased cerebral palsy rate in a given population. The BPP evaluates five characteristics: fetal movement, tone, breathing, heart reactivity, and amniotic fluid (AF volume estimation. The purpose of study was to determine whether there are different degree of acidosis at which the biophysical activity (acute marker are affected. "nMethods: In a prospective study of 140 patients undergoing cesarean section before onset of labor, the fetal biophysical profile was performed 24h before the time of cesarean and was matched with cord arterial PH that was obtained from a cord segment (10-20cm that was double clamped after delivery of newborn. (using cord arterial PH less than 7.20 for the diagnosis of acidosis. "nResults: The fetal biophysical profile was found to have a significant relationship with umbilical blood PH. The sensitivity, specificity, positive predictive value, negative predictive value of fetal biophysical profile score were: 88.9%, 88.6%, 50%, 98.1%. "nConclusion: The first manifestations of fetal acidosis are nonreactive nonstress testing and fetal breathing loss; in advanced acidemia fetal movements and fetal tone are compromised. A protocol of antepartum fetal evaluation is suggested based upon the individual biophysical components rather than the score alone.

  1. Modelling Biophysical Parameters of Maize Using Landsat 8 Time Series

    Science.gov (United States)

    Dahms, Thorsten; Seissiger, Sylvia; Conrad, Christopher; Borg, Erik

    2016-06-01

    Open and free access to multi-frequent high-resolution data (e.g. Sentinel - 2) will fortify agricultural applications based on satellite data. The temporal and spatial resolution of these remote sensing datasets directly affects the applicability of remote sensing methods, for instance a robust retrieving of biophysical parameters over the entire growing season with very high geometric resolution. In this study we use machine learning methods to predict biophysical parameters, namely the fraction of absorbed photosynthetic radiation (FPAR), the leaf area index (LAI) and the chlorophyll content, from high resolution remote sensing. 30 Landsat 8 OLI scenes were available in our study region in Mecklenburg-Western Pomerania, Germany. In-situ data were weekly to bi-weekly collected on 18 maize plots throughout the summer season 2015. The study aims at an optimized prediction of biophysical parameters and the identification of the best explaining spectral bands and vegetation indices. For this purpose, we used the entire in-situ dataset from 24.03.2015 to 15.10.2015. Random forest and conditional inference forests were used because of their explicit strong exploratory and predictive character. Variable importance measures allowed for analysing the relation between the biophysical parameters with respect to the spectral response, and the performance of the two approaches over the plant stock evolvement. Classical random forest regression outreached the performance of conditional inference forests, in particular when modelling the biophysical parameters over the entire growing period. For example, modelling biophysical parameters of maize for the entire vegetation period using random forests yielded: FPAR: R² = 0.85; RMSE = 0.11; LAI: R² = 0.64; RMSE = 0.9 and chlorophyll content (SPAD): R² = 0.80; RMSE=4.9. Our results demonstrate the great potential in using machine-learning methods for the interpretation of long-term multi-frequent remote sensing datasets to model

  2. Molecular dynamics simulation: at a crossroad between molecular biophysics and petascale computing

    Science.gov (United States)

    Cheng, Xiaolin

    2015-03-01

    High-performance computing (HPC) has become crucial for most advances made in chemistry and biology today. In particular, biophysical simulation is capable of helping generate critical new insights and drive the direction of experimentation. In this talk, I will discuss our work towards addressing some fundamental membrane biophysical questions using HPC capabilities at Oak Ridge National Laboratory. I will first provide a synopsis of our current progress in developing molecular dynamics (MD) techniques that make efficient use of massively parallel supercomputers. I will then discuss a few examples of large-scale MD simulations of biomembrane vesicles, an effort aimed at shedding light on the lateral organization and cross-layer coupling in biologically-relevant membranes. In conclusion, I will discuss a few scientific and technical challenges faced by MD simulation at the exascale. This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725.

  3. Estimation of rice biophysical parameters using multitemporal RADARSAT-2 images

    Science.gov (United States)

    Li, S.; Ni, P.; Cui, G.; He, P.; Liu, H.; Li, L.; Liang, Z.

    2016-04-01

    Compared with optical sensors, synthetic aperture radar (SAR) has the capability of acquiring images in all-weather conditions. Thus, SAR images are suitable for using in rice growth regions that are characterized by frequent cloud cover and rain. The objective of this paper was to evaluate the probability of rice biophysical parameters estimation using multitemporal RADARSAT-2 images, and to develop the estimation models. Three RADARSTA-2 images were acquired during the rice critical growth stages in 2014 near Meishan, Sichuan province, Southwest China. Leaf area index (LAI), the fraction of photosynthetically active radiation (FPAR), height, biomass and canopy water content (WC) were observed at 30 experimental plots over 5 periods. The relationship between RADARSAT-2 backscattering coefficients (σ 0) or their ratios and rice biophysical parameters were analysed. These biophysical parameters were significantly and consistently correlated with the VV and VH σ 0 ratio (σ 0 VV/ σ 0 VH) throughout all growth stages. The regression model were developed between biophysical parameters and σ 0 VV/ σ 0 VH. The results suggest that the RADARSAT-2 data has great potential capability for the rice biophysical parameters estimation and the timely rice growth monitoring.

  4. 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...

  5. Lidar remote sensing of savanna biophysical attributes

    Science.gov (United States)

    Gwenzi, David

    plot level biomass into wall-to-wall maps that provide more ecological information. We evaluated the utility of three spatial modeling approaches to address this problem: deterministic methods, geostatistical methods and an image segmentation approach. Overall, the mean pixel biomass estimated by the 3 approaches did not differ significantly but the output maps showed marked differences in the estimation precision and ability of each model to mimic the primary variable's trend across the landscape. The results emphasized the need for future satellite lidar missions to consider increasing the sampling intensity across track so that biomass observations are made and characterized at the scale at which they vary. We used data from the Multiple Altimeter Beam Experimental Lidar (MABEL), an airborne photon counting lidar sensor developed by NASA Goddard to simulate ICESat-2 data. We segmented each transect into different block sizes and calculated canopy top and mean ground elevation based on the structure of the histogram of the block's aggregated photons. Our algorithm was able to compute canopy height and generate visually meaningful vegetation profiles at MABEL's signal and noise levels but a simulation of the expected performance of ICESat-2 by adjusting MABEL data's detected number of signal and noise photons to that predicted using ATLAS instrument model design cases indicated that signal photons will be substantially lower. The lower data resolution reduces canopy height estimation precision especially in areas of low density vegetation cover. Given the clear difficulties in processing simulated ATLAS data, it appears unlikely that it will provide the kind of data required for mapping of the biophysical properties of savanna vegetation. Rather, resources are better concentrated on preparing for the Global Ecosystem Dynamics Investigation (GEDI) mission, a waveform lidar mission scheduled to launch by the end of this decade. In addition to the full waveform technique

  6. 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

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

    International Nuclear Information System (INIS)

    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

  8. Biophysical characterization of a model antibody drug conjugate.

    Science.gov (United States)

    Arakawa, Tsutomu; Kurosawa, Yasunori; Storms, Michael; Maruyama, Toshiaki; Okumura, C J; Maluf, Nasib Karl

    2016-01-01

    Antibody drug conjugates (ADC) are important next-generation biopharmaceuticals and thus require stringent structure characterization as is the case for monoclonal antibodies. We have tested several biophysical techniques, i.e., circular dichroism, analytical ultracentrifugation, differential scanning calorimetry and fluorescence spectroscopy, to characterize a fluorescein-labeled monoclonal antibody as a model ADC. These techniques indicated possible small structure and stability changes by the conjugation, while largely retaining the tertiary structure of the antibody, consistent with unaltered biological activities. Thus, the above biophysical techniques are effective at detecting changes in the structural properties of ADC. PMID:27534450

  9. The Twilight of Determinism: At Least in Biophysical Novelties

    CERN Document Server

    Gilead, Amihud

    2015-01-01

    In the 1990s, Richard Lewontin referred to what appeared to be the twilight of determinism in biology. He pointed out that DNA determines only a little part of life phenomena, which are very complex. In fact, organisms determine the environment and vice versa in a nonlinear way. Very recently, biophysicists, Shimon Marom and Erez Braun, have demonstrated that controlled biophysical systems have shown a relative autonomy and flexibility in response which could not be predicted. Within the boundaries of some restraints, most of them genetic, this freedom from determinism is well maintained. Marom and Braun have challenged not only biophysical determinism but also reverse-engineering, naive reductionism, mechanism, and systems biology.

  10. Radiation physics, biophysics, and radiation biology

    International Nuclear Information System (INIS)

    An important event of the year was the designation of our Laboratory as a Center for Radiological Research by the Dean of the Faculty of Medicine and Vice-President for Health Sciences. Center status acknowledges the size and importance of the research efforts in this area, and allows a greater measure of independence in administrative matters. While the name has changed from a Laboratory to a Center within the Medical School, the mission and charge remain the same. The efforts of the Center are a multidisciplinary mix of physics, chemistry, and biology, mostly at a basic level, with the admixture of a small proportion of pragmatic or applied research in support of radiation protection or radiation therapy. About a quarter of our funding, mostly individual research awards, could be regarded as in direct support of radiotherapy, with the remainder (an NCI program project grant and DOE grants) being in support of research addressing more basic issues. An important effort currently underway concerns ab-initio calculations of the dielectric response function of condensed water. This investigation has received the coveted designation, ''Grand Challenge Project,'' awarded by DOE to research work which represents ''distinct advance on a major scientific or engineering problem that is broadly recognized as important within the mission of the Department.''

  11. Radiation physics, biophysics, and radiation biology

    International Nuclear Information System (INIS)

    Research at the Radiological Research Laboratory is a blend of physics, chemistry, and biology, involving research at the basic level with the admixture of a small proportion of pragmatic or applied research in support of radiation protection and/or radiotherapy. Current research topics include: oncogenic transformation assays, mutation studies involving interactions between radiation and environmental contaminants, isolation, characterization and sequencing of a human repair gene, characterization of a dominant transforming gene found in C3H 10T1/2 cells, characterize ab initio the interaction of DNA and radiation, refine estimates of the radiation quality factor Q, a new mechanistic model of oncogenesis showing the role of long-term low dose medium LET radiation, and time dependent modeling of radiation induced chromosome damage and subsequent repair or misrepair

  12. Delineating Biophysical Environments of the Sunda Banda Seascape, Indonesia

    Directory of Open Access Journals (Sweden)

    Mingshu Wang

    2015-01-01

    Full Text Available The Sunda Banda Seascape (SBS, located in the center of the Coral Triangle, is a global center of marine biodiversity and a conservation priority. We proposed the first biophysical environmental delineation of the SBS using globally available satellite remote sensing and model-assimilated data to categorize this area into unique and meaningful biophysical classes. Specifically, the SBS was partitioned into eight biophysical classes characterized by similar sea surface temperature, chlorophyll a concentration, currents, and salinity patterns. Areas within each class were expected to have similar habitat types and ecosystem functions. Our work supplemented prevailing global marine management schemes by focusing in on a regional scale with finer spatial resolution. It also provided a baseline for academic research, ecological assessments and will facilitate marine spatial planning and conservation activities in the area. In addition, the framework and methods of delineating biophysical environments we presented can be expanded throughout the whole Coral Triangle to support research and conservation activities in this important region.

  13. Skin Biophysical Characteristics in Patients with Keratoconus: A Controlled Study

    Directory of Open Access Journals (Sweden)

    Reza M. Robati

    2016-01-01

    Full Text Available Background. Keratoconus is a relatively common corneal disease causing significant visual disability. Individuals with connective tissue disorders that affect the skin such as Marfan’s syndrome and Ehlers-Danlos syndrome or patients with atopic dermatitis show an increased prevalence of keratoconus. It seems that there are some concurrent alterations of skin and cornea in patients with keratoconus. Objective. We plan to compare skin biophysical characteristics in patients with keratoconus and healthy controls. Methods. Forty patients with keratoconus (18 females and 22 males with mean (SD age of 33.32 (9.55 years (range 19–56 and 40 healthy controls were recruited to this study. Skin biophysical characteristics including cutaneous resonance running time (CRRT, stratum corneum hydration, and melanin values were measured in patients and controls. Results. The median CRRT, stratum corneum hydration, and melanin measurements were significantly lower in patients with keratoconus in comparison with healthy controls. Conclusion. There are some alterations of skin biophysical properties in patients with keratoconus. Therefore, the assessment of these skin parameters could provide us some clues to the possible common biophysical variations of cornea and skin tissue in diseases such as keratoconus.

  14. Skin Biophysical Characteristics in Patients with Keratoconus: A Controlled Study

    Science.gov (United States)

    Robati, Reza M.; Einollahi, Bahram; Einollahi, Hoda; Younespour, Shima; Fadaifard, Shahed

    2016-01-01

    Background. Keratoconus is a relatively common corneal disease causing significant visual disability. Individuals with connective tissue disorders that affect the skin such as Marfan's syndrome and Ehlers-Danlos syndrome or patients with atopic dermatitis show an increased prevalence of keratoconus. It seems that there are some concurrent alterations of skin and cornea in patients with keratoconus. Objective. We plan to compare skin biophysical characteristics in patients with keratoconus and healthy controls. Methods. Forty patients with keratoconus (18 females and 22 males) with mean (SD) age of 33.32 (9.55) years (range 19–56) and 40 healthy controls were recruited to this study. Skin biophysical characteristics including cutaneous resonance running time (CRRT), stratum corneum hydration, and melanin values were measured in patients and controls. Results. The median CRRT, stratum corneum hydration, and melanin measurements were significantly lower in patients with keratoconus in comparison with healthy controls. Conclusion. There are some alterations of skin biophysical properties in patients with keratoconus. Therefore, the assessment of these skin parameters could provide us some clues to the possible common biophysical variations of cornea and skin tissue in diseases such as keratoconus. PMID:27403376

  15. Biophysical characterisation of GlycoPEGylated recombinant human factor VIIa

    DEFF Research Database (Denmark)

    Plesner, Bitten; Westh, Peter; Nielsen, Anders D.

    ) both increased with GlycoPEGylation. Both Tm and Tagg were independent of the molecular weight and the shape of the PEG chain. From the present biophysical characterisation it is concluded that after GlycoPEGylation, rFVIIa appears to be unaffected structurally (secondary and tertiary structure...

  16. 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 abili...

  17. 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...

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

    International Nuclear Information System (INIS)

    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

  19. 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.

  20. How can biophysical models be tested experimentally?

    International Nuclear Information System (INIS)

    Seldom are experiments designed from the outset for the primary purpose of testing a particular model. Rather, experiments should be designed and carried out in such a way that the data can be fitted to several models so that differences in the basic hypotheses upon which the models are based can be tested and compared. In the present context the ultimate aim is to arrive at cancer risk estimates in the human based on laboratory data. Two general points are made with respect to this aim. The first is that it would be highly desirable to obtain a consistent, coherent set of data by the same group of investigators using the same cell lines, that encompass double strand breaks, exchange type chromosome aberrations cell lethality, mutation and transformation. At the present time, the data available to the modelers are fragmentary; seldom are more than one or two endpoints available from the same investigator, involving the same biological system. The second is that a major goal for the future must be to improve communication between experiments and modelers. Particular comments are made on the following research areas; assays for oncogenic transformation; oncogenic transformation; dominant acting transforming genes; recessive suppressor genes; cytogenetics and transformation. (author)

  1. Incorporating modeling and simulations in undergraduate biophysical chemistry course to promote understanding of structure-dynamics-function relationships in proteins.

    Science.gov (United States)

    Hati, Sanchita; Bhattacharyya, Sudeep

    2016-03-01

    A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and simulations. In particular, modern computational tools are employed to elucidate the relationship between structure, dynamics, and function in proteins. Computer-based laboratory protocols that we introduced in three modules allow students to visualize the secondary, super-secondary, and tertiary structures of proteins, analyze non-covalent interactions in protein-ligand complexes, develop three-dimensional structural models (homology model) for new protein sequences and evaluate their structural qualities, and study proteins' intrinsic dynamics to understand their functions. In the fourth module, students are assigned to an authentic research problem, where they apply their laboratory skills (acquired in modules 1-3) to answer conceptual biophysical questions. Through this process, students gain in-depth understanding of protein dynamics-the missing link between structure and function. Additionally, the requirement of term papers sharpens students' writing and communication skills. Finally, these projects result in new findings that are communicated in peer-reviewed journals. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:140-159, 2016. PMID:26801683

  2. The 1989 progress report: Polytechnic school laboratories' Direction

    International Nuclear Information System (INIS)

    The 1989 progress report of the laboratories' Direction of the Polytechnic School (France) is presented. The research activities carried out in each laboratory are summarized. Scientific and technical cooperation, financial and employement aspects are included. The main fields of research are: biochemistry, chemistry, reaction mechanisms, organic synthesis, mechanics of solids, meteorology, irradiated solids, optics, physics, biophysics, lasers, mathematics, econometrics, epistemology, management and computer science

  3. PCSB--a program collection for structural biology and biophysical chemistry.

    Science.gov (United States)

    Hofmann, A; Wlodawer, A

    2002-01-01

    We present the first package of Java classes specifically aimed at the handling of structural and biophysical problems. To enable object-oriented programming a basis of fundamental Java classes is required which deals with basic operations of vectors, matrices, amino acid sequences, crystal symmetries and PDB files. Five classes, which carry out these basic operations, were constructed and bundled together with several utility functions in the PCSB package. Furthermore, to demonstrate their applicability and to obtain programs handling common tasks in structural laboratories, we present the first six applications of PCSB. All applications are portable to different platforms and require only the Java Runtime Environment to be installed on the system. available as PDF file. PMID:11836236

  4. Biophysical Insights from Temperature-Dependent Single-Molecule Förster Resonance Energy Transfer

    Science.gov (United States)

    Holmstrom, Erik D.; Nesbitt, David J.

    2016-05-01

    Single-molecule fluorescence microscopy techniques can be used in combination with micrometer length-scale temperature control and Förster resonance energy transfer (FRET) in order to gain detailed information about fundamental biophysical phenomena. In particular, this combination of techniques has helped foster the development of remarkable quantitative tools for studying both time- and temperature-dependent structural kinetics of biopolymers. Over the past decade, multiple research efforts have successfully incorporated precise spatial and temporal control of temperature into single-molecule FRET (smFRET)-based experiments, which have uncovered critical thermodynamic information on a wide range of biological systems such as conformational dynamics of nucleic acids. This review provides an overview of various temperature-dependent smFRET approaches from our laboratory and others, highlighting efforts in which such methods have been successfully applied to studies of single-molecule nucleic acid folding.

  5. Linking Gap Model with MODIS Biophysical Products for Biomass Estimation

    Science.gov (United States)

    Wang, D.; Sun, G.; Cai, Y.; Guo, Z.; Fu, A.; Ni, W.; Liu, D.

    With the development of earth observation technology and data processing technology biophysical data from remote sensing means such as MODIS LAI and NPP are accessible now However it is still difficult for direct measurement of biomass from remote sensors One possibility for overcoming this problem is using ecological models to link the vegetation parameters currently available from remote sensing to biomass In this paper a combined work is done for estimating forest biomass A calibrated gap model ZELIG was run to simulate the forest development in a temperate forested area in NE China The output relationship between age and biomass was linked to registered MODIS LAI NPP and land cover type images of the same area From the above work forest age or biomass was estimated from existing remote sensed data Obviously there is a lot of work to be done such as optimal combination of biophysical parameters to improve the linkage between MODIS product and ecological modeling

  6. Elucidating diversity of exosomes: biophysical and molecular characterization methods.

    Science.gov (United States)

    Khatun, Zamila; Bhat, Anjali; Sharma, Shivani; Sharma, Aman

    2016-09-01

    Exosomes are cell-secreted nanovesicles present in biological fluids in normal and diseased conditions. Owing to their seminal role in cell-cell communication, emerging evidences suggest that exosomes are fundamental regulators of various diseases. Due to their potential usefulness in disease diagnosis, robust isolation and characterization of exosomes is critical in developing exosome-based assays. In the last few years, different exosome characterization methods, both biophysical and molecular, have been developed to characterize these tiny vesicles. Here, in this review we summarize: first, biophysical techniques based on spectroscopy (e.g., Raman spectroscopy, dynamic light scattering) and other principles, for example, scanning electron microscopy, atomic force microscopy; second, antibody-based molecular techniques including flow cytometry, transmission electron microscopy and third, nanotechnology-dependent exosome characterization methodologies. PMID:27488053

  7. 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.

  8. 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.

  9. "The Physics of Life," an undergraduate general education biophysics course

    CERN Document Server

    Parthasarathy, Raghuveer

    2014-01-01

    Improving the scientific literacy of non-scientists is an important goal, both because of the ever-increasing impact of science and technology on our lives, and because understanding science enriches our experience of the natural world. One route to improving scientific literacy is via general education undergraduate courses -- i.e. courses intended for students not majoring in the sciences or engineering -- which in many cases provide these students' last formal exposure to science. I describe here a course on biophysics for non-science-major undergraduates recently developed at the University of Oregon (Eugene, OR, USA). Biophysics, I claim, is a particularly useful vehicle for addressing scientific literacy. It involves important and general scientific concepts, demonstrates connections between basic science and tangible, familiar phenomena related to health and disease, and illustrates that scientific insights develop by applying tools and perspectives from disparate fields in creative ways. In addition, ...

  10. Biophysical and economic limits to negative CO2 emissions

    OpenAIRE

    Smith, P; Davis, S J; Creutzig, F.; Minx, J.

    2016-01-01

    To have a >50% chance of limiting warming below 2 °C, most recent scenarios from integrated assessment models (IAMs) require large-scale deployment of negative emissions technologies (NETs). These are technologies that result in the net removal of greenhouse gases from the atmosphere. We quantify potential global impacts of the different NETs on various factors (such as land, greenhouse gas emissions, water, albedo, nutrients and energy) to determine the biophysical limits to, and economic co...

  11. The problem of morphogenesis: unscripted biophysical control systems in plants

    OpenAIRE

    Lintilhac, Philip M.

    2013-01-01

    The relative simplicity of plant developmental systems, having evolved within the universal constraints imposed by the plant cell wall, may allow us to outline a consistent developmental narrative that is not currently possible in the animal kingdom. In this article, I discuss three aspects of the development of the mature form in plants, approaching them in terms of the role played by the biophysics and mechanics of the cell wall during growth. First, I discuss axis extension in terms of a l...

  12. Free-electron-laser-based biophysical and biomedical instrumentation

    International Nuclear Information System (INIS)

    A survey of biophysical and biomedical applications of free-electron lasers (FELs) is presented. FELs are pulsed light sources, collectively operating from the microwave through the x-ray range. This accelerator-based technology spans gaps in wavelength, pulse structure, and optical power left by conventional sources. FELs are continuously tunable and can produce high-average and high-peak power. Collectively, FEL pulses range from quasicontinuous to subpicosecond, in some cases with complex superpulse structures. Any given FEL, however, has a more restricted set of operational parameters. FELs with high-peak and high-average power are enabling biophysical and biomedical investigations of infrared tissue ablation. A midinfrared FEL has been upgraded to meet the standards of a medical laser and is serving as a surgical tool in ophthalmology and human neurosurgery. The ultrashort pulses produced by infrared or ultraviolet FELs are useful for biophysical investigations, both one-color time-resolved spectroscopy and when coupled with other light sources, for two-color time-resolved spectroscopy. FELs are being used to drive soft ionization processes in mass spectrometry. Certain FELs have high repetition rates that are beneficial for some biophysical and biomedical applications, but confound research for other applications. Infrared FELs have been used as sources for inverse Compton scattering to produce a pulsed, tunable, monochromatic x-ray source for medical imaging and structural biology. FEL research and FEL applications research have allowed the specification of spin-off technologies. On the horizon is the next generation of FELs, which is aimed at producing ultrashort, tunable x rays by self-amplified spontaneous emission with potential applications in biology

  13. Biophysics of protein-DNA interactions and chromosome organization

    OpenAIRE

    Marko, John F.

    2015-01-01

    The function of DNA in cells depends on its interactions with protein molecules, which recognize and act on base sequence patterns along the double helix. These notes aim to introduce basic polymer physics of DNA molecules, biophysics of protein-DNA interactions and their study in single-DNA experiments, and some aspects of large-scale chromosome structure. Mechanisms for control of chromosome topology will also be discussed.

  14. 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: 1.222, year: 2014

  15. Biophysical mechanism determining dental implants biocompatibility and conditioning their oseintegration

    Czech Academy of Sciences Publication Activity Database

    Vetterl, Vladimír; Hasoň, Stanislav; Silvennoinen, R.; Cvrček, L.; Vaněk, J.; Bartáková, S.; Strašák, L.; Fojt, Lukáš

    Beijing, 2009. s. 1. [The 60th Annual Meeting of the International Society of Electrochemistry. 16.08.2009-21.08.2009, Beijing] R&D Projects: GA MŠk(CZ) 1M0528; GA ČR(CZ) GA202/08/1688; GA AV ČR(CZ) KAN200040651 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : fibrinogene * oseointegration * titanium Subject RIV: BO - Biophysics

  16. Biophysical basis for the geometry of conical stromatolites

    OpenAIRE

    Petroff, Alexander P.; Sim, Min Sub; Maslov, Andrey; Krupenin, Mikhail; Rothman, Daniel H.; Bosak, Tanja

    2010-01-01

    Stromatolites may be Earth’s oldest macroscopic fossils; however, it remains controversial what, if any, biological processes are recorded in their morphology. Although the biological interpretation of many stromatolite morphologies is confounded by the influence of sedimentation, conical stromatolites form in the absence of sedimentation and are, therefore, considered to be the most robust records of biophysical processes. A qualitative similarity between conical stromatolites and some moder...

  17. PREFACE: Nanoelectronics, sensors and single molecule biophysics Nanoelectronics, sensors and single molecule biophysics

    Science.gov (United States)

    Tao, Nongjian

    2012-04-01

    This special section of Journal of Physics: Condensed Matter (JPCM) is dedicated to Professor Stuart M Lindsay on the occasion of his 60th birthday and in recognition of his outstanding contributions to multiple research areas, including light scattering spectroscopy, scanning probe microscopy, biophysics, solid-liquid interfaces and molecular and nanoelectronics. It contains a collection of 14 papers in some of these areas, including a feature article by Lindsay. Each paper was subject to the normal rigorous review process of JPCM. In Lindsay's paper, he discusses the next generations of hybrid chemical-CMOS devices for low cost and personalized medical diagnosis. The discussion leads to several papers on nanotechnology for biomedical applications. Kawaguchi et al report on the detection of single pollen allergen particles using electrode embedded microchannels. Stern et al describe a structural study of three-dimensional DNA-nanoparticle assemblies. Hihath et al measure the conductance of methylated DNA, and discuss the possibility of electrical detection DNA methylation. Portillo et al study the electrostatic effects on the aggregation of prion proteins and peptides with atomic force microscopy. In an effort to understand the interactions between nanostructures and cells, Lamprecht et al report on the mapping of the intracellular distribution of carbon nanotubes with a confocal Raman imaging technique, and Wang et al focus on the intracellular delivery of gold nanoparticles using fluorescence microscopy. Park and Kristic provide theoretical analysis of micro- and nano-traps and their biological applications. This section also features several papers on the fundamentals of electron transport in single atomic wires and molecular junctions. The papers by Xu et al and by Wandlowksi et al describe new methods to measure conductance and forces in single molecule junctions and metallic atomic wires. Scullion et al report on the conductance of molecules with similar

  18. A quantitative overview of biophysical forces impinging on neural function

    International Nuclear Information System (INIS)

    The fundamentals of neuronal membrane excitability are globally described using the Hodgkin-Huxley (HH) model. The HH model, however, does not account for a number of biophysical phenomena associated with action potentials or propagating nerve impulses. Physical mechanisms underlying these processes, such as reversible heat transfer and axonal swelling, have been compartmentalized and separately investigated to reveal neuronal activity is not solely influenced by electrical or biochemical factors. Instead, mechanical forces and thermodynamics also govern neuronal excitability and signaling. To advance our understanding of neuronal function and dysfunction, compartmentalized analyses of electrical, chemical, and mechanical processes need to be revaluated and integrated into more comprehensive theories. The present perspective is intended to provide a broad overview of biophysical forces that can influence neural function, but which have been traditionally underappreciated in neuroscience. Further, several examples where mechanical forces have been shown to exert their actions on nervous system development, signaling, and plasticity are highlighted to underscore their importance in sculpting neural function. By considering the collective actions of biophysical forces influencing neuronal activity, our working models can be expanded and new paradigms can be applied to the investigation and characterization of brain function and dysfunction. (topical review)

  19. 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.

  20. Structural, biological and biophysical properties of glycated and glycoxidized phosphatidylethanolamines.

    Science.gov (United States)

    Annibal, Andrea; Riemer, Thomas; Jovanovic, Olga; Westphal, Dennis; Griesser, Eva; Pohl, Elena E; Schiller, Jürgen; Hoffmann, Ralf; Fedorova, Maria

    2016-06-01

    Glycation and glycoxidation of proteins and peptides have been intensively studied and are considered as reliable diagnostic biomarkers of hyperglycemia and early stages of type II diabetes. However, glucose can also react with primary amino groups present in other cellular components, such as aminophospholipids (aminoPLs). Although it is proposed that glycated aminoPLs can induce many cellular responses and contribute to the development and progression of diabetes, the routes of their formation and their biological roles are only partially revealed. The same is true for the influence of glucose-derived modifications on the biophysical properties of PLs. Here we studied structural, signaling, and biophysical properties of glycated and glycoxidized phosphatidylethanolamines (PEs). By combining high resolution mass spectrometry and nuclear magnetic resonance spectroscopy it was possible to deduce the structures of several intermediates indicating an oxidative cleavage of the Amadori product yielding glycoxidized PEs including advanced glycation end products, such as carboxyethyl- and carboxymethyl-ethanolamines. The pro-oxidative role of glycated PEs was demonstrated and further associated with several cellular responses including activation of NFκB signaling pathways. Label free proteomics indicated significant alterations in proteins regulating cellular metabolisms. Finally, the biophysical properties of PL membranes changed significantly upon PE glycation, such as melting temperature (Tm), membrane surface charge, and ion transport across the phospholipid bilayer. PMID:27012418

  1. Biophysical Discovery through the Lens of a Computational Microscope

    Science.gov (United States)

    Amaro, Rommie

    With exascale computing power on the horizon, improvements in the underlying algorithms and available structural experimental data are enabling new paradigms for chemical discovery. My work has provided key insights for the systematic incorporation of structural information resulting from state-of-the-art biophysical simulations into protocols for inhibitor and drug discovery. We have shown that many disease targets have druggable pockets that are otherwise ``hidden'' in high resolution x-ray structures, and that this is a common theme across a wide range of targets in different disease areas. We continue to push the limits of computational biophysical modeling by expanding the time and length scales accessible to molecular simulation. My sights are set on, ultimately, the development of detailed physical models of cells, as the fundamental unit of life, and two recent achievements highlight our efforts in this arena. First is the development of a molecular and Brownian dynamics multi-scale modeling framework, which allows us to investigate drug binding kinetics in addition to thermodynamics. In parallel, we have made significant progress developing new tools to extend molecular structure to cellular environments. Collectively, these achievements are enabling the investigation of the chemical and biophysical nature of cells at unprecedented scales.

  2. 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.

  3. Relevance of experiments with different charged particles having the same LET for biophysical modelling of radiation effects

    International Nuclear Information System (INIS)

    Extensive experimental data have been collected on the cellular and molecular effects produced on V79 cells by low energy protons and alpha-particles of comparable linear energy transfer (LET) at Legnaro and Harwell laboratories. Protons were the more effective in inducing cell inactivation and mutation, while this was not observed for initial production of DNA double strand breaks which is quite insensitive to radiation type and LET. These experimental results provide new constraints for biophysical modelling of radiation action with respect to both the relevant molecular damage and the relevant microscopic properties of radiation tracks. (author)

  4. 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.

  5. Biophysical and economic limits to negative CO2 emissions

    Science.gov (United States)

    Smith, Pete; Davis, Steven J.; Creutzig, Felix; Fuss, Sabine; Minx, Jan; Gabrielle, Benoit; Kato, Etsushi; Jackson, Robert B.; Cowie, Annette; Kriegler, Elmar; van Vuuren, Detlef P.; Rogelj, Joeri; Ciais, Philippe; Milne, Jennifer; Canadell, Josep G.; McCollum, David; Peters, Glen; Andrew, Robbie; Krey, Volker; Shrestha, Gyami; Friedlingstein, Pierre; Gasser, Thomas; Grübler, Arnulf; Heidug, Wolfgang K.; Jonas, Matthias; Jones, Chris D.; Kraxner, Florian; Littleton, Emma; Lowe, Jason; Moreira, José Roberto; Nakicenovic, Nebojsa; Obersteiner, Michael; Patwardhan, Anand; Rogner, Mathis; Rubin, Ed; Sharifi, Ayyoob; Torvanger, Asbjørn; Yamagata, Yoshiki; Edmonds, Jae; Yongsung, Cho

    2016-01-01

    To have a >50% chance of limiting warming below 2 °C, most recent scenarios from integrated assessment models (IAMs) require large-scale deployment of negative emissions technologies (NETs). These are technologies that result in the net removal of greenhouse gases from the atmosphere. We quantify potential global impacts of the different NETs on various factors (such as land, greenhouse gas emissions, water, albedo, nutrients and energy) to determine the biophysical limits to, and economic costs of, their widespread application. Resource implications vary between technologies and need to be satisfactorily addressed if NETs are to have a significant role in achieving climate goals.

  6. Biophysical modelling of radiation induced damage in chromosomes

    International Nuclear Information System (INIS)

    A computational biophysical model is described which simulates radiation damage to human blood lymphocytes by photon and electron radiation. The model includes a realistic simulation of the geometrical structure of lymphocytes (plasma, nucleus, chromatin, DNA) and its chemical constituents. The simulation of damage to DNA, which is the critical target for the induction of chromosome aberrations, takes into account direct effects (energy deposition) and indirect effects (radical attack). Furthermore, an attempt has been made to correlate DNA damage within the cell nucleus to the coefficients of the dose effect relationships for the induction of dicentric chromosomes; reasonable agreement is found with relevant experimental data. (author)

  7. Plant Sucrose Transporters from a Biophysical Point of View

    Institute of Scientific and Technical Information of China (English)

    Dietmar Geiger

    2011-01-01

    T The majority of higher plants use sucrose as their main mobile carbohydrate. Proton-driven sucrose transporters play a crucial role in cell-to-cell and long-distance distribution of sucrose throughout the plant. A very negative plant membrane potential and the ability of sucrose transporters to accumulate sucrose concentrations of more than 1 M indicate that plants evolved transporters with unique structural and functional features. The knowledge about the transport mechanism and structural/functional domains of these nano-machines is, however, still fragmentary. In this review,the current knowledge about the biophysical properties of plant sucrose transporters is summarized and discussed.

  8. Radio biophysical studies on some fresh water biota

    International Nuclear Information System (INIS)

    The present study includes biophysical measurements of uptake and release of Co-60 by aquatic biota, water hyacinth plant (Eichhronia Crassipes ) and biomphalaria alexandrina snails placed in ismailia canal water. The uptake of co-60 was studied under different experimental conditions, namely the effect of contact time, variation of p H of the cobalt solution, the presence of competing ions and variation of cobalt carrier concentration. The experimental results of Co-60 uptake and release by the aquatic biota are described using the compartmental model, and also using the well known freudlich isotherm equation model

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

    International Nuclear Information System (INIS)

    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

  10. Neurophysiological and biophysical evidence on the mechanism of electric taste

    OpenAIRE

    1985-01-01

    The phenomenon of electric taste was investigated by recording from the chorda tympani nerve of the rat in response to both electrical and chemical stimulations of the tongue with electrolytes in order to gain some insight into its mechanism on both a neurophysiological and biophysical basis. The maximum neural response levels were identical for an individual salt (LiCl, NaCl, KCl, or CaCl2), whether it was presented as a chemical solution or as an anodal stimulus through a subthreshold solut...

  11. 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

  12. Methods of high throughput biophysical characterization in biopharmaceutical development.

    Science.gov (United States)

    Razinkov, Vladimir I; Treuheit, Michael J; Becker, Gerald W

    2013-03-01

    Discovery and successful development of biopharmaceutical products depend on a thorough characterization of the molecule both before and after formulation. Characterization of a formulated biotherapeutic, typically a protein or large peptide, requires a rigorous assessment of the molecule's physical stability. Stability of a biotherapeutic includes not only chemical stability, i.e., degradation of the molecule to form undesired modifications, but also structural stability, including the formation of aggregates. In this review, high throughput biophysical characterization techniques are described according to their specific applications during biopharmaceutical discovery, development and manufacturing. The methods presented here are classified according to these attributes, and include spectroscopic assays based on absorbance, polarization, intrinsic and extrinsic fluorescence, surface plasmon resonance instrumentation, calorimetric methods, dynamic and static light scattering techniques, several visible particle counting and sizing methods, new viscosity assay, based on light scattering and mass spectrometry. Several techniques presented here are already implemented in industry; but, many high throughput biophysical methods are still in the initial stages of implementation or even in the prototype stage. Each technique in this report is judged by the specific application of the method through the biopharmaceutical development process. PMID:22725690

  13. Constructing Dual Beam Optical Tweezers for Undergraduate Biophysics Research

    Science.gov (United States)

    Daudelin, Brian; West-Coates, Devon; Del'Etoile, Jon; Grotzke, Eric; Paramanathan, Thayaparan

    Optical tweezing, or trapping, is a modern physics technique which allows us to use the radiation pressure from laser beams to trap micron sized particles. Optical tweezers are commonly used in graduate level biophysics research but seldom used at the undergraduate level. Our goal is to construct a dual beam optical tweezers for future undergraduate biophysical research. Dual beam optical tweezers use two counter propagating laser beams to provide a stronger trap. In this study we discuss how the assembly of the dual beam optical tweezers is done through three main phases. The first phase was to construct a custom compressed air system to isolate the optical table from the vibrations from its surroundings so that we can measure pico-newton scale forces that are observed in biological systems. In addition, the biomaterial flow system was designed with a flow cell to trap biomolecules by combining several undergraduate semester projects. During the second phase we set up the optics to image and display the inside of the flow cell. Currently we are in the process of aligning the laser to create an effective trap and developing the software to control the data collection. This optical tweezers set up will enable us to study potential cancer drug interactions with DNA at the single molecule level and will be a powerful tool in promoting interdisciplinary research at the undergraduate level.

  14. 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.

  15. Biophysics of filament length regulation by molecular motors

    Science.gov (United States)

    Kuan, Hui-Shun; Betterton, M. D.

    2013-06-01

    Regulating physical size is an essential problem that biological organisms must solve from the subcellular to the organismal scales, but it is not well understood what physical principles and mechanisms organisms use to sense and regulate their size. Any biophysical size-regulation scheme operates in a noisy environment and must be robust to other cellular dynamics and fluctuations. This work develops theory of filament length regulation inspired by recent experiments on kinesin-8 motor proteins, which move with directional bias on microtubule filaments and alter microtubule dynamics. Purified kinesin-8 motors can depolymerize chemically-stabilized microtubules. In the length-dependent depolymerization model, the rate of depolymerization tends to increase with filament length, because long filaments accumulate more motors at their tips and therefore shorten more quickly. When balanced with a constant filament growth rate, this mechanism can lead to a fixed polymer length. However, the mechanism by which kinesin-8 motors affect the length of dynamic microtubules in cells is less clear. We study the more biologically realistic problem of microtubule dynamic instability modulated by a motor-dependent increase in the filament catastrophe frequency. This leads to a significant decrease in the mean filament length and a narrowing of the filament length distribution. The results improve our understanding of the biophysics of length regulation in cells.

  16. 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.

  17. Biophysical basis for noninvasive skin cancer detection using Raman spectroscopy

    Science.gov (United States)

    Feng, Xu; Moy, Austin J.; Markey, Mia K.; Fox, Matthew C.; Reichenberg, Jason S.; Tunnell, James W.

    2016-03-01

    Raman spectroscopy (RS) is proving to be a valuable tool for real time noninvasive skin cancer detection via optical fiber probe. However, current methods utilizing RS for skin cancer diagnosis rely on statistically based algorithms to provide tissue classification and do not elucidate the underlying biophysical changes of skin tissue. Therefore, we aim to use RS to explore skin biochemical and structural characteristics and then correlate the Raman spectrum of skin tissue with its disease state. We have built a custom confocal micro-Raman spectrometer system with an 830nm laser light. The high resolution capability of the system allows us to measure spectroscopic features from individual tissue components in situ. Raman images were collected from human skin samples from Mohs surgical biopsy, which were then compared with confocal laser scanning, two-photon fluorescence and hematoxylin and eosin-stained images to develop a linear model of skin tissue Raman spectra. In this model, macroscopic tissue spectra obtained from RS fiber probe were fit into a linear combination of individual basis spectra of primary skin constituents. The fit coefficient of the model explains the biophysical changes spanning a range of normal and various disease states. The model allows for determining parameters similar to that a pathologist is familiar reading and will be a significant guidance in developing RS diagnostic decision schemes.

  18. Complexation of insecticide chlorantraniliprole with human serum albumin: Biophysical aspects

    International Nuclear Information System (INIS)

    Chlorantraniliprole is a novel insecticide belonging to the diamide class of selective ryanodine receptor agonists. A biophysical study on the binding interaction of a novel diamide insecticide, chlorantraniliprole, with staple in vivo transporter, human serum albumin (HSA) has been investigated utilizing a combination of steady-state and time-resolved fluorescence, circular dichroism (CD), and molecular modeling methods. The interaction of chlorantraniliprole with HSA gives rise to fluorescence quenching through static mechanism, this corroborates the fluorescence lifetime outcomes that the ground state complex formation and the predominant forces in the HSA-chlorantraniliprole conjugate are van der Waals forces and hydrogen bonds, as derived from thermodynamic analysis. The definite binding site of chlorantraniliprole in HSA has been identified from the denaturation of protein, competitive ligand binding, and molecular modeling, subdomain IIIA (Sudlow's site II) was designated to possess high-affinity binding site for chlorantraniliprole. Moreover, using synchronous fluorescence, CD, and three-dimensional fluorescence we testified some degree of HSA structure unfolding upon chlorantraniliprole binding. - Highlights: → Our study highlights for the first time how binding dynamics can predominate for the new diamide insecticide, chlorantraniliprole. → Chlorantraniliprole is situated within subdomain IIIA, Sudlow's site II, which is the same as that of indole-benzodiazepine site. → Biophysical and molecular modeling approaches are useful to resolve the ligand interaction with biomacromolecule. → It serves as a protective device in binding and in inactivating potential toxic compounds to which the body is exposed.

  19. Complexation of insecticide chlorantraniliprole with human serum albumin: Biophysical aspects

    Energy Technology Data Exchange (ETDEWEB)

    Ding Fei [Department of Chemistry, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193 (China); Liu Wei [College of Economics and Management, China Agricultural University, Beijing 100083 (China); Diao Jianxiong [Department of Chemistry, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193 (China); Yin Bin [Key Laboratory of Pesticide Chemistry and Application Technology, Ministry of Agriculture, Department of Applied Chemistry, China Agricultural University, Beijing 100193 (China); Zhang Li, E-mail: zhli.work@gmail.co [Key Laboratory of Pesticide Chemistry and Application Technology, Ministry of Agriculture, Department of Applied Chemistry, China Agricultural University, Beijing 100193 (China); Sun Ying, E-mail: sunying@cau.edu.c [Department of Chemistry, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193 (China)

    2011-07-15

    Chlorantraniliprole is a novel insecticide belonging to the diamide class of selective ryanodine receptor agonists. A biophysical study on the binding interaction of a novel diamide insecticide, chlorantraniliprole, with staple in vivo transporter, human serum albumin (HSA) has been investigated utilizing a combination of steady-state and time-resolved fluorescence, circular dichroism (CD), and molecular modeling methods. The interaction of chlorantraniliprole with HSA gives rise to fluorescence quenching through static mechanism, this corroborates the fluorescence lifetime outcomes that the ground state complex formation and the predominant forces in the HSA-chlorantraniliprole conjugate are van der Waals forces and hydrogen bonds, as derived from thermodynamic analysis. The definite binding site of chlorantraniliprole in HSA has been identified from the denaturation of protein, competitive ligand binding, and molecular modeling, subdomain IIIA (Sudlow's site II) was designated to possess high-affinity binding site for chlorantraniliprole. Moreover, using synchronous fluorescence, CD, and three-dimensional fluorescence we testified some degree of HSA structure unfolding upon chlorantraniliprole binding. - Highlights: {yields} Our study highlights for the first time how binding dynamics can predominate for the new diamide insecticide, chlorantraniliprole. {yields} Chlorantraniliprole is situated within subdomain IIIA, Sudlow's site II, which is the same as that of indole-benzodiazepine site. {yields} Biophysical and molecular modeling approaches are useful to resolve the ligand interaction with biomacromolecule. {yields} It serves as a protective device in binding and in inactivating potential toxic compounds to which the body is exposed.

  20. 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.

  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. Annual report of the Laboratory for Condensed Matter Physics, and the Biophysics Group

    International Nuclear Information System (INIS)

    Research on photoemission and photoluminescence in quantum wells; photoemission assisted by electric fields; the electrochemistry of the semiconductor-electrolyte interface; MESFET's; fractal physics; amorphous silicon; superionic and mixed conductors; solids chemistry and NMR; internal motion of nucleic acids; cardiophysiology; imaging of microscopic internal motions; and Ap4A metabolism is presented

  3. Annual report of the Laboratory of Condensed Matter Physics, and the Biophysics Group, 1985

    International Nuclear Information System (INIS)

    Research on photoemission and photoluminescence in quantum wells; photoemission assisted by electric fields; the electrochemistry of the semiconductor-electrolyte interface; transport properties of MESFET's; fractal physics; amorphous silicon; superionic and mixed conductors; solids chemistry and NMR; internal motion of nucleic acids; cardiophysiology; imaging of microscopic internal motions; and Ap4A metabolism is presented

  4. HYDROMECHANICS LABORATORY

    Data.gov (United States)

    Federal Laboratory Consortium — Naval Academy Hydromechanics Laboratory The Naval Academy Hydromechanics Laboratory (NAHL) began operations in Rickover Hall in September 1976. The primary purpose...

  5. 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

  6. Fluorescence Quantum Yield Measurements of Fluorescent Proteins: A Laboratory Experiment for a Biochemistry or Molecular Biophysics Laboratory Course

    Science.gov (United States)

    Wall, Kathryn P.; Dillon, Rebecca; Knowles, Michelle K.

    2015-01-01

    Fluorescent proteins are commonly used in cell biology to assess where proteins are within a cell as a function of time and provide insight into intracellular protein function. However, the usefulness of a fluorescent protein depends directly on the quantum yield. The quantum yield relates the efficiency at which a fluorescent molecule converts…

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

    DEFF Research Database (Denmark)

    Tian, Xinsheng; Langkilde, Annette Eva; Thorolfsson, Matthias; Rasmussen, Hanne B; Vestergaard, Bente

    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 a...

  8. Biophysics and Structure to Counter Threats and Challenges

    CERN Document Server

    Margaris, Manolia

    2013-01-01

    This ASI brought together a diverse group of experts who span virology, biology, biophysics, chemistry, physics and engineering.  Prominent lecturers representing world renowned scientists from nine (9) different countries, and students from around the world representing eighteen (18) countries, participated in the 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 chemical and bioterrorism agents, lead to cleaner environments and improved energy sources, and help propel development in NATO partner countries.  At the end of the ASI students had an appreciation of how to apply each technique to their own particular research problem and to demonstrate that multifaceted approaches and new technologies are needed to solve the biological challenges of our time.  The course...

  9. Biophysics of selectin-ligand interactions in inflammation and cancer

    Science.gov (United States)

    Siu-Lun Cheung, Luthur; Raman, Phrabha S.; Balzer, Eric M.; Wirtz, Denis; Konstantopoulos, Konstantinos

    2011-02-01

    Selectins (l-, e- and p-selectin) are calcium-dependent transmembrane glycoproteins that are expressed on the surface of circulating leukocytes, activated platelets, and inflamed endothelial cells. Selectins bind predominantly to sialofucosylated glycoproteins and glycolipids (e-selectin only) present on the surface of apposing cells, and mediate transient adhesive interactions pertinent to inflammation and cancer metastasis. The rapid turnover of selectin-ligand bonds, due to their fast on- and off-rates along with their remarkably high tensile strengths, enables them to mediate cell tethering and rolling in shear flow. This paper presents the current body of knowledge regarding the role of selectins in inflammation and cancer metastasis, and discusses experimental methodologies and mathematical models used to resolve the biophysics of selectin-mediated cell adhesion. Understanding the biochemistry and biomechanics of selectin-ligand interactions pertinent to inflammatory disorders and cancer metastasis may provide insights for developing promising therapies and/or diagnostic tools to combat these disorders.

  10. Biophysical and Physiological Basis of Human Cold Acclimatization

    Directory of Open Access Journals (Sweden)

    Bal Krishna

    1968-05-01

    Full Text Available On exposure to cold, the problem is to maintain internal temperature of the human body in the presence of an increased thermal gradient between the core and the external environment. The ability to maintain homeothermy in the cold environment is enhanced in the acclimatized man. Superimposed upon the adaptive responses of the whole body to cold exposure are the adaptive responses of the extermities to avoid severe cold injury. The two major methods of adjustment to cold exposure are metabolic adjustments and peripheral cooling. Metabolic adjustment involve an increase in heat production in response to a cold stress such as shivering and non shivering thermogenesis and voluntary muscular activity. Peripheral cooling reduce the loss of heat from the skin by effectively increasing the thickness of relatively cooler peripheral tissues. The available literature on human cold acclimatization has been surveyed with a view to explain the biophysical and physiological mechanisms involved in the process of acclimatization.

  11. 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...

  12. Biophysics of filament length regulation by molecular motors

    CERN Document Server

    Kuan, Hui-Shun

    2013-01-01

    Regulating physical size is an essential problem that biological organisms must solve from the subcellular to the organismal scales, but it is not well understood what physical principles and mechanisms organisms use to sense and regulate their size. Any biophysical size-regulation scheme operates in a noisy environment and must be robust to other cellular dynamics and fluctuations. This work develops theory of filament length regulation inspired by recent experiments on kinesin-8 motor proteins, which move with directional bias on microtubule filaments and alter microtubule dynamics. Purified kinesin-8 motors can depolymerize chemically-stabilized microtubules. In the length-dependent depolymerization model, the rate of depolymerization tends to increase with filament length, because long filaments accumulate more motors at their tips and therefore shorten more quickly. When balanced with a constant filament growth rate, this mechanism can lead to a fixed polymer length. However, the mechanism by which kines...

  13. The physics, biophysics and technology of photodynamic therapy

    International Nuclear Information System (INIS)

    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)

  14. 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)

  15. 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.

  16. Biophysics of magnetic orientation: strengthening the interface between theory and experimental design

    Science.gov (United States)

    Kirschvink, Joseph L.; Winklhofer, Michael; Walker, Michael M.

    2010-01-01

    The first demonstrations of magnetic effects on the behaviour of migratory birds and homing pigeons in laboratory and field experiments, respectively, provided evidence for the longstanding hypothesis that animals such as birds that migrate and home over long distances would benefit from possession of a magnetic sense. Subsequent identification of at least two plausible biophysical mechanisms for magnetoreception in animals, one based on biogenic magnetite and another on radical-pair biochemical reactions, led to major efforts over recent decades to test predictions of the two models, as well as efforts to understand the ultrastructure and function of the possible magnetoreceptor cells. Unfortunately, progress in understanding the magnetic sense has been challenged by: (i) the availability of a relatively small number of techniques for analysing behavioural responses to magnetic fields by animals; (ii) difficulty in achieving reproducible results using the techniques; and (iii) difficulty in development and implementation of new techniques that might bring greater experimental power. As a consequence, laboratory and field techniques used to study the magnetic sense today remain substantially unchanged, despite the huge developments in technology and instrumentation since the techniques were developed in the 1950s. New methods developed for behavioural study of the magnetic sense over the last 30 years include the use of laboratory conditioning techniques and tracking devices based on transmission of radio signals to and from satellites. Here we consider methodological developments in the study of the magnetic sense and present suggestions for increasing the reproducibility and ease of interpretation of experimental studies. We recommend that future experiments invest more effort in automating control of experiments and data capture, control of stimulation and full blinding of experiments in the rare cases where automation is impossible. We also propose new

  17. 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.

  18. Space Based Ornithology: On the Wings of Migration and Biophysics

    Science.gov (United States)

    Smith, James A.

    2005-01-01

    The study of bird migration on a global scale is one of the compelling and challenging problems of modern biology with major implications for human health and conservation biology. Migration and conservation efforts cross national boundaries and are subject to numerous international agreements and treaties. Space based technology offers new opportunities to shed understanding on the distribution and migration of organisms on the planet and their sensitivity to human disturbances and environmental changes. Migration is an incredibly diverse and complex behavior. A broad outline of space based research must address three fundamental questions: (1) where could birds be, i.e. what is their fundamental niche constrained by their biophysical limits? (2) where do we actually find birds, i.e. what is their realizable niche as modified by local or regional abiotic and biotic factors, and (3) how do they get there (and how do we know?), that is what are their migration patterns and associated mechanisms? Our working hypothesis is that individual organism biophysical models of energy and water balance, driven by satellite measurements of spatio-temporal gradients in climate and habitat, will help us to explain the variability in avian species richness and distribution. Dynamic state variable modeling provides one tool for studying bird migration across multiple scales and can be linked to mechanistic models describing the time and energy budget states of migrating birds. Such models yield an understanding of how a migratory flyway and its component habitats function as a whole and link stop-over ecology with biological conservation and management. Further these models provide an ecological forecasting tool for science and application users to address what are the possible consequences of loss of wetlands, flooding, drought or other natural disasters such as hurricanes on avian biodiversity and bird migration.

  19. The BIOMAT facility at FAIR: a new tool for ground-based research in space radiation biophysics

    Science.gov (United States)

    Durante, Marco

    The BIOMAT facility at FAIR: a new tool for ground-based research in space radiation biophysics M.Durante The FAIR accelerator complex at GSI (placeCityDarmstadt, country-regionGermany) will be a unique facility, where heavy ions with energies up to about 45 A GeV can be used for radiation biology experiments. The study of these very high charge and energy (HZE) particles is not only interesting for understanding the mechanisms of radiation action in living system, but also for radiation protection purposes. For space radiobiology, it is generally acknowledged that accelerator-based experiments are preferable to expensive and poorly reproducible flight tests, which are also presently unable to simulate the space radiation field beyond Earth's geomagnetic field. For these very reason, NASA has started the Space Radiation Health Program, building the 34 M NASA Space Radiation Laboratory (NSRL) at the Brookhaven National Laboratory (NY), and funding several research groups for studying biological effects of heavy ions with mass up to 56 (iron) and energy up to metricconverterProductID1 A1 A GeV. FAIR offers a number of unique opportunities in this frame. First, the beamtime available at NSRL is not sufficient to accommodate many non-US research groups, while the research needs are becoming urgent: uncertainty should be reduced to ±50% and effective countermeasures (physical and medical) developed by 2025 if a mission to Mars has to be performed within the first half of the XXI century. FAIR can be used to test a higher energy range (1- metricconverterProductID35 A35 A GeV), which has a low flux in space but is particularly penetrating and consequently impossible to shield. Finally, the raster scanning system used at GSI offers unique opportunities for biological experiments requiring precise exposures of parts of tissue or animal targets. The group of Biophysics at GSI has along experience in the field of space radiation protection, which naturally stems from heavy

  20. Empirical and biophysical estimations of human cochlea's psychophysical tuning curve sharpness

    Science.gov (United States)

    Chan, Wei Xuan; Kim, Namkeun; Yoon, Yong-Jin

    2016-01-01

    Despite the advances in cochlear research, the estimation of auditory nerve fiber frequency tuning of human cochlea is mostly based on psychophysical measurements. Although efforts had been made to estimate human frequency tuning sharpness from various physiological measurements which are less species dependent such as the compound action potential and stimulus-frequency otoacoustic emission delay, conclusions on the relative frequency tuning sharpness compared with that of other mammals vary. We simulated the biophysical human cochlea's tuning curve based on physiological measurements of human cochlea and compared the human frequency tuning sharpness with results from empirical methods as well as experimental data of other mammalian cochleae. The compound action potential are more accurate at frequencies below 3 kHz while the stimulus frequency-otoacoustic emission delay are more accurate at frequencies above 1 kHz regions. The results from mechanical cochlear models, with support from conclusions of the other two empirical methodologies, suggest that the human frequency tuning sharpness at frequencies below 1 kHz is similar to common laboratory mammals but is exceptionally sharp at higher frequencies.

  1. 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

  2. Biophysical Aspects of Radiation Quality. Second Panel Report

    International Nuclear Information System (INIS)

    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

  3. A biophysical understanding of the applications and implications of nanomaterials

    Science.gov (United States)

    Geitner, Nicholas K.

    The last few decades have seen an explosion in the study and application of nanomaterials that continues to grow at a dizzying pace. Despite exciting applications in nano-enabled electronics, materials, medicine, and environmental remediation, an understanding of the interactions of these materials with natural materials and systems and the resulting implications lags severely behind. The purpose of this dissertation is to illuminate these interactions as well as develop novel environmental applications from a biophysical perspective. Following an introduction and literature review in Chapter 1, Chapters 2-4 will explore the application of dendritic polymers as novel and biocompatible oil dispersants for more environmentally conscious response to catastrophic oil spills. Chapter 2 will serve as a proof-of-concept, exploring the interactions between two model dendritic polymers and two model oil hydrocarbons. Next, the biocompatibility of these nanoscale dispersing agents is addressed in Chapter 3, using a soil amoeba as the primary model organism with emphasis on the mechanisms of any observed toxicity. Finally, in an effort to minimize cationic charge-induced cytotoxicity, the cationic terminal functional groups of poly(amidoamine) (PAMAM) dendrimers are replaced with either anionic or neutral functional groups. The resulting changes in structure and oil-dispersing function of the original and modified dendrimers are then investigated. Chapter 5 details a study of the applications and implications of graphene derivatives. Specifically, the environmental persistence of graphene and graphene oxide are assessed by studying their interactions with natural amphiphiles using synergistic experiments and molecular dynamics simulations. The application of graphene oxide for the removal of polyaromatic hydrocarbons from aquatic systems is also investigated and compared to the efficacy of PAMAM dendrimers in the same application. Finally, Chapter 6 explores the interactions

  4. Diagnostic efficacy of biophysical tests and cerebral-umbilical index when assessing fetal oxygenation

    Directory of Open Access Journals (Sweden)

    Čančarević-Đajić Branka

    2013-01-01

    Full Text Available Introduction. Perinatal morbidity and mortality are the ultimate indicators of antenatal care today, whose responsible task is to assess the respiratory function of the placenta, fetal growth and placental maturation in order to provide conditions for the delivery of a living and viable newborn. The diagnostic procedures of antenatal care tested within this study were the biophysical tests of cardiotocography and the fetal biophysical profile, along with the colour doppler evaluation of the cerebral-umbilical ratio. The objective of this study was to determine the most effective diagnostic procedure when assessing fetal oxygenation. Materials and Methods. The prospective study included 119 pregnant women. They all underwent cardiotocography, biophysical profile and colour doppler evaluation of the cerebral-umbilical ratio. The babies’ umbilical artery blood pH was determined in the first minute upon birth, along with the Apgar score. Results. The results were processed statistically and the most effective diagnostic procedure for the evaluation of fetal oxygenation was selected, after which the rates of perinatal morbidity and mortality were calculated. The findings revealed that cardiotocography was the most sensitive antepartal predictor of fetal acidosis, while the fetal biophysical profile proved the most specific. The rates of perinatal morbidity and of perinatal mortality were 24.37% and 1.68%, respectively. Conclusion. The findings analysis revealed a high statistical significance of both biophysical tests and the cerebral-umbilical ratio evaluation as predictors of the fetal distress syndrome. The analysis of the cerebral-umbilical ratio and biophysical tests showed that the cerebral-umbilical ratio evaluation not only was more sensitive as a parameter compared to biophysical tests but it was also more specific than cardiotocography. Cardiotocography is the most sensitive antepartal predictor of fetal acidosis, followed by the cerebral

  5. Biophysical mechanism of transient retinal phototropism in rod photoreceptors

    Science.gov (United States)

    Zhao, Xiaohui; Thapa, Damber; Wang, Benquan; Gai, Shaoyan; Yao, Xincheng

    2016-03-01

    Oblique light stimulation evoked transient retinal phototropism (TRP) has been recently detected in frog and mouse retinas. High resolution microscopy of freshly isolated retinas indicated that the TRP is predominated by rod photoreceptors. Comparative confocal microscopy and optical coherence tomography (OCT) revealed that the TRP predominantly occurred from the photoreceptor outer segment (OS). However, biophysical mechanism of rod OS change is still unknown. In this study, frog retinal slices, which open a cross section of retinal photoreceptor and other functional layers, were used to test the effect of light stimulation on rod OS. Near infrared light microscopy was employed to monitor photoreceptor changes in retinal slices stimulated by a rectangular-shaped visible light flash. Rapid rod OS length change was observed after the stimulation delivery. The magnitude and direction of the rod OS change varied with the position of the rods within the stimulated area. In the center of stimulated region the length of the rod OS shrunk, while in the peripheral region the rod OS tip swung towards center region in the plane perpendicular to the incident stimulus light. Our experimental result and theoretical analysis suggest that the observed TRP may reflect unbalanced disc-shape change due to localized pigment bleaching. Further investigation is required to understand biochemical mechanism of the observed rod OS kinetics. Better study of the TRP may provide a noninvasive biomarker to enable early detection of age-related macular degeneration (AMD) and other diseases that are known to produce retinal photoreceptor dysfunctions.

  6. 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.

  7. Alteration of biophysical activity of pulmonary surfactant by aluminosilicate nanoparticles.

    Science.gov (United States)

    Kondej, Dorota; Sosnowski, Tomasz R

    2013-02-01

    The influence of five different types of aluminosilicate nanoparticles (NPs) on the dynamic surface activity of model pulmonary surfactant (PS) (Survanta) was studied experimentally using oscillating bubble tensiometry. Bentonite, halloysite and montmorillonite (MM) NPs, which are used as fillers of polymer composites, were characterized regarding the size distribution, morphology and surface area. Particle doses applied in the studies were estimated based on the inhalation rate and duration, taking into account the expected aerosol concentration and deposition efficiency after penetration of NPs into the alveolar region. The results indicate that aluminosilicate NPs at concentrations in the pulmonary liquid above 0.1 mg cm(-3) are capable of promoting alterations of the original dynamic biophysical activity of the PS. This effect is indicated by deviation of the minimum surface tension, stability index and the size of surface tension hysteresis. Such response is dependent on the type of NPs present in the system and is stronger when particle concentration increases. It is suggested that interactions between NPs and the PS must be related to the surfactant adsorption on the suspended particles, while in the case of surface-modified clay NPs the additional washout of surface-active components may be expected. It is speculated that observed changes in surface properties of the surfactant may be associated with undesired health effects following extensive inhalation of aluminosilicate NPs in the workplace. PMID:23363039

  8. The biophysical bases of will-less behaviours

    Directory of Open Access Journals (Sweden)

    Jose Luis Perez 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.

  9. 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.

  10. Identification of spatiotemporal patterns of biophysical droughts in Iran

    Science.gov (United States)

    Kamali, Bahareh; Abbaspour, Karim; Yang, Hong

    2015-04-01

    This study aims to identify historical patterns of meteorological, hydrological, and agricultural (inclusively biophysical) droughts in Iran over the last forty years. Standardized precipitation index (SPI), standardized runoff index (SRI), and soil moisture deficit index (SMDI) were used to represent the three types of droughts, respectively. Variables required for calculating the indices were obtained from a SWAT (Soil and Water Assessment Tool) model constructed for the country. The model was calibrated based on monthly runoff using the Sequential Uncertainty Fitting (SUFI-2) algorithm in SWAT-CUP. The indices were compared across temporal and spatial dimensions. Drought characteristics including number of events, start, end, duration and severity were derived to identify areas most prone to drought events. The results on provincial level show a variety of spatiotemporal patterns in different drought aspects over the country. The summary of analysis ranked drought events based on short-term severe droughts to multi-year duration events. Our analyses on three types of droughts provide a basis for further studies concerning drought impacts under future climate change and water resource management strategies in semi-arid areas.

  11. Biophysical principles predict fitness landscapes of drug resistance.

    Science.gov (United States)

    Rodrigues, João V; Bershtein, Shimon; Li, Anna; Lozovsky, Elena R; Hartl, Daniel L; Shakhnovich, Eugene I

    2016-03-15

    Fitness landscapes of drug resistance constitute powerful tools to elucidate mutational pathways of antibiotic escape. Here, we developed a predictive biophysics-based fitness landscape of trimethoprim (TMP) resistance for Escherichia coli dihydrofolate reductase (DHFR). We investigated the activity, binding, folding stability, and intracellular abundance for a complete set of combinatorial DHFR mutants made out of three key resistance mutations and extended this analysis to DHFR originated from Chlamydia muridarum and Listeria grayi We found that the acquisition of TMP resistance via decreased drug affinity is limited by a trade-off in catalytic efficiency. Protein stability is concurrently affected by the resistant mutants, which precludes a precise description of fitness from a single molecular trait. Application of the kinetic flux theory provided an accurate model to predict resistance phenotypes (IC50) quantitatively from a unique combination of the in vitro protein molecular properties. Further, we found that a controlled modulation of the GroEL/ES chaperonins and Lon protease levels affects the intracellular steady-state concentration of DHFR in a mutation-specific manner, whereas IC50 is changed proportionally, as indeed predicted by the model. This unveils a molecular rationale for the pleiotropic role of the protein quality control machinery on the evolution of antibiotic resistance, which, as we illustrate here, may drastically confound the evolutionary outcome. These results provide a comprehensive quantitative genotype-phenotype map for the essential enzyme that serves as an important target of antibiotic and anticancer therapies. PMID:26929328

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

    International Nuclear Information System (INIS)

    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. A Biophysical Neural Model To Describe Spatial Visual Attention

    Science.gov (United States)

    Hugues, Etienne; José, Jorge V.

    2008-02-01

    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.

  14. Biophysical characterization of gold nanoparticles-loaded liposomes.

    Science.gov (United States)

    Mady, Mohsen Mahmoud; Fathy, Mohamed Mahmoud; Youssef, Tareq; Khalil, Wafaa Mohamed

    2012-10-01

    Gold nanoparticles were prepared and loaded into the bilayer of dipalmitoylphosphatidylcholine (DPPC) liposomes, named as gold-loaded liposomes. Biophysical characterization of gold-loaded liposomes was studied by transmission electron microscopy (TEM) and Fourier transform infrared (FTIR) spectroscopy as well as turbidity and rheological measurements. FTIR measurements showed that gold nanoparticles made significant changes in the frequency of the CH(2) stretching bands, revealing that gold nanoparticles increased the number of gauche conformers and create a conformational change within the acyl chains of phospholipids. The transmission electron micrographs (TEM) revealed that gold nanoparticles were loaded in the liposomal bilayer. The zeta potential of DPPC liposomes had a more negative value after incorporating of Au NPs into liposomal membranes. Turbidity studies revealed that the loading of gold nanoparticles into DPPC liposomes results in shifting the temperature of the main phase transition to a lower value. The membrane fluidity of DPPC bilayer was increased by loading the gold nanoparticles as shown from rheological measurements. Knowledge gained in this study may open the door to pursuing liposomes as a viable strategy for Au NPs delivery in many diagnostic and therapeutic applications. PMID:22027546

  15. 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.

  16. 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...

  17. Evolutionary and biophysical relationships among the papillomavirus E2 proteins.

    Science.gov (United States)

    Blakaj, Dukagjin M; Fernandez-Fuentes, Narcis; Chen, Zigui; Hegde, Rashmi; Fiser, Andras; Burk, Robert D; Brenowitz, Michael

    2009-01-01

    Infection by human papillomavirus (HPV) may result in clinical conditions ranging from benign warts to invasive cancer. The HPV E2 protein represses oncoprotein transcription and is required for viral replication. HPV E2 binds to palindromic DNA sequences of highly conserved four base pair sequences flanking an identical length variable 'spacer'. E2 proteins directly contact the conserved but not the spacer DNA. Variation in naturally occurring spacer sequences results in differential protein affinity that is dependent on their sensitivity to the spacer DNA's unique conformational and/or dynamic properties. This article explores the biophysical character of this core viral protein with the goal of identifying characteristics that associated with risk of virally caused malignancy. The amino acid sequence, 3d structure and electrostatic features of the E2 protein DNA binding domain are highly conserved; specific interactions with DNA binding sites have also been conserved. In contrast, the E2 protein's transactivation domain does not have extensive surfaces of highly conserved residues. Rather, regions of high conservation are localized to small surface patches. Implications to cancer biology are discussed. PMID:19273107

  18. Biophysical interactions between plant and soil: theory and practice

    Science.gov (United States)

    van der Ploeg, Martine

    2016-04-01

    Vegetation plays an essential role in the hydrological cycle, as it regulates the water flux to the atmosphere through evapotranspiration, while it is dependent on adequate water supply. Vegetation shapes the land surface by changing infiltration characteristics as a result of root growth, and controls soil moisture storage, which in turn affect runoff characteristics and groundwater recharge. Vegetation and the underlying geology are in constant interaction, wherein water plays a key role. The resilience of the coupled vegetation-soil system critically depends on its sensitivity to environmental changes. Models are a useful tool to explore interaction and feedbacks between vegetation, soil and landscape. Plants respond biochemically to their environment, while the models used for hydrology are often based on physical interactions. Gene-expression and genotype adaptation may complicate our modelling efforts in for example climate change impacts. Combination of new techniques to assess soil and plant properties facilitates assessment of biophysical interactions. This poster will review these techniques and compare the obtained insights of soil-plant relationships with the current modeling approaches.

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

    International Nuclear Information System (INIS)

    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

  20. Unofficial Road Building in the Amazon: Socioeconomic and Biophysical Explanations

    Science.gov (United States)

    Perz, Stephen G.; Caldas, Marcellus M.; Arima, Eugenio; Walker, Robert J.

    2007-01-01

    Roads have manifold social and environmental impacts, including regional development, social conflicts and habitat fragmentation. 'Road ecology' has emerged as an approach to evaluate the various ecological and hydrological impacts of roads. This article aims to complement road ecology by examining the socio-spatial processes of road building itself. Focusing on the Brazilian Amazon, a heavily-studied context due to forest fragmentation by roads, the authors consider non-state social actors who build 'unofficial roads' for the purpose of gaining access to natural resources to support livelihoods and community development. They examine four case studies of roads with distinct histories in order to explain the socio-spatial processes behind road building in terms of profit maximization, land tenure claims, co-operative and conflictive political ecologies, and constraints as well as opportunities afforded by the biophysical environment. The study cases illustrate the need for a multi-pronged theoretical approach to understanding road building, and call for more attention to the role of non-state actors in unofficial road construction.

  1. Mesenchymal morphogenesis of embryonic stem cells dynamically modulates the biophysical microtissue niche

    Science.gov (United States)

    Kinney, Melissa A.; Saeed, Rabbia; McDevitt, Todd C.

    2014-01-01

    Stem cell fate and function are dynamically modulated by the interdependent relationships between biochemical and biophysical signals constituting the local 3D microenvironment. While approaches to recapitulate the stem cell niche have been explored for directing stem cell differentiation, a quantitative relationship between embryonic stem cell (ESC) morphogenesis and intrinsic biophysical cues within three-dimensional microtissues has not been established. In this study, we demonstrate that mesenchymal embryonic microtissues induced by BMP4 exhibited increased stiffness and viscosity accompanying differentiation, with cytoskeletal tension significantly contributing to multicellular stiffness. Perturbation of the cytoskeleton during ESC differentiation led to modulation of the biomechanical and gene expression profiles, with the resulting cell phenotype and biophysical properties being highly correlated by multivariate analyses. Together, this study elucidates the dynamics of biophysical and biochemical signatures within embryonic microenvironments, with broad implications for monitoring tissue dynamics, modeling pathophysiological and embryonic morphogenesis and directing stem cell patterning and differentiation. PMID:24598818

  2. 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: 2.219, year: 2014

  3. 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

  4. Comparison of biophysical and satellite predictors for wheat yield forecasting in Ukraine

    OpenAIRE

    Kolotii, A.; Kussul, N.; A. Shelestov; Skakun, S.; Yailymov, B.; R. Basarab; M. Lavreniuk; T. Oliinyk; Ostapenko, V.

    2015-01-01

    Winter wheat crop yield forecasting at national, regional and local scales is an extremely important task. This paper aims at assessing the efficiency (in terms of prediction error minimization) of satellite and biophysical model based predictors assimilation into winter wheat crop yield forecasting models at different scales (region, county and field) for one of the regions in central part of Ukraine. Vegetation index NDVI, as well as different biophysical parameters (LAI and fAPAR)...

  5. Diagnostic efficacy of biophysical tests and cerebral-umbilical index when assessing fetal oxygenation

    OpenAIRE

    Čančarević-Đajić Branka; Vilendečić Rade

    2013-01-01

    Introduction. Perinatal morbidity and mortality are the ultimate indicators of antenatal care today, whose responsible task is to assess the respiratory function of the placenta, fetal growth and placental maturation in order to provide conditions for the delivery of a living and viable newborn. The diagnostic procedures of antenatal care tested within this study were the biophysical tests of cardiotocography and the fetal biophysical profile, along with the colour doppler evaluation of...

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

    International Nuclear Information System (INIS)

    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)

  7. The problem of the competitiveness of nuclear energy : a biophysical explanation

    OpenAIRE

    Diaz Maurin, François

    2011-01-01

    In this study I try to explain the systemic problem of the low economic competitiveness of nuclear energy for the production of electricity by carrying out a biophysical analysis of its production process. Given the fact that neither econometric approaches nor onedimensional methods of energy analyses are effective, I introduce the concept of biophysical explanation as a quantitative analysis capable of handling the inherent ambiguity associated with the concept of energy. In particular, the...

  8. Mesenchymal morphogenesis of embryonic stem cells dynamically modulates the biophysical microtissue niche

    OpenAIRE

    Kinney, Melissa A.; Rabbia Saeed; McDevitt, Todd C.

    2014-01-01

    Stem cell fate and function are dynamically modulated by the interdependent relationships between biochemical and biophysical signals constituting the local 3D microenvironment. While approaches to recapitulate the stem cell niche have been explored for directing stem cell differentiation, a quantitative relationship between embryonic stem cell (ESC) morphogenesis and intrinsic biophysical cues within three-dimensional microtissues has not been established. In this study, we demonstrate that ...

  9. Extraction of Mangrove Biophysical Parameters Using Airborne LiDAR

    OpenAIRE

    Poonsak Miphokasap; Phisan Santitamnont; Kiyoshi Honda; Wasinee Wannasiri; Masahiko Nagai

    2013-01-01

    Tree parameter determinations using airborne Light Detection and Ranging (LiDAR) have been conducted in many forest types, including coniferous, boreal, and deciduous. However, there are only a few scientific articles discussing the application of LiDAR to mangrove biophysical parameter extraction at an individual tree level. The main objective of this study was to investigate the potential of using LiDAR data to estimate the biophysical parameters of mangrove trees at an individual tree scal...

  10. Biophysical characterization of G-protein coupled receptor-peptide ligand binding

    OpenAIRE

    Langelaan, David N.; Ngweniform, Pascaline; Rainey, Jan K.

    2011-01-01

    G-protein coupled receptors (GPCRs) are ubiquitous membrane proteins allowing intracellular response to extracellular factors that range from photons of light to small molecules to proteins. Despite extensive exploitation of GRCRs as therapeutic targets, biophysical characterization of GPCR-ligand interactions remains challenging. In this minireview, we focus on techniques which have been successfully employed for structural and biophysical characterization of peptide ligands binding to their...

  11. Dlk1 Promotes a Fast Motor Neuron Biophysical Signature Required for Peak Force Execution

    OpenAIRE

    Muller, D.; Cherukuri, P; Henningfeld, K.; Poh, C. H.; Wittler, L; Grote, P.; Schluter, O.; Schmidt, J.; Laborda, J.; Bauer, S R; Brownstone, R M; Marquardt, T

    2014-01-01

    Motor neurons, which relay neural commands to drive skeletal muscle movements, encompass types ranging from "slow" to "fast," whose biophysical properties govern the timing, gradation, and amplitude of muscle force. Here we identify the noncanonical Notch ligand Delta-like homolog 1 (Dlk1) as a determinant of motor neuron functional diversification. Dlk1, expressed by ~30% of motor neurons, is necessary and sufficient to promote a fast biophysical signature in the mouse and chick. Dlk1 suppre...

  12. 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. PMID:25393245

  13. 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.

  14. Electron paramagnetic resonance biophysical radiation dosimetry with tooth enamel

    International Nuclear Information System (INIS)

    This thesis deals with the 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 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 100 mGy ranges can be easily reconstructed in teeth that 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 the 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 neutrons

  15. Structural features underlying raloxifene's biophysical interaction with bone matrix.

    Science.gov (United States)

    Bivi, Nicoletta; Hu, Haitao; Chavali, Balagopalakrishna; Chalmers, Michael J; Reutter, Christopher T; Durst, Gregory L; Riley, Anna; Sato, Masahiko; Allen, Matthew R; Burr, David D; Dodge, Jeffrey A

    2016-02-15

    Raloxifene, a selective estrogen receptor modulator (SERM), reduces fracture risk at least in part by improving the mechanical properties of bone in a cell- and estrogen receptor-independent manner. In this study, we determined that raloxifene directly interacts with the bone tissue. Through the use of multiple and complementary biophysical techniques including nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy (FTIR), we show that raloxifene interacts specifically with the organic component or the organic/mineral composite, and not with hydroxyapatite. Structure-activity studies reveal that the basic side chain of raloxifene is an instrumental determinant in the interaction with bone. Thus, truncation of portions of the side chain reduces bone binding and also diminishes the increase in mechanical properties. Our results support a model wherein the piperidine interacts with bone matrix through electrostatic interactions with the piperidine nitrogen and through hydrophobic interactions (van der Waals) with the aliphatic groups in the side chain and the benzothiophene core. Furthermore, in silico prediction of the potential binding sites on the surface of collagen revealed the presence of a groove with sufficient space to accommodate raloxifene analogs. The hydroxyl groups on the benzothiophene nucleus, which are necessary for binding of SERMs to the estrogen receptor, are not required for binding to the bone surface, but mediate a more robust binding of the compound to the bone powder. In conclusion, we report herein a novel property of raloxifene analogs that allows them to interact with the bone tissue through potential contacts with the organic matrix and in particular collagen. PMID:26795112

  16. Analytical Laboratories

    Data.gov (United States)

    Federal Laboratory Consortium — NETL’s analytical laboratories in Pittsburgh, PA, and Albany, OR, give researchers access to the equipment they need to thoroughly study the properties of materials...

  17. National laboratories

    International Nuclear Information System (INIS)

    The foundation of a 'National Laboratory' which would support a Research center in synchrotron radiation applications is proposed. The essential features of such a laboratory differing of others centers in Brazil are presented. (L.C.)

  18. Laboratory Tests

    Science.gov (United States)

    Laboratory tests check a sample of your blood, urine, or body tissues. A technician or your doctor ... compare your results to results from previous tests. Laboratory tests are often part of a routine checkup ...

  19. Computational Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory contains a number of commercial off-the-shelf and in-house software packages allowing for both statistical analysis as well as mathematical modeling...

  20. Biophysics and bioinformatics of transcription regulation in bacteria and bacteriophages

    Science.gov (United States)

    Djordjevic, Marko

    2005-11-01

    Due to rapid accumulation of biological data, bioinformatics has become a very important branch of biological research. In this thesis, we develop novel bioinformatic approaches and aid design of biological experiments by using ideas and methods from statistical physics. Identification of transcription factor binding sites within the regulatory segments of genomic DNA is an important step towards understanding of the regulatory circuits that control expression of genes. We propose a novel, biophysics based algorithm, for the supervised detection of transcription factor (TF) binding sites. The method classifies potential binding sites by explicitly estimating the sequence-specific binding energy and the chemical potential of a given TF. In contrast with the widely used information theory based weight matrix method, our approach correctly incorporates saturation in the transcription factor/DNA binding probability. This results in a significant reduction in the number of expected false positives, and in the explicit appearance---and determination---of a binding threshold. The new method was used to identify likely genomic binding sites for the Escherichia coli TFs, and to examine the relationship between TF binding specificity and degree of pleiotropy (number of regulatory targets). We next address how parameters of protein-DNA interactions can be obtained from data on protein binding to random oligos under controlled conditions (SELEX experiment data). We show that 'robust' generation of an appropriate data set is achieved by a suitable modification of the standard SELEX procedure, and propose a novel bioinformatic algorithm for analysis of such data. Finally, we use quantitative data analysis, bioinformatic methods and kinetic modeling to analyze gene expression strategies of bacterial viruses. We study bacteriophage Xp10 that infects rice pathogen Xanthomonas oryzae. Xp10 is an unusual bacteriophage, which has morphology and genome organization that most closely

  1. Energy return on investment: Theory and application to biophysical economics

    Science.gov (United States)

    Murphy, David J.

    This dissertation is comprised of an introduction and five manuscripts split into two main sections: theory and application. Manuscripts one and four have been published, manuscript three has been accepted for publication, and manuscripts two and five are currently in review for publication. The theory sections contains the first two manuscripts. The first manuscript is a review of the literature on Energy Return on Investment (EROI) analysis. I cover five areas in this manuscript, including: (1) EROI and corn ethanol, (2) EROI for most major fuels, (3) alternative EROI applications, (4) EROI and the economy, and (5) the minimum EROI for society. The second manuscript provides a methodological framework for performing EROI analysis. I cover the following areas in this manuscript: (1) boundaries of analysis, (2) energy quality corrections, (3) energy intensity values, and lastly (4) alternative EROI statistics. The applications section contains manuscripts three through five. The third manuscript provides a biophysical model of economic growth indicating that the feedback mechanisms between oil supply and oil price have created a growth paradox: maintaining business as usual economic growth will require the production of new sources of oil, yet the only sources of oil remaining require high oil prices, thus hampering economic growth. The fourth manuscript is a study on the geographic variability of corn ethanol production. The main conclusions of this study were: (1) the statistical error associated with calculating the EROI of corn ethanol was enough to cast doubt as to whether corn ethanol yields net energy, and (2) failure to account for the geographic variation in corn yields and fertilizer inputs artificially inflated previous estimates of the EROI or corn ethanol. In the fifth manuscript I measure the impact of the Urban Heat Island within the metropolitan area of San Juan, Puerto Rico, on the electricity demand within the city. I calculated that the UHI

  2. Comparison of biophysical factors influencing on emphysema quantification with low-dose CT

    Science.gov (United States)

    Heo, Chang Yong; Kim, Jong Hyo

    2014-03-01

    Emphysema Index(EI) measurements in MDCT is known to be influenced by various biophysical factors such as total lung volume, and body size. We investigated the association of the four biophysical factors with emphysema index in low-dose MDCT. In particular, we attempted to identify a potentially stronger biophysical factor than total lung volume. A total of 400 low-dose MDCT volumes taken at 120kVp, 40mAs, 1mm thickness, and B30f reconstruction kernel were used. The lungs, airways, and pulmonary vessels were automatically segmented, and two Emphysema Indices, relative area below -950HU(RA950) and 15th percentile(Perc15), were extracted from the segmented lungs. The biophysical factors such as total lung volume(TLV), mode of lung attenuation(ModLA), effective body diameter(EBD), and the water equivalent body diameter(WBD) were estimated from the segmented lung and body area. The association of biophysical factors with emphysema indices were evaluated by correlation coefficients. The mean emphysema indices were 8.3±5.5(%) in RA950, and -930±18(HU) in Perc15. The estimates of biophysical factors were 4.7±1.0(L) in TLV, -901±21(HU) in ModLA, 26.9±2.2(cm) in EBD, and 25.9±2.6(cm) in WBD. The correlation coefficients of biophysical factors with RA950 were 0.73 in TLV, 0.94 in ModLA, 0.31 in EBD, and 0.18 WBD, the ones with Perc15 were 0.74 in TLV, 0.98 in ModLA, 0.29 in EBD, and 0.15 WBD. Study results revealed that two biophysical factors, TLV and ModLA, mostly affects the emphysema indices. In particular, the ModLA exhibited strongest correlation of 0.98 with Perc15, which indicating the ModLA is the most significant confounding biophysical factor in emphysema indices measurement.

  3. Agriculture sector resource and environmental policy analysis: an economic and biophysical approach.

    Science.gov (United States)

    House, R; McDowell, H; Peters, M; Heimlich, R

    1999-01-01

    Agricultural pollution of the environment is jointly determined by economic decisions driving land use, production practices, and stochastic biophysical processes associated with agricultural production, land and climate characteristics. It follows that environmental and economic statistics, traditionally collected independently of each other, offer little insight into non-point pollutant loadings. We argue that effective policy development would be facilitated by integrating environmental and economic data gathering, combined with simulation modelling linking economic and biophysical components. Integrated data collection links economics, land use, production methods and environmental loadings. An integrated economic/biophysical modelling framework facilitates policy analysis because monetary incentives to reduce pollution can be evaluated in the context of market costs and returns that influence land use and production activity. This allows prediction of environmental and economic outcomes from alternative policies to solve environmental problems. We highlight steps taken to merge economic and biophysical modelling for policy analysis within the Economic Research Service of the United States Department of Agriculture. An example analysis of a policy to reduce agricultural nitrogen pollution is presented, with the economic and environmental results illustrating the value of linked economic and biophysical analysis. PMID:10231835

  4. 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.

  5. 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.

  6. Unexplored biophysical problem of manned flight to Mars

    Science.gov (United States)

    Avakyan, Sergey; Voronin, Nikolai; Kovalenok, Vladimir; Trchounian, Armen

    The presentation discusses so far unexplored biophysical problem of manned flight to the Mars, scheduled for the next decade. In long-term manned space flights on the orbital stations "Salyut-6" Soviet cosmonaut crews under the command of one of the co-authors (cosmonaut V.V. Kovalenok) had repeatedly observed the effect of certain geophysical conditions on the psychological state of each crew. These effects were coinciding with the increased intensity of global illumination in the upper ionosphere space on flight altitudes (300-360 km). It is important that, during all these periods, the geomagnetic pulsation's were completely absent. Previously a new but very important for long interplanetary expeditions problem of psychophysical state of the crew in the absence of alternating electromagnetic fields and radiation, including the ionosphere one, was first raised for evolutionarily adapted humanity. However, up to date, this subject, particularly during the long simulation experiments such as "Mars 500", which eliminates much of their value and contribution to the Mars mission, has almost no attention. Indeed, the obtained results have clearly shown that the cosmonaut crews in orbital flight, even deep one within geomagnetic sphere, might experience severe psychological discomfort, the nature of which is fully defined. This is the appearance of such rather unusual geophysical periods of different durations (from minutes to days) those are in the form of an almost complete lack of geomagnetic pulsations on the Earth. The aim is to confirm the need of considering possible pathological effects of the complete lack of rhythm forming, inherent for terrestrial environment geomagnetic pulsation's on psychological and physical state of the cosmonaut crew. This is important for the preparation and conducting the manned flights beyond the Earth's magnetosphere, particularly to the Mars. The influence of the presence of different types of geomagnetic pulsation's recorded by

  7. 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

  8. Introducing interdisciplinary science to second year undergraduates in a Current Topics in Biophysics course

    CERN Document Server

    Jerzak, Stanislaw

    2015-01-01

    We offer second year students the opportunity to explore Current Topics in Biophysics in a course co-taught by a physicist and a biologist. The interdisciplinary course allows university students to engage in analytical thinking that integrates physics and biology. The students are either biophysics majors (50%) or from a diversity of science majors (about 30% life sciences). All will have taken first year courses in biology, physics and mathematics. The course is divided into: 1) The application of physical approaches to biological problems using case studies (how high can a tree grow? and biological pumps are two examples); 2) An introduction to physics concepts for which potential applications are explored (biophotonics and its application in fluorescence microscopy and photodynamic therapy is one example); and 3) Presentations from industry and university researchers who describe careers, research and clinical applications of biophysics. Over the six years the course has been offered, students have achiev...

  9. 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.

  10. 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...

  11. Laboratory Building.

    Energy Technology Data Exchange (ETDEWEB)

    Herrera, Joshua M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-03-01

    This report is an analysis of the means of egress and life safety requirements for the laboratory building. The building is located at Sandia National Laboratories (SNL) in Albuquerque, NM. The report includes a prescriptive-based analysis as well as a performance-based analysis. Following the analysis are appendices which contain maps of the laboratory building used throughout the analysis. The top of all the maps is assumed to be north.

  12. Visualization Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Evaluates and improves the operational effectiveness of existing and emerging electronic warfare systems. By analyzing and visualizing simulation results...

  13. Dynamics Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Dynamics Lab replicates vibration environments for every Navy platform. Testing performed includes: Flight Clearance, Component Improvement, Qualification, Life...

  14. Chemistry Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — Purpose: To conduct fundamental studies of highway materials aimed at understanding both failure mechanisms and superior performance. New standard test methods are...

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

    International Nuclear Information System (INIS)

    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

  16. Synthesis and biophysical properties of (l)-aTNA based G-quadruplexes

    DEFF Research Database (Denmark)

    Gothelf, Kurt Vesterager; Kumar, Vipin

    2016-01-01

    Novel G-quadruplex structures are constructed by acyclic (l)-threninol nucleic acid and their synthesis and biophysical properties are described. Pyrene excimer fluorescence and circular dichroism (CD) data revealed that four strands of aTNA are oriented in antiparallel direction.......Novel G-quadruplex structures are constructed by acyclic (l)-threninol nucleic acid and their synthesis and biophysical properties are described. Pyrene excimer fluorescence and circular dichroism (CD) data revealed that four strands of aTNA are oriented in antiparallel direction....

  17. Measurement of bio-physical signals for posture movement on the transformation system

    OpenAIRE

    Kim, Jeong-lae; Kim, Kyu-dong

    2014-01-01

    A signal transformation system of posture movement for the stable state was designed in order to measure the bio-physical signal. To estimate the subject in a stable state on the basis of the bio-physical signal in the posture movement, the conditions of vision, vestibular, somatosensory apparatus and the central nervous system (CNS) were detected. Based on the vision condition, there was a greater average variation (Vi-αAVG-MAX and Vi-αAVG-MIN) in position with eyes closed and eyes opened (P...

  18. Biophysical characterization of the recombinant fusion two-domain proteins composed of PDZ3, SH3 and small artificial proteins

    Czech Academy of Sciences Publication Activity Database

    Boušová, Kristýna; Bednárová, Lucie; Hofbauerová, K.; Obšilová, Veronika; Vondrášek, Jiří

    Praha: Ústav organické chemie a biochemie AV ČR, 2016. s. 61. ISBN 978-80-86241-55-5. [Prague Protein Spring Meeting 2016: Proteins and their Design /4./. 05.05.2016-08.05.2016, Praha] Institutional support: RVO:61388963 ; RVO:67985823 Keywords : two-domain proteins * biophysical characterization Subject RIV: BO - Biophysics

  19. Learning from Our Evolving Understanding of Biophysical Interactions to Improve River Restoration Practice.

    Science.gov (United States)

    Sear, D. A.

    2014-12-01

    Restoration of riverine habitats has largely proceeded on the assumption that by improving physical habitat, and more latterly processes, biophysical interactions will reassemble to a state similar to that prior to the disturbance event. Whilst there had been little monitoring to support this view, there is increasing evidence that the complexity of ecological systems demands a greater understanding of these biophysical interactions before we can state that a restoration has succeeded. In this paper I will draw on two examples to demonstrate the importance of understanding the spatial as well as the temporal scale of biophysical interactions. In the first example, field and modelling was used to demonstrate how different location of large wood and forest restoration can result in different hydrological outcomes. Similarly, as the forest matures it is possible to see change in restoration outcomes, extending beyond the lifetime of the project. In the second example I demonstrate how climate and land use drive the biophysical interactions within spawning salmonid habitats, research that questions accepted models used in the restoration of salmonid spawning habitat. Finally the paper reflects on the problems of restoring complex ecosystems; and points towards the need for improvements in how we research and communicate with stakeholders who ultimately live by the streams we restore.

  20. Biophysical properties of membrane lipids of anammox bacteria : I. Ladderane phospholipids form highly organized fluid membranes

    NARCIS (Netherlands)

    Boumann, Henry A.; Longo, Marjorie L.; Stroeve, Pieter; Poolman, Bert; Hopmans, Ellen C.; Stuart, Marc C. A.; Damste, Jaap S. Sinninghe; Schouten, Stefan

    2009-01-01

    Anammox bacteria that are capable of anaerobically oxidizing ammonium (anammox) with nitrite to nitrogen gas produce unique membrane phospholipids that comprise hydrocarbon chains with three or five linearly condensed cyclobutane rings. To gain insight into the biophysical properties of these 'ladde

  1. Absorption and Scattering Coefficients: A Biophysical-Chemistry Experiment Using Reflectance Spectroscopy

    Science.gov (United States)

    Cordon, Gabriela B.; Lagorio, M. Gabriela

    2007-01-01

    A biophysical-chemistry experiment, based on the reflectance spectroscopy for calculating the absorption and scattering coefficients of leaves is described. The results show that different plants species exhibit different values for both the coefficients because of their different pigment composition.

  2. Biophysical characterization of the proton-coupled oligopeptide transporter YjdL

    DEFF Research Database (Denmark)

    Jensen, Johanne Mørch; Simonsen, Fie C.; Mastali, Amir; Hald, Helle; Lillebro, Ida; Diness, Frederik; Olsen, Lars; Mirza, Osman Asghar

    2012-01-01

    significantly different from prototypical POTs such as the human hPepT1. Nonetheless YjdL contains several highly conserved POT residues, which include Glu388 that is located in the putative substrate binding cavity. Here we present biophysical characterization of WT-YjdL and Glu388Gln. Isothermal titration...

  3. Summaries of fiscal year 1994 projects in medical applications and biophysical research

    International Nuclear Information System (INIS)

    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

  4. X-ray structure and biophysical properties of rabbit fibroblast growth factor 1

    International Nuclear Information System (INIS)

    This report shows that the tertiary structure of rabbit FGF-1 is essentially identical to that of human FGF-1, with four surface mutations (140-amino-acid form). Biophysical data indicate that rabbit FGF-1 is less thermostable than human FGF-1 and has a slower association rate with the FGF-1 receptor. Mitogenic assays indicate that rabbit FGF-1 is tenfold less potent than human FGF-1; however, rabbit FGF-1 exhibits greater heparin stimulation such that its mitogenic activity in the presence of heparin is essentially indistinguishable from that of human FGF-1. 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

  5. Lessons from the biophysics of interfaces: Lung surfactant and tear fluid

    DEFF Research Database (Denmark)

    Rantamaki, A.; Telenius, J.; Koivuniemi, A.;

    2011-01-01

    The purpose of this review is to provide insight into the biophysical properties and functions of tear fluid and lung surfactant - two similar fluids covering the epithelium of two distinctive organs. Both fluids form a layer-like structure that essentially comprise of an aqueous layer next to the...

  6. Coupling Biophysical and Socioeconomic Models for Coral Reef Systems in Quintana Roo, Mexican Caribbean

    Directory of Open Access Journals (Sweden)

    Elizabeth A. Fulton

    2011-09-01

    Full Text Available Transdisciplinary approaches that consider both socioeconomic and biophysical processes are central to understanding and managing rapid change in coral reef systems worldwide. To date, there have been limited attempts to couple the two sets of processes in dynamic models for coral reefs, and these attempts are confined to reef systems in developed countries. We present an approach to coupling existing biophysical and socioeconomic models for coral reef systems in the Mexican state of Quintana Roo. The biophysical model is multiscale, using dynamic equations to capture local-scale ecological processes on individual reefs, with reefs connected at regional scales by the ocean transport of larval propagules. The agent-based socioeconomic model simulates changes in tourism, fisheries, and urbanization in the Quintana Roo region. Despite differences in the formulation and currencies of the two models, we were able to successfully modify and integrate them to synchronize and define information flows and feedbacks between them. A preliminary evaluation of the coupled model system indicates that the model gives reasonable predictions for fisheries and ecological variables and can be used to examine scenarios for future social–ecological change in Quintana Roo. We provide recommendations for where efforts might usefully be focused in future attempts to integrate models of biophysical and socioeconomic processes, based on the limitations of our coupled system.

  7. Laboratory Tests

    Science.gov (United States)

    ... Medical Devices Radiation-Emitting Products Vaccines, Blood & Biologics Animal & ... or conditions. What are lab tests? Laboratory tests are medical procedures that involve testing samples of blood, urine, or other tissues or ...

  8. 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.

    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.

  9. An ethnographic study: Becoming a physics expert in a biophysics research group

    Science.gov (United States)

    Rodriguez, Idaykis

    Expertise in physics has been traditionally studied in cognitive science, where physics expertise is understood through the difference between novice and expert problem solving skills. The cognitive perspective of physics experts only create a partial model of physics expertise and does not take into account the development of physics experts in the natural context of research. This dissertation takes a social and cultural perspective of learning through apprenticeship to model the development of physics expertise of physics graduate students in a research group. I use a qualitative methodological approach of an ethnographic case study to observe and video record the common practices of graduate students in their biophysics weekly research group meetings. I recorded notes on observations and conduct interviews with all participants of the biophysics research group for a period of eight months. I apply the theoretical framework of Communities of Practice to distinguish the cultural norms of the group that cultivate physics expert practices. Results indicate that physics expertise is specific to a topic or subfield and it is established through effectively publishing research in the larger biophysics research community. The participant biophysics research group follows a learning trajectory for its students to contribute to research and learn to communicate their research in the larger biophysics community. In this learning trajectory students develop expert member competencies to learn to communicate their research and to learn the standards and trends of research in the larger research community. Findings from this dissertation expand the model of physics expertise beyond the cognitive realm and add the social and cultural nature of physics expertise development. This research also addresses ways to increase physics graduate student success towards their PhD. and decrease the 48% attrition rate of physics graduate students. Cultivating effective research

  10. 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.

  11. Hydrogen-rich gas production via fast pyrolysis of biophysical dried sludge: Effect of particle size and moisture content on product yields and syngas composition.

    Science.gov (United States)

    Han, Rong; Liu, Jinwen; Zhao, Chenxi; Li, Yuliang; Chen, Aixia

    2016-06-01

    After biophysical drying, a novel biophysical dried sludge particle was obtained. This work aims to investigate the function and effects of particle sizes and moisture contents on the fast pyrolysis of biophysical dried sludge particles. The results showed that large particles (>4 mm) favoured the oil generation with a maximum value of 19.0%, and small particles (pyrolysis. PMID:27118735

  12. Biophysical and medical safety basis of laser emission

    Science.gov (United States)

    Paltsev, Yu.; Levina, A.

    1996-01-01

    Laser equipment may inflict serious losses to human health if safety norms established by relevant standards and other documentation are not properly observed. It is explained by physical properties of laser emission (LE) which differs from general light sources by quantitative behavior of such parameters as the degrees of coherence, monochromaticity, brightness, polarization. Thus, biological effects due to laser emission, as a rule, are more expressed comparing with other types of emission from other spontaneous light sources. LE effects biological tissues through the density of energy flow and impulse duration. It is common knowledge nowadays that LE biological action is assessed by two criteria: physical parameters and absorptive properties of tissues exposed to rays. LE causes the greatest danger to the eyes due to their specific structure. The next target organ vulnerable to LE is skin. Pathological changes of skin depend on the LE power, time of exposure, wave length, and the extent of skin pigmentation. Along with different kinds of damage directly in the tissues exposed to rays, LE may cause changes in organs and body systems subject to indirect exposure. It is important that these changes may develop due to low intensity levels of LE that do not cause local damage. National and international standards on LE safety are based on maximum allowable levels (MAL) of exposure. It has been generally accepted that the main MAL criterion is LE threshold minimal exposure which causes damage to retina, eyes, and skin. As distinct from foreign safety standards, hygienic norms and regulations are in force in the Russian Federation where additional co-efficients along with standard generally accepted MAL values have been introduced for the persons who are subject to occupational regular exposure to lasers. This approach has been chosen after the results of follow-up and health studies of these occupational contingents have been analyzed, and experiments on laboratory

  13. A selective view of stochastic inference and modeling problems in nanoscale biophysics

    Institute of Scientific and Technical Information of China (English)

    KOU S. C.

    2009-01-01

    Advances in nanotechnology enable scientists for the first time to study biological processes on a nanoscale molecule-by-molecule basis. They also raise challenges and opportunities for statisticians and applied probabilists. To exemplify the stochastic inference and modeling problems in the field, this paper discusses a few selected cases, ranging from likelihood inference, Bayesian data augmentation, and semi- and non-parametric inference of nanometric biochemical systems to the utilization of stochastic integro-differential equations and stochastic networks to model single-molecule biophysical processes. We discuss the statistical and probabilistic issues as well as the biophysical motivation and physical meaning behind the problems, emphasizing the analysis and modeling of real experimental data.

  14. A selective view of stochastic inference and mod-eling problems in nanoscale biophysics

    Institute of Scientific and Technical Information of China (English)

    KOU; S.C.

    2009-01-01

    Advances in nanotechnology enable scientists for the first time to study biological pro-cesses on a nanoscale molecule-by-molecule basis.They also raise challenges and opportunities for statisticians and applied probabilists.To exemplify the stochastic inference and modeling problems in the field,this paper discusses a few selected cases,ranging from likelihood inference,Bayesian data augmentation,and semi-and non-parametric inference of nanometric biochemical systems to the uti-lization of stochastic integro-differential equations and stochastic networks to model single-molecule biophysical processes.We discuss the statistical and probabilistic issues as well as the biophysical motivation and physical meaning behind the problems,emphasizing the analysis and modeling of real experimental data.

  15. Biophysical regions identification using an artificial neuronal network: A case study in the South Western Atlantic

    Science.gov (United States)

    Saraceno, Martin; Provost, Christine; Lebbah, Mustapha

    A classification method based on an artificial neuronal network is used to identify biophysical regions in the South Western Atlantic (SWA). The method comprises a probabilistic version of the Kohonen’s self-organizing map and a Hierarchical Ascending Clustering algorithm. It objectively defines the optimal number of classes and the class boundaries. The method is applied to ocean surface data provided by satellite: chlorophyll-a, sea surface temperature and sea surface temperature gradient, first to means and then, in an attempt to examine seasonal variations, to monthly climatologies. Both results reflect the presence of the major circulation patterns and frontal positions in the SWA. The provinces retrieved using mean fields are compared to previous results and show a more accurate description of the SWA. The classification obtained with monthly climatologies offers the flexibility to include the time dimension; the boundaries of biophysical regions established are not fixed, but vary in time. Perspectives and limitations of the methodology are discussed.

  16. Testing the Simple Biosphere model (SiB) using point micrometeorological and biophysical data

    Science.gov (United States)

    Sellers, P. J.; Dorman, J. L.

    1987-01-01

    The suitability of the Simple Biosphere (SiB) model of Sellers et al. (1986) for calculation of the surface fluxes for use within general circulation models is assessed. The structure of the SiB model is described, and its performance is evaluated in terms of its ability to realistically and accurately simulate biophysical processes over a number of test sites, including Ruthe (Germany), South Carolina (U.S.), and Central Wales (UK), for which point biophysical and micrometeorological data were available. The model produced simulations of the energy balances of barley, wheat, maize, and Norway Spruce sites over periods ranging from 1 to 40 days. Generally, it was found that the model reproduced time series of latent, sensible, and ground-heat fluxes and surface radiative temperature comparable with the available data.

  17. Large-Scale Overexpression and Purification of ADARs from Saccharomyces cerevisiae for Biophysical and Biochemical Studies

    OpenAIRE

    Macbeth, Mark R.; Bass, Brenda L.

    2007-01-01

    Many biochemical and biophysical analyses of enzymes require quantities of protein that are difficult to obtain from expression in an endogenous system. To further complicate matters, native adenosine deaminases that act on RNA (ADARs) are expressed at very low levels, and overexpression of active protein has been unsuccessful in common bacterial systems. Here we describe the plasmid construction, expression, and purification procedures for ADARs overexpressed in the yeast Saccharomyces cerev...

  18. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Wahl, U., E-mail: uwahl@itn.pt [Instituto Tecnologico e Nuclear, Estrada Nacional 10, 2686-953 Sacavem (Portugal); Centro de Fisica Nuclear da Universidade de Lisboa, Av. Prof. Gama Pinto 2, 1649-003 Lisboa (Portugal)

    2011-12-15

    The ISOLDE isotope separator facility at CERN provides a variety of radioactive ion beams, currently more than 800 different isotopes from {approx}70 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 {approx}15%) of the delivered beam time, requested by 18 different experiments. The ISOLDE materials science and biophysics community currently consists of {approx}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 in biological systems. The characterisation methods used are typical radioactive probe techniques such as Moessbauer spectroscopy, perturbed angular correlation, emission channeling, and tracer diffusion studies. In addition to these 'classic' methods of nuclear solid state physics, also standard semiconductor analysis techniques such as photoluminescence or deep level transient spectroscopy profit from the application of radioactive isotopes, which helps them to overcome their chemical 'blindness' since the nuclear half life of radioisotopes provides a signal that changes in time with characteristic exponential decay or saturation curves. In this presentation an overview will be given on the recent research activities in materials science and biophysics at ISOLDE, presenting some of the highlights during the last five years, together with a short outlook on the new developments under way.

  20. 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.

  1. Biophysical Properties of Scaffolds Modulate Human Blood Vessel Formation from Circulating Endothelial Colony-Forming Cells

    Science.gov (United States)

    Critser, Paul J.; Yoder, Mervin C.

    A functional vascular system forms early in development and is continually remodeled throughout the life of the organism. Impairment to the regeneration or repair of this system leads to tissue ischemia, dysfunction, and disease. The process of vascular formation and remodeling is complex, relying on local microenvironmental cues, cytokine signaling, and multiple cell types to function properly. Tissue engineering strategies have attempted to exploit these mechanisms to develop functional vascular networks for the generation of artificial tissues and therapeutic strategies to restore tissue homeostasis. The success of these strategies requires the isolation of appropriate progenitor cell sources which are straightforward to obtain, display high proliferative potential, and demonstrate an ability to form functional vessels. Several populations are of interest including endothelial colony-forming cells, a subpopulation of endothelial progenitor cells. Additionally, the development of scaffolds to deliver and support progenitor cell survival and function is crucial for the formation of functional vascular networks. The composition and biophysical properties of these scaffolds have been shown to modulate endothelial cell behavior and vessel formation. However, further investigation is needed to better understand how these mechanical properties and biophysical properties impact vessel formation. Additionally, several other cell populations are involved in neoangiogenesis and formation of tissue parenchyma and an understanding of the potential impact of these cell populations on the biophysical properties of scaffolds will also be needed to advance these strategies. This chapter examines how the biophysical properties of matrix scaffolds can influence vessel formation and remodeling and, in particular, the impact on in vivo human endothelial progenitor cell vessel formation.

  2. Biophysical Model of Ion Transport across Human Respiratory Epithelia Allows Quantification of Ion Permeabilities

    OpenAIRE

    Garcia, Guilherme J.M.; Boucher, Richard C.; Elston, Timothy C.

    2013-01-01

    Lung health and normal mucus clearance depend on adequate hydration of airway surfaces. Because transepithelial osmotic gradients drive water flows, sufficient hydration of the airway surface liquid depends on a balance between ion secretion and absorption by respiratory epithelia. In vitro experiments using cultures of primary human nasal epithelia and human bronchial epithelia have established many of the biophysical processes involved in airway surface liquid homeostasis. Most experimental...

  3. Biophysical Characterization of the Centromere-specific Nucleosome from Budding Yeast*

    OpenAIRE

    Kingston, Isabel J.; Yung, Jasmine S. Y.; Singleton, Martin R

    2010-01-01

    The centromeric DNA of all eukaryotes is assembled upon a specialized nucleosome containing a histone H3 variant known as CenH3. Despite the importance and conserved nature of this protein, the characteristics of the centromeric nucleosome are still poorly understood. In particular, the stoichiometry and DNA-binding properties of the CenH3 nucleosome have been the subject of some debate. We have characterized the budding yeast centromeric nucleosome by biochemical and biophysical methods and ...

  4. THE INFLUENCE OF THE NUTRITIONAL FACTORS ON SOME BIOPHYSICAL PARAMETERS OF THE RUMINAL FLUID

    OpenAIRE

    IULIANA CREłESCU; RODICA CĂPRIłĂ; D. DRÎNCEANU; RODICA CHEREJI; MIHAELA PETCU; C-TIN MATEESCU

    2013-01-01

    At this hour, a large part of the products obtained through biotechnologies are used in animal fodder, thus contributing to the enhancement of the animal products obtained in economical conditions through optimising the nutrition. In the present study, we wanted to pursue the influence of a high level of cereal in fodder rations, as well as the effect of the yeast Saccharomyces cerevisiae, Yea Sacc1026 strain on some biophysical parameters of the ruminal fluid, such as: pH, density and superf...

  5. Proceedings of the anatomical society of great britain and ireland, and the british biophysical society.

    Science.gov (United States)

    1999-05-01

    A joint meeting of the Anatomical Society of Great Britain and Ireland and the British Biophysical Society was held at the School of Biomedical Sciences, University of Leeds, from 5th to 7th January 1999. It included a symposium on 'Structure and function of molecular motors' and the Annual General Meetings of both Societies. The following are abstracts of communications and posters presented at the meeting. PMID:17103658

  6. Polish Academy of Sciences. Institute of Biochemistry and Biophysics. Research Report 1998-1999

    International Nuclear Information System (INIS)

    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

  7. 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.

  8. Simulation of Tillage Systems Impact on Soil Biophysical Properties Using the SALUS Model

    OpenAIRE

    2011-01-01

    A sustainable land management has been defined as the management system that allows for production, while minimizing risk, maintaining quality of soil and water. Tillage systems can significantly decrease soil carbon storage and influence the soil environment of a crop. Crop growth models can be useful tools in evaluating the impact of different tillage systems on soil biophysical properties and on the growth and final yield of the crops. The objectives of this paper were i) to illustrate the...

  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. REMOTE-SENSING-BASED BIOPHYSICAL MODELS FOR ESTIMATING LAI OF IRRIGATED CROPS IN MURRY DARLING BASIN

    OpenAIRE

    Wittamperuma, I.; M. Hafeez; Pakparvar, M.; Louis, J.

    2012-01-01

    Remote sensing is a rapid and reliable method for estimating crop growth data from individual plant to crops in irrigated agriculture ecosystem. The LAI is one of the important biophysical parameter for determining vegetation health, biomass, photosynthesis and evapotranspiration (ET) for the modelling of crop yield and water productivity. Ground measurement of this parameter is tedious and time-consuming due to heterogeneity across the landscape over time and space. This study deals with the...

  11. Biophysical criteria used by farmers for fallow selection in West and Central Africa

    OpenAIRE

    Norgrove, Lindsey; Hauser, Stefan

    2016-01-01

    In many parts of the humid Tropics, slash and burn shifting cultivation, incorporating a fallow phase, is the most common farming method, encompassing a broad diversity of techniques. The ecological productivity and sustainability of such systems depend upon the crop:fallow time ratio. Farmers often have biophysical criteria by which to match parcels to cropping systems and decide, for example, when to recultivate a fallow. In this paper, we collate reports of indicators used by farmers to ai...

  12. Biophysical and Economic Uncertainty in the Analysis of Poverty Impacts of Climate Change

    OpenAIRE

    Hertel, Thomas W.; Lobell, David; Verma, Monika

    2011-01-01

    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 productivity shocks reflecting the impacts of climate on agricultural yields in 2030. These shocks, in turn, affect the global economy. The response of economic agents to climate change is the second source of uncertainty in our estimates. We find that, even ...

  13. Comparison of biophysical and satellite predictors for wheat yield forecasting in Ukraine

    Science.gov (United States)

    Kolotii, A.; Kussul, N.; Shelestov, A.; Skakun, S.; Yailymov, B.; Basarab, R.; Lavreniuk, M.; Oliinyk, T.; Ostapenko, V.

    2015-04-01

    Winter wheat crop yield forecasting at national, regional and local scales is an extremely important task. This paper aims at assessing the efficiency (in terms of prediction error minimization) of satellite and biophysical model based predictors assimilation into winter wheat crop yield forecasting models at different scales (region, county and field) for one of the regions in central part of Ukraine. Vegetation index NDVI, as well as different biophysical parameters (LAI and fAPAR) derived from satellite data and WOFOST crop growth model are considered as predictors of winter wheat crop yield forecasting model. Due to very short time series of reliable statistics (since 2000) we consider single factor linear regression. It is shown that biophysical parameters (fAPAR and LAI) are more preferable to be used as predictors in crop yield forecasting regression models at each scale. Correspondent models possess much better statistical properties and are more reliable than NDVI based model. The most accurate result in current study has been obtained for LAI values derived from SPOT-VGT (at 1 km resolution) on county level. At field level, a regression model based on satellite derived LAI significantly outperforms the one based on LAI simulated with WOFOST.

  14. Evolutionary dynamics of viral escape under antibodies stress: A biophysical model.

    Science.gov (United States)

    Chéron, Nicolas; Serohijos, Adrian W R; Choi, Jeong-Mo; Shakhnovich, Eugene I

    2016-07-01

    Viruses constantly face the selection pressure of antibodies, either from innate immune response of the host or from administered antibodies for treatment. We explore the interplay between the biophysical properties of viral proteins and the population and demographic variables in the viral escape. The demographic and population genetics aspect of the viral escape have been explored before; however one important assumption was the a priori distribution of fitness effects (DFE). Here, we relax this assumption by instead considering a realistic biophysics-based genotype-phenotype relationship for RNA viruses escaping antibodies stress. In this model the DFE is itself an evolvable property that depends on the genetic background (epistasis) and the distribution of biophysical effects of mutations, which is informed by biochemical experiments and theoretical calculations in protein engineering. We quantitatively explore in silico the viability of viral populations under antibodies pressure and derive the phase diagram that defines the fate of the virus population (extinction or escape from stress) in a range of viral mutation rates and antibodies concentrations. We find that viruses are most resistant to stress at an optimal mutation rate (OMR) determined by the competition between supply of beneficial mutation to facilitate escape from stressors and lethal mutagenesis caused by excess of destabilizing mutations. We then show the quantitative dependence of the OMR on genome length and viral burst size. We also recapitulate the experimental observation that viruses with longer genomes have smaller mutation rate per nucleotide. PMID:26939576

  15. Identification of Optimal Hyperspectral Bands for Estimation of Rice Biophysical Parameters

    Institute of Scientific and Technical Information of China (English)

    Fu-Min Wang; Jing-Feng Huang; Xiu-Zhen Wang

    2008-01-01

    The present study aims to identify the narrow spectral bands that are most suitable for characterizing rice biophysical parameters. The data used for this study come from ground-level hyperspectral reflectance measurements for five rice species at three levels of nitrogen fertilization during the growing period. Reflectance was measured in discrete narrow bands between 350 and 2 500 nm. Observed rice biophysical parameters included leaf area index (LAI), wet biomass and dry biomass. The stepwise regression method was applied to identify the optimal bands for rice biophysical parameter estimation. This research indicated that combinations of four narrow bands in stepwise regression models explained 69% to 83% variability for LAI, 56% to 73% for aboveground wet biomass and 70% to 83% for leaf wet biomass. An overwhelming proportion of rice information was in a particular portion of near infrared (NIR) (1 100-1 150 nm), red-edge (700-750 nm), and a longer portion of green (550-600 nm). These were followed by the moisture-sensitive NIR (950-1 000 nm), the intermediate portion of shortwave infrared (SWIR) (1 650-1 700 nm), and another portion of NIR (t 000-1 050 nm).

  16. 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.

  17. 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.

  18. 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.

  19. Land-use Change and Biophysical Accounting in Forest Carbon Projects

    Science.gov (United States)

    Jackson, R. B.

    2014-12-01

    Biological carbon sequestration by reforestation and afforestation is being promoted as an opportunity to help mitigate global warming and climate change. The scientific basis to support such forestry activities is shifting to include many biophysical dimensions beyond carbon storage. In this talk I address two questions: 1) Where can forests help slow the buildup of greenhouse gases in the atmosphere while also providing beneficial biophysical feedbacks? and (2) How many extra resources, including water and nutrients, may be needed to achieve this carbon storage and climate benefit? By comparing the biophysical forcings and climatic impact of vegetation replacement across North America using satellite-derived albedo, land surface temperature (LST), and evapotranspiration (ET) between adjacent vegetation types, we show that a carbon-centric accounting is, in most cases, insufficient for climate mitigation policies. Where afforestation or reforestation occurs, deciduous broadleaf trees are likely to produce stronger cooling benefits than evergreen needleleaf trees provide in temperate ecosystems. Our analyses also suggest that forestry activities will have the most climatic benefits at locations where background albedo prior to landscape change is low, snow cover is minimal, cloud cover is high, and soil water availability is ample.

  20. 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.

  1. Saxton Transportation Operations Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Saxton Transportation Operations Laboratory (Saxton Laboratory) is a state-of-the-art facility for conducting transportation operations research. The laboratory...

  2. Annual report No. 5 for Institute of Molecular Biophysics of Florida State University, September 1, 1964-August 31, 1965

    Energy Technology Data Exchange (ETDEWEB)

    1965-06-01

    This document contains the results of one years work by the members of the Institute of Molecular Biophysics at Florida State University. Research summaries for 29 programs covering 18 disciplines are included. 45 refs. (TEM)

  3. Virtual Laboratories

    CERN Document Server

    Hut, P

    2006-01-01

    At the frontier of most areas in science, computer simulations play a central role. The traditional division of natural science into experimental and theoretical investigations is now completely outdated. Instead, theory, simulation, and experimentation form three equally essential aspects, each with its own unique flavor and challenges. Yet, education in computational science is still lagging far behind, and the number of text books in this area is minuscule compared to the many text books on theoretical and experimental science. As a result, many researchers still carry out simulations in a haphazard way, without properly setting up the computational equivalent of a well equipped laboratory. The art of creating such a virtual laboratory, while providing proper extensibility and documentation, is still in its infancy. A new approach is described here, Open Knowledge, as an extension of the notion of Open Source software. Besides open source code, manuals, and primers, an open knowledge project provides simul...

  4. Laboratory investigations

    International Nuclear Information System (INIS)

    Our task is to design mined-repository systems that will adequately secure high-level nuclear waste for at least 10,000 yr and that will be mechanically stable for 50 to 100-yr periods of retrievability during which mistakes could be corrected and a valuable source of energy could be reclaimed, should national policy on the reprocessing of spent fuel ever change. The only credible path for the escape of radionuclides from the repository to the biosphere is through ground-water, and in hard rock, bulk permeability is largely governed by natural and artificial fracture systems. Catastrophic failure of an excavation in hard rock is likely to occur at the weakest links - the discontinuities in the rock mass that is perturbed first by mining and then by radiogenic heating. The laboratory can contribute precise measurements of the pertinent thermomechanical, hydrological and chemical properties and improve our understanding of the fundamental processes through careful experiments under well controlled conditions that simulate the prototype environment. Thus laboratory investigations are necessary, but they are not sufficient, for conventional sample sizes are small relative to natural defects like joints - i.e., the rock mass is not a continuum - and test durations are short compared to those that predictive modeling must take into account. Laboratory investigators can contribute substantially more useful data if they are provided facilities for testing large specimens(say one cubic meter) and for creep testing of all candidate host rocks. Even so, extrapolations of laboratory data to the field in neither space nor time are valid without the firm theoretical foundations yet to be built. Meanwhile in-situ measurements of structure-sensitive physical properties and access to direct observations of rock-mass character will be absolutely necessary

  5. Culham Laboratory

    International Nuclear Information System (INIS)

    The report contains summaries of work carried out under the following headings: fusion research experiments; U.K. contribution to the JET project; supporting studies; theoretical plasma physics, computational physics and computing; fusion reactor studies; engineering and technology; contract research; external relations; staff, finance and services. Appendices cover main characteristics of Culham fusion experiments, staff, extra-mural projects supported by Culham Laboratory, and a list of papers written by Culham staff. (U.K.)

  6. Activity and biophysical inhibition resistance of a novel synthetic lung surfactant containing Super-Mini-B DATK peptide

    OpenAIRE

    Notter, Robert H.; Wang, Zhengdong; Walther, Frans J

    2016-01-01

    Background/objectives. This study examines the surface activity, resistance to biophysical inhibition, and pulmonary efficacy of a synthetic lung surfactant containing glycerophospholipids combined with Super Mini-B (S-MB) DATK, a novel and stable molecular mimic of lung surfactant protein (SP)-B. The objective of the work is to test whether S-MB DATK synthetic surfactant has favorable biophysical and physiological activity for future use in treating surfactant deficiency or dysfunction in lu...

  7. 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

  8. Biophysical and Socioeconomic Factors Associated with Forest Transitions at Multiple Spatial and Temporal Scales

    Directory of Open Access Journals (Sweden)

    Patricia Adame

    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

  9. Severity of climate change dictates the direction of biophysical feedbacks of vegetation change to Arctic climate

    Science.gov (United States)

    Zhang, Wenxin; Jansson, Christer; Miller, Paul; Smith, Ben; Samuelsson, Patrick

    2014-05-01

    Vegetation-climate feedbacks induced by vegetation dynamics under climate change alter biophysical properties of the land surface that regulate energy and water exchange with the atmosphere. Simulations with Earth System Models applied at global scale suggest that the current warming in the Arctic has been amplified, with large contributions from positive feedbacks, dominated by the effect of reduced surface albedo as an increased distribution, cover and taller stature of trees and shrubs mask underlying snow, darkening the surface. However, these models generally employ simplified representation of vegetation dynamics and structure and a coarse grid resolution, overlooking local or regional scale details determined by diverse vegetation composition and landscape heterogeneity. In this study, we perform simulations using an advanced regional coupled vegetation-climate model (RCA-GUESS) applied at high resolution (0.44×0.44° ) over the Arctic Coordinated Regional Climate Downscaling Experiment (CORDEX-Arctic) domain. The climate component (RCA4) is forced with lateral boundary conditions from EC-EARTH CMIP5 simulations for three representative concentration pathways (RCP 2.6, 4.5, 8.5). Vegetation-climate response is simulated by the individual-based dynamic vegetation model (LPJ-GUESS), accounting for phenology, physiology, demography and resource competition of individual-based vegetation, and feeding variations of leaf area index and vegetative cover fraction back to the climate component, thereby adjusting surface properties and surface energy fluxes. The simulated 2m air temperature, precipitation, vegetation distribution and carbon budget for the present period has been evaluated in another paper. The purpose of this study is to elucidate the spatial and temporal characteristics of the biophysical feedbacks arising from vegetation shifts in response to different CO2 concentration pathways and their associated climate change. Our results indicate that the

  10. Photobiology Research Laboratory (Fact Sheet)

    Energy Technology Data Exchange (ETDEWEB)

    2012-06-01

    This fact sheet provides information about Photobiology Research Laboratory capabilities and applications at NREL. The photobiology group's research is in four main areas: (1) Comprehensive studies of fuel-producing photosynthetic, fermentative, and chemolithotrophic model microorganisms; (2) Characterization and engineering of redox enzymes and proteins for fuel production; (3) Genetic and pathway engineering of model organisms to improve production of hydrogen and hydrocarbon fuels; and (4) Studies of nanosystems using biological and non-biological materials in hybrid generation. NREL's photobiology research capabilities include: (1) Controlled and automated photobioreactors and fermenters for growing microorganisms under a variety of environmental conditions; (2) High-and medium-throughput screening of H{sub 2}-producing organisms; (3) Homologous and heterologous expression, purification, and biochemical/biophysical characterization of redox enzymes and proteins; (4) Qualitative and quantitative analyses of gases, metabolites, carbohydrates, lipids, and proteins; (5) Genetic and pathway engineering and development of novel genetic toolboxes; and (6) Design and spectroscopic characterization of enzyme-based biofuel cells and energy conversion nanodevices.

  11. 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.

  12. Effects of LiDAR point density, sampling size and height threshold on estimation accuracy of crop biophysical parameters.

    Science.gov (United States)

    Luo, Shezhou; Chen, Jing M; Wang, Cheng; Xi, Xiaohuan; Zeng, Hongcheng; Peng, Dailiang; Li, Dong

    2016-05-30

    Vegetation leaf area index (LAI), height, and aboveground biomass are key biophysical parameters. Corn is an important and globally distributed crop, and reliable estimations of these parameters are essential for corn yield forecasting, health monitoring and ecosystem modeling. Light Detection and Ranging (LiDAR) is considered an effective technology for estimating vegetation biophysical parameters. However, the estimation accuracies of these parameters are affected by multiple factors. In this study, we first estimated corn LAI, height and biomass (R2 = 0.80, 0.874 and 0.838, respectively) using the original LiDAR data (7.32 points/m2), and the results showed that LiDAR data could accurately estimate these biophysical parameters. Second, comprehensive research was conducted on the effects of LiDAR point density, sampling size and height threshold on the estimation accuracy of LAI, height and biomass. Our findings indicated that LiDAR point density had an important effect on the estimation accuracy for vegetation biophysical parameters, however, high point density did not always produce highly accurate estimates, and reduced point density could deliver reasonable estimation results. Furthermore, the results showed that sampling size and height threshold were additional key factors that affect the estimation accuracy of biophysical parameters. Therefore, the optimal sampling size and the height threshold should be determined to improve the estimation accuracy of biophysical parameters. Our results also implied that a higher LiDAR point density, larger sampling size and height threshold were required to obtain accurate corn LAI estimation when compared with height and biomass estimations. In general, our results provide valuable guidance for LiDAR data acquisition and estimation of vegetation biophysical parameters using LiDAR data. PMID:27410085

  13. Unravel biophysical factors on river water quality response in Chilean Central-Southern watersheds.

    Science.gov (United States)

    Yevenes, Mariela A; Arumí, José L; Farías, Laura

    2016-05-01

    Identifying the key anthropogenic (land uses) and natural (topography and climate) biophysical drivers affecting river water quality is essential for efficient management of water resources. We tested the hypothesis that water quality can be predicted by different biophysical factors. Multivariate statistics based on a geographical information system (GIS) were used to explore the influence of factors (i.e., precipitation, topography, and land uses) on water quality (i.e., nitrate (NO 3 (-) ), phosphate (PO 4 (3 -) ), silicate (Si(OH)4), dissolved oxygen (DO), suspended solids (TSS), biological oxygen demand (DO), temperature (T), conductivity (EC), and pH) for two consecutive years in the Itata and Biobío river watersheds, Central Chile (36° 00' and 38° 30'). The results showed that (NO 3 (-) ), (PO 4 (3 -) ), Si(OH)4, TSS, EC, and DO were higher during rainy season (austral fall, winter, and spring), whereas BOD and temperature were higher during dry season. The spatial variation of these parameters in both watersheds was related to land use, topography (e.g., soil moisture, soil hydrological group, and erodability), and precipitation. Soil hydrological group and soil moisture were the strongest explanatory predictors for PO 4 (3 -) , Si(OH)4 and EC in the river, followed by land use such as agriculture for NO 3 (-) and DO and silviculture for TSS and Si(OH)4. High-resolution water leaching and runoff maps allowed us to identify agriculture areas with major probability of water leaching and higher probability of runoff in silviculture areas. Moreover, redundancy analysis (RDA) revealed that land uses (agriculture and silviculture) explained in 60 % the river water quality variation. Our finding highlights the vulnerability of Chilean river waters to different biophysical drivers, rather than climate conditions alone, which is amplified by human-induced degradation. PMID:27038616

  14. 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. PMID:26771181

  15. 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.

  16. Photobiology of Symbiodinium revisited: bio-physical and bio-optical signatures

    Science.gov (United States)

    Hennige, S. J.; Suggett, D. J.; Warner, M. E.; McDougall, K. E.; Smith, D. J.

    2009-03-01

    Light is often the most abundant resource within the nutrient-poor waters surrounding coral reefs. Consequently, zooxanthellae ( Symbiodinium spp.) must continually photoacclimate to optimise productivity and ensure coral success. In situ coral photobiology is becoming dominated by routine assessments using state-of-the-art non-invasive bio-optical or chlorophyll a fluorescence (bio-physical) techniques. Multiple genetic types of Symbiodinium are now known to exist; however, little focus has been given as to how these types differ in terms of characteristics that are observable using these techniques. Therefore, this investigation aimed to revisit and expand upon a pivotal study by Iglesias-Prieto and Trench (1994) by comparing the photoacclimation characteristics of different Symbiodinium types based on their bio-physical (chlorophyll a fluorescence, reaction centre counts) and bio-optical (optical absorption, pigment concentrations) ‘signatures’. Signatures described here are unique to Symbiodinium type and describe phenotypic responses to set conditions, and hence are not suitable to describe taxonomic structure of in hospite Symbiodinium communities. In this study, eight Symbiodinium types from clades and sub-clades (A-B, F) were grown under two PFDs (Photon Flux Density) and examined. The photoacclimation response by Symbiodinium was highly variable between algal types for all bio-physical and for many bio-optical measurements; however, a general preference to modifying reaction centre content over effective antennae-absorption was observed. Certain bio-optically derived patterns, such as light absorption, were independent of algal type and, when considered per photosystem, were matched by reaction centre stoichiometry. Only by better understanding genotypic and phenotypic variability between Symbiodinium types can future studies account for the relative taxonomic and physiological contribution by Symbiodinium to coral acclimation.

  17. From autopoiesis to neurophenomenology: Francisco Varela's exploration of the biophysics of being.

    Science.gov (United States)

    Rudrauf, David; Lutz, Antoine; Cosmelli, Diego; Lachaux, Jean-Philippe; Le Van Quyen, Michel

    2003-01-01

    This paper reviews in detail Francisco Varela's work on subjectivity and consciousness in the biological sciences. His original approach to this "hard problem" presents a subjectivity that is radically intertwined with its biological and physical roots. It must be understood within the framework of his theory of a concrete, embodied dynamics, grounded in his general theory of autonomous systems. Through concepts and paradigms such as biological autonomy, embodiment and neurophenomenology, the article explores the multiple levels of circular causality assumed by Varela to play a fundamental role in the emergence of human experience. The concept of biological autonomy provides the necessary and sufficient conditions for characterizing biological life and identity as an emergent and circular self-producing process. Embodiment provides a systemic and dynamical framework for understanding how a cognitive self--a mind--can arise in an organism in the midst of its operational cycles of internal regulation and ongoing sensorimotor coupling. Global subjective properties can emerge at different levels from the interactions of components and can reciprocally constrain local processes through an ongoing, recursive morphodynamics. Neurophenomenology is a supplementary step in the study of consciousness. Through a rigorous method, it advocates the careful examination of experience with first-person methodologies. It attempts to create heuristic mutual constraints between biophysical data and data produced by accounts of subjective experience. The aim is to explicitly ground the active and disciplined insight the subject has about his/her experience in a biophysical emergent process. Finally, we discuss Varela's essential contribution to our understanding of the generation of consciousness in the framework of what we call his "biophysics of being." PMID:12795206

  18. Mesoscale simulations of two model systems in biophysics: from red blood cells to DNAs

    Science.gov (United States)

    Peng, Zhangli; Chen, Yeng-Long; Lu, Huijie; Pan, Zehao; Chang, Hsueh-Chia

    2015-12-01

    Computational modeling has become increasingly important in biophysics, but the great challenge in numerical simulations due to the multiscale feature of biological systems limits the capability of modeling in making discoveries in biology. Innovative multiscale modeling approaches are desired to bridge different scales from nucleic acids and proteins to cells and tissues. Although all-atom molecular dynamics has been successfully applied in many microscale biological processes such as protein folding, it is still prohibitively expensive for studying macroscale problems such as biophysics of cells and tissues. On the other hand, continuum-based modeling has become a mature procedure for analysis and design in many engineering fields, but new insights for biological systems in the microscale are limited when molecular details are missing in continuum-based modeling. In this context, mesoscale modeling approaches such as Langevin dynamics, lattice Boltzmann method, and dissipative particle dynamics have become popular by simultaneously incorporating molecular interactions and long-range hydrodynamic interactions, providing insights to properties on longer time and length scales than molecular dynamics. In this review, we summarized several mesoscale simulation approaches for studying two model systems in biophysics: red blood cells (RBCs) and deoxyribonucleic acids (DNAs). The RBC is a model system for cell mechanics and biological membranes, while the DNA represents a model system for biopolymers. We introduced the motivations of studying these problems and presented the key features of different mesoscale methods. Furthermore, we described the latest progresses in these methods and highlighted the major findings for modeling RBCs and DNAs. Finally, we also discussed the challenges and potential issues of different approaches.

  19. River bank burrowing by invasive crayfish: Spatial distribution, biophysical controls and biogeomorphic significance.

    Science.gov (United States)

    Faller, Matej; Harvey, Gemma L; Henshaw, Alexander J; Bertoldi, Walter; Bruno, Maria Cristina; England, Judy

    2016-11-01

    Invasive species generate significant global environmental and economic costs and represent a particularly potent threat to freshwater systems. The biogeomorphic impacts of invasive aquatic and riparian species on river processes and landforms remain largely unquantified, but have the potential to generate significant sediment management issues within invaded catchments. Several species of invasive (non-native) crayfish are known to burrow into river banks and visual evidence of river bank damage is generating public concern and media attention. Despite this, there is a paucity of understanding of burrow distribution, biophysical controls and the potential significance of this problem beyond a small number of local studies at heavily impacted sites. This paper presents the first multi-catchment analysis of this phenomenon, combining existing data on biophysical river properties and invasive crayfish observations with purpose-designed field surveys across 103 river reaches to derive key trends. Crayfish burrows were observed on the majority of reaches, but burrowing tended to be patchy in spatial distribution, concentrated in a small proportion (bank biophysical properties than by reach-scale properties, and burrowed banks were more likely to be characterised by cohesive bank material, steeper bank profiles with large areas of bare bank face, often on outer bend locations. Burrow excavation alone has delivered a considerable amount of sediment to invaded river systems in the surveyed sites (3tkm(-1) impacted bank) and this represents a minimum contribution and certainly an underestimate of the absolute yield (submerged burrows were not recorded). Furthermore, burrowing was associated with bank profiles that were either actively eroding or exposed to fluvial action and/or mass failure processes, providing the first quantitative evidence that invasive crayfish may cause or accelerate river bank instability and erosion in invaded catchments beyond the scale of

  20. Modeling crop water use in an irrigated maize cropland using a biophysical process-based model

    Science.gov (United States)

    Ding, Risheng; Kang, Shaozhong; Du, Taisheng; Hao, Xinmei; Tong, Ling

    2015-10-01

    Accurate modeling of crop water use or evapotranspiration (ET) is needed to understand the hydrologic cycle and improve water use efficiency. Biophysical process-based multilayer models can capture details of the nonlinear interaction between microclimate and physiology within the canopy and thus accurately simulate ET. In this study, we extended a process-based multilayer model, ACASA, which explicitly simulated many of the nonlinear biophysical processes within each of ten crop canopy sublayers and then integrated to represent the complete crop canopy. Based on the original ACASA model, we made the improved modifications including four added modules (C4 crop photosynthesis, water stress response of stomatal conductance, crop morphological changes, and heterogeneous root water uptake), and two adjusted calculation procedures (soil evaporation resistance and hydraulic characteristic parameters). Key processes were parameterized for the improved ACASA model using observations. The simulated canopy ET was validated using eddy covariance measurements over an irrigated maize field in an arid inland region of northwest China. The improved ACASA model predicted maize ET for both half-hourly and daily time-scales. The improved model also predicted the reduction in maize ET under the condition of soil water deficit. Soil evaporation, an important component of maize ET, was also satisfactorily simulated in the improved model. Compared to the original ACASA model, the improved model yielded an improved estimation of maize ET. Using the improved model, we found that maize ET was nonlinearly affected by changes in leaf area index and photosynthetic capacity through canopy conductance. In general, the improved ACASA model, a biophysical process-based multilayer model, can be used to diagnose and predict crop ET, and draw some insights into the nonlinear interactions between crop canopy and ambient environment.

  1. Long-Term Data Records of Biophysical Parameters from Multiple Satellite Systems

    Science.gov (United States)

    Ganguly, S.; Nemani, R. R.; Baret, F.; Myneni, R.; Zhang, G.; Milesi, C.; Hashimoto, H.

    2014-12-01

    Long-term satellite-derived vegetation biophysical products like the Leaf Area Index (LAI) and the Fraction of Photosynthetically Active Radiation (FPAR) are widely popular in the scientific research community for monitoring ecosystem health and vegetation dynamics as well as for a number of climate-ecosystem models that use LAI/FPAR as an input. The availability of continuous time series data from heritage sensors like the MODIS, AVHRR, SPOT, Landsat and MISR have allowed a number of research teams to generate biophysical products from these sensors using a wide variety of physical and emperical modeling techniques. However, the consistency and the continuity in the generated products from these various sensors have always been a concern for application scientists. Deriving consistent products require sophisticated algorithm formulation that takes into account the differences in sensor characteristics like spectral response function, field of view, spatial resolution and view/azimuth angle, to name a few. There have been recent advances in algorithms that take into account these differences in order to create a consistent long-term data. Another important advancement has been the generation of hybrid products that use information from two different sensors to drive a physical model. This paper presents a treatise on the existing long-term biophysical products and their usability in terms of global change research and applications that may range from a watershed level to climate model simulations. In addition, the paper will present (a) state-of-the-art LAI/FPAR products that are being generated from the Landsat sensor at a continental scale and its application to the NASA Carbon Monitoring System (CMS) and, (b) some of the recent efforts on extending the physical algorithm to next generation satellite sensor systems like the Landsat 8 and Sentinel-2.

  2. Biophysical and Biochemical Studies of the FMDV and EMCV IRES Elements

    OpenAIRE

    Onuegbu, Anthonia Chinwe

    2013-01-01

    The biophysical properties of the hairpin loop structures in the FMDV and EMCV IRES domains three and I, J were studied using UV melting and Circular Dichroism studies. The apical region consists of the hammerhead region that is made up of hairpin loop structures such as the GNRA motifs in the 16mer hairpin loop, (FMDV and EMCV), the heptaloop 15mer in the FMDV and 17mer in the EMCV, The RAAA motif in the 11mer (FMDV and EMCV). The empirical calculations on the folding of the RNA motifs were ...

  3. Biophysical Insights into the Inhibitory Mechanism of Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitors

    Directory of Open Access Journals (Sweden)

    Nicolas Sluis-Cremer

    2013-11-01

    Full Text Available HIV-1 reverse transcriptase (RT plays a central role in HIV infection. Current United States Federal Drug Administration (USFDA-approved antiretroviral therapies can include one of five approved non-nucleoside RT inhibitors (NNRTIs, which are potent inhibitors of RT activity. Despite their crucial clinical role in treating and preventing HIV-1 infection, their mechanism of action remains elusive. In this review, we introduce RT and highlight major advances from experimental and computational biophysical experiments toward an understanding of RT function and the inhibitory mechanism(s of NNRTIs.

  4. 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...... 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 into these...

  5. Extended ground truth : a new methodology for biophysical and geophysical surface parameters extraction at subject scale

    OpenAIRE

    Gademer, Antoine

    2010-01-01

    Retrieval of land surface parameters is an essential part of life and Earth sciences activities, as they are the key to understand the complex phenomena that take place in the biosphere. This thesis proposes a new methodology for biophysical and geophysical surface para-meters analysis, that we call Extended Ground Truth, and that mix the advantages of the field ope-rations and those of remote sensing. We have especially focused our work on the benefits of low altitude remote sensing with a m...

  6. On the Semi-Automatic Retrieval of Biophysical Parameters Based on Spectral Index Optimization

    Directory of Open Access Journals (Sweden)

    Juan Pablo Rivera

    2014-05-01

    Full Text Available Regression models based on spectral indices are typically empirical formulae enabling the mapping of biophysical parameters derived from Earth Observation (EO data. Due to its empirical nature, it remains nevertheless uncertain to what extent a selected regression model is the most appropriate one, until all band combinations and curve fitting functions are assessed. This paper describes the application of a Spectral Index (SI assessment toolbox in the Automated Radiative Transfer Models Operator (ARTMO package. ARTMO enables semi-automatic retrieval and mapping of biophysical parameters from optical remote sensing observations. The SI toolbox facilitates the assessment of biophysical parameter retrieval accuracy of established as well as new and generic SIs. For instance, based on the SI formulation used, all possible band combinations of formulations with up to ten bands can be defined and evaluated. Several options are available in the SI assessment: calibration/validation data partitioning, the addition of noise and the definition of curve fitting models. To illustrate its functioning, all two-band combinations according to simple ratio (SR and normalized difference (ND formulations as well as various fitting functions (linear, exponential, power, logarithmic, polynomial have been assessed. HyMap imaging spectrometer (430–2490 nm data obtained during the SPARC-2003 campaign in Barrax, Spain, have been used to extract leaf area index (LAI and leaf chlorophyll content (LCC estimates. For both SR and ND formulations the most sensitive regions have been identified for two-band combinations of green (539–570 nm with longwave SWIR (2421–2453 nm for LAI (r2: 0.83 and far-red (692 nm with NIR (1340 nm or shortwave SWIR (1661–1686 nm for LCC (r2: 0.93. Polynomial, logarithmic and linear fitting functions led to similar best correlations, though spatial differences emerged when applying the functions to HyMap imagery. We suggest that a

  7. Biophysical characterization of KV3.1 potassium channel activating compounds

    DEFF Research Database (Denmark)

    Taskin, Bahar; von Schoubye, Nadia Lybøl; Sheykhzade, Majid; Frank Bastlund, Jesper; Grunnet, Morten; Jespersen, Thomas

    2015-01-01

    The effect of two positive modulators, RE1 and EX15, on the voltage-gated K(+) channel Kv3.1 was investigated using the whole-cell patch-clamp technique on HEK293 cells expressing Kv3.1a. RE1 and EX15 increased the Kv3.1 currents in a concentration-dependent manner with an EC50 value of 4.5 and 1...... present study introduces the first detailed biophysical characterization of two new Kv3.1 channel modifying compounds with different modulating properties....

  8. Covariance of biophysical data with digital topographic and land use maps over the FIFE site

    Science.gov (United States)

    Davis, F. W.; Schimel, D. S.; Friedl, M. A.; Michaelsen, J. C.; Kittel, T. G. F.; Dubayah, R.; Dozier, J.

    1992-11-01

    Sampling design is critical in locating ground sampling stations for large-scale climatological field experiments. In the stratified sampling design adopted for the First International Satellite Land Surface Climatology Project (ISLSCP) Field Experiment (FIFE), the study region was stratified into 14 different terrain units based on land use/land cover and topographic variables that were hypothesized to have a strong influence on surface biophysical properties. Digital terrain maps were produced to facilitate ground data integration and extrapolation. This paper describes the biophysical stratification of the FIFE site, implementation of the stratification using geographic information system (GIS) techniques, and validation of the stratification with respect to field measurements of biomass, soil moisture, Bowen ratio (β), and the greenness vegetation index (GVI) derived from thematic mapper satellite data. Maps of burning and topographic position were significantly associated with variation in biomass, GVI, and β. The effects of burning and topography were stronger for the Konza Prairie Long-Term Ecological Research (KPLTER) site than for the rest of the FIFE site, where cattle grazing was a major confounding effect. The stratified design did not appreciably change the estimated site-wide means for surface climate parameters but accounted for between 25 and 45% of the sample variance depending on the variable. The design was weakened by undersampling of several strata, by high within-station variance in soil and vegetation data, and by failure to account for diverse land management practices on private lands surrounding KPLTER. We recommend that future large-scale climatological studies include the development of a digital terrain data base well in advance of field campaigns and that multitemporal imagery be used to obtain preliminary estimates of spatial and temporal variance in surface biophysical properties. We also recommend that sampling for the most

  9. Type A and B RNase P RNAs are interchangeable in vivo despite substantial biophysical differences

    OpenAIRE

    Wegscheid, Barbara; Condon, Ciarán; Hartmann, Roland K.

    2006-01-01

    We show that structural type A and B bacterial ribonuclease P (RNase P) RNAs can fully replace each other in vivo despite the many reported differences in their biogenesis, biochemical/biophysical properties and enzyme function in vitro. Our findings suggest that many of the reported idiosyncrasies of type A and B enzymes either do not reflect the in vivo situation or are not crucial for RNase P function in vivo, at least under standard growth conditions. The discrimination of mature tRNA by ...

  10. Fluctuation theory of solutions applications in chemistry, chemical engineering, and biophysics

    CERN Document Server

    Smith, Paul E

    2013-01-01

    There are essentially two theories of solutions that can be considered exact: the McMillan-Mayer theory and Fluctuation Solution Theory (FST). The first is mostly limited to solutes at low concentrations, while FST has no such issue. It is an exact theory that can be applied to any stable solution regardless of the number of components and their concentrations, and the types of molecules and their sizes. Fluctuation Theory of Solutions: Applications in Chemistry, Chemical Engineering, and Biophysics outlines the general concepts and theoretical basis of FST and provides a range of applications

  11. Distributed Energy Technology Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Distributed Energy Technologies Laboratory (DETL) is an extension of the power electronics testing capabilities of the Photovoltaic System Evaluation Laboratory...

  12. FOOTWEAR PERFORMANCE LABORATORY

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory provides biomechanical and physical analyses for both military and commercial footwear. The laboratory contains equipment that is integral to the us...

  13. Bio Engineering Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — Description/History: Chemistry and biology laboratories The Bio Engineering Laboratory (BeL) is theonly full spectrum biotechnology capability within the Department...

  14. Physical Sciences Laboratory (PSL)

    Data.gov (United States)

    Federal Laboratory Consortium — PNNL's Physical Sciences Laboratory (PSL) houses 22 research laboratories for conducting a wide-range of research including catalyst formulation, chemical analysis,...

  15. Large-Scale Overexpression and Purification of ADARs from Saccharomyces cerevisiae for Biophysical and Biochemical Studies

    Science.gov (United States)

    Macbeth, Mark R.; Bass, Brenda L.

    2008-01-01

    Many biochemical and biophysical analyses of enzymes require quantities of protein that are difficult to obtain from expression in an endogenous system. To further complicate matters, native adenosine deaminases that act on RNA (ADARs) are expressed at very low levels, and overexpression of active protein has been unsuccessful in common bacterial systems. Here we describe the plasmid construction, expression, and purification procedures for ADARs overexpressed in the yeast Saccharomyces cerevisiae. ADAR expression is controlled by the Gal promoter, which allows for rapid induction of transcription when the yeast are grown in media containing galactose. The ADAR is translated with an N-terminal histidine tag that is cleaved by the tobacco etch virus protease, generating one nonnative glycine residue at the N-terminus of the ADAR protein. ADARs expressed using this system can be purified to homogeneity, are highly active in deaminating RNA, and are produced in quantities (from 3 to 10 mg of pure protein per liter of yeast culture) that are sufficient for most biophysical studies. PMID:17662848

  16. Incorporating Bio-Physical Sciences into a Decision Support Tool for Sustainable Urban Planning

    Directory of Open Access Journals (Sweden)

    Zina Mitraka

    2014-11-01

    Full Text Available Deciding upon optimum planning actions in terms of sustainable urban planning involves the consideration of multiple environmental and socio-economic criteria. The transformation of natural landscapes to urban areas affects energy and material fluxes. An important aspect of the urban environment is the urban metabolism, and changes in such metabolism need to be considered for sustainable planning decisions. A spatial Decision Support System (DSS prototyped within the European FP7-funded project BRIDGE (sustainaBle uRban plannIng Decision support accountinG for urban mEtabolism, enables accounting for the urban metabolism of planning actions, by exploiting the current knowledge and technology of biophysical sciences. The main aim of the BRIDGE project was to bridge the knowledge and communication gap between urban planners and environmental scientists and to illustrate the advantages of considering detailed environmental information in urban planning processes. The developed DSS prototype integrates biophysical observations and simulation techniques with socio-economic aspects in five European cities, selected as case studies for the pilot application of the tool. This paper describes the design and implementation of the BRIDGE DSS prototype, illustrates some examples of use, and highlights the need for further research and development in the field.

  17. Guidance for Large-scale Implementation of Alternate Wetting and Drying: A Biophysical Suitability Assessment

    Science.gov (United States)

    Sander, B. O.; Wassmann, R.; Nelson, A.; Palao, L.; Wollenberg, E.; Ishitani, M.

    2014-12-01

    The alternate wetting and drying (AWD) technology for rice production does not only save 15-30% of irrigation water, it also reduces methane emissions by up to 70%. AWD is defined by periodic drying and re-flooding of a rice field. Due to its high mitigation potential and its simplicity to execute this practice AWD has gained a lot of attention in recent years. The Climate and Clean Air Coalition (CCAC) has put AWD high on its agenda and funds a project to guide implementation of this technology in Vietnam, Bangladesh and Colombia. One crucial activity is a biophysical suitability assessment for AWD in the three countries. For this, we analyzed rainfall and soil data as well as potential evapotranspiration to assess if the water balance allows practicing AWD or if precipitation is too high for rice fields to fall dry. In my talk I will outline key factors for a successful large-scale implementation of AWD with a focus on the biophysical suitability assessment. The seasonal suitability maps that we generated highlight priority areas for AWD implementation and guide policy makers to informed decisions about meaningful investments in infrastructure and extension work.

  18. Biophysical regulation of Chlamydia pneumoniae-infected monocyte recruitment to atherosclerotic foci

    Science.gov (United States)

    Evani, Shankar J.; Ramasubramanian, Anand K.

    2016-01-01

    Chlamydia pneumoniae infection is implicated in atherosclerosis although the contributory mechanisms are poorly understood. We hypothesize that C. pneumoniae infection favors the recruitment of monocytes to atherosclerotic foci by altering monocyte biophysics. Primary, fresh human monocytes were infected with C. pneumoniae for 8 h, and the interactions between monocytes and E-selectin or aortic endothelium under flow were characterized by video microscopy and image analysis. The distribution of membrane lipid rafts and adhesion receptors were analyzed by imaging flow cytometry. Infected cells rolled on E-selectin and endothelial surfaces, and this rolling was slower, steady and uniform compared to uninfected cells. Infection decreases cholesterol levels, increases membrane fluidity, disrupts lipid rafts, and redistributes CD44, which is the primary mediator of rolling interactions. Together, these changes translate to higher firm adhesion of infected monocytes on endothelium, which is enhanced in the presence of LDL. Uninfected monocytes treated with LDL or left untreated were used as baseline control. Our results demonstrate that the membrane biophysical changes due to infection and hyperlipidemia are one of the key mechanisms by which C. pneumoniae can exacerbate atherosclerotic pathology. These findings provide a framework to characterize the role of ‘infectious burden’ in the development and progression of atherosclerosis.

  19. NS3 Protease from Hepatitis C Virus: Biophysical Studies on an Intrinsically Disordered Protein Domain

    Directory of Open Access Journals (Sweden)

    Adrian Velazquez-Campoy

    2013-06-01

    Full Text Available The nonstructural protein 3 (NS3 from the hepatitis C virus (HCV is responsible for processing the non-structural region of the viral precursor polyprotein in infected hepatic cells. NS3 protease activity, located at the N-terminal domain, is a zinc-dependent serine protease. A zinc ion, required for the hydrolytic activity, has been considered as a structural metal ion essential for the structural integrity of the protein. In addition, NS3 interacts with another cofactor, NS4A, an accessory viral protein that induces a conformational change enhancing the hydrolytic activity. Biophysical studies on the isolated protease domain, whose behavior is similar to that of the full-length protein (e.g., catalytic activity, allosteric mechanism and susceptibility to inhibitors, suggest that a considerable global conformational change in the protein is coupled to zinc binding. Zinc binding to NS3 protease can be considered as a folding event, an extreme case of induced-fit binding. Therefore, NS3 protease is an intrinsically (partially disordered protein with a complex conformational landscape due to its inherent plasticity and to the interaction with its different effectors. Here we summarize the results from a detailed biophysical characterization of this enzyme and present new experimental data.

  20. ‘The physics of life,’ an undergraduate general education biophysics course

    Science.gov (United States)

    Parthasarathy, Raghuveer

    2015-05-01

    Improving the scientific literacy of non-scientists is an important aim, both because of the ever-increasing impact of science on our lives and because understanding science enriches our experience of the natural world. One route to improving scientific literacy is via general education undergraduate courses—i.e. courses for students not majoring in the sciences or engineering. Because it encompasses a variety of important scientific concepts, demonstrates connections between basic science and real-world applications and illustrates the creative ways in which scientific insights develop, biophysics is a useful subject with which to promote scientific literacy. I describe here a course on biophysics for non-science-major undergraduates recently developed at the University of Oregon (Eugene, OR, USA), noting its design, which spans both macroscopic and microscopic topics, and the specific content of a few of its modules. I also describe evidence-based pedagogical approaches adopted in teaching the course and aspects of course enrollment and evaluation.

  1. Synergistic linkage between remote sensing and biophysical models for estimating plant ecophysiological and ecosystem processes

    International Nuclear Information System (INIS)

    Abstract Information on the ecological and physiological status of crops is essential for growth diagnostics and yield prediction. Within-field or between-field spatial information is required, especially with the recent trend toward precision agriculture, which seeks the efficient use of agrochemicals, water, and energy. The study of carbon and nitrogen cycles as well as environmental management on local and regional scales requires assessment of the spatial variability of biophysical and ecophysiological variables, scaling up of which is also needed for scientific and decision-making purposes. Remote sensing has great potential for these applications because it enables wide-area non-destructive, and real-time acquisition of information about ecophysiological conditions of vegetation. With recent advances in sensor technology, a variety of electromagnetic signatures, such as hyperspectral reflectance, thermal-infrared temperature, and microwave backscattering coefficients, can be acquired for both plants and ecosystems using ground-based, airborne, and satellite platforms. Their spatial and temporal resolutions have both recently been improved. This article reviews the state of the art in the remote sensing of plant ecophysiological data, with special emphasis on the synergy between remote sensing signatures and biophysical and ecophysiological process models. Several case studies for the optical, thermal, and microwave domains have demonstrated the potential of this synergistic linkage. Remote sensing and process modeling methods complement each other when combined synergistically. Further research on this approach is needed f or a wide range of ecophysiological and ecosystem studies, as well as for practical crop management

  2. Biophysical and biochemical constraints imposed by salt stress:Learning from halophyte

    Directory of Open Access Journals (Sweden)

    Bernardo eDuarte

    2014-12-01

    Full Text Available Soil salinization is one of the most important factors impacting plant productivity. About 3.6 billion of the world’s 5.2 billion ha of agricultural dryland have already suffered erosion, degradation and salinization. Halophytes typically are considered as plants able to complete their life cycle in environments where the salt concentration is 200 mM NaCl or higher. Different strategies are known to overcome salt stress, as adaptation mechanisms from this type of plants. Salinity adjustment is a complex phenomenon characterized by both biochemical and biophysical adaptations. As photosynthesis is a prerequisite for biomass production, halophytes adapted their electronic transduction pathways and the entire energetic metabolism to overcome the salt excess. The maintenance of ionic homeostasis is in the basis of all cellular stress in particular in terms of redox potential and energy transduction. In the present work the biophysical mechanisms underlying energy capture and transduction in halophytes are discussed alongside with their relation to biochemical mechanisms, integrating data from photosystem light harvesting complexes, electronic transport chains to the quinone pools, carbon harvesting and energy dissipation metabolism.

  3. Market research on garment-based "wearables" and biophysical monitoring and a new monitoring method.

    Science.gov (United States)

    Schultze, Claudia; Burr, Stacey

    2004-01-01

    Technology advancements are foremost on the minds of scientists and developers who are working to overcome the many hurdles associated with bringing consumers the enhanced benefits associated with next generation wearable health systems. Often the technology work takes a front seat to the basic requirements of traditional consumer apparel. The choices of what consumers elect to place and carry on their body can be practical, logical, emotional and sometimes seemingly random. By providing insights and data to support the claims, developers of wearable health systems of the future will be able improve their chance of consumer adoption and continued use by gaining a clearer picture of the people that will be wearing the systems. Results from 5 different consumer research studies are presented, examining consumer buying patterns, gender differences, regional differences, their receptivity to health benefits delivered via clothing and what they want from technology enhanced clothing. Market research related to biophysical monitoring utilizing smart fabrics or interactive textiles show a critical level of commercial activity. Medical applications focused on the aged, infant and critical patient care are taking the lead. This paper presents a look at the biophysical monitoring market and discusses new materials useful in garment systems and the challenges remaining for their development and integration with textiles. A new method of non-invasive monitoring of periodic activity is discussed. PMID:15718637

  4. Simulation of Tillage Systems Impact on Soil Biophysical Properties Using the SALUS Model

    Directory of Open Access Journals (Sweden)

    Luigi Sartori

    2011-02-01

    Full Text Available A sustainable land management has been defined as the management system that allows for production, while minimizing risk, maintaining quality of soil and water. Tillage systems can significantly decrease soil carbon storage and influence the soil environment of a crop. Crop growth models can be useful tools in evaluating the impact of different tillage systems on soil biophysical properties and on the growth and final yield of the crops. The objectives of this paper were i to illustrate the SALUS model and its tillage component; ii to evaluate the effects of different tillage systems on water infiltration and time to ponding, iii to simulate the effect of tillage systems on some soil biophysical properties. The SALUS (System Approach to Land Use Sustainability model is designed to simulate continuous crop, soil, water and nutrient conditions under different tillage and crop residues management strategies for multiple years. Predictions of changes in surface residue, bulk density, runoff, drainage and evaporation were consistent with expected behaviours of these parameters as described in the literature. The experiment to estimate the time to ponding curve under different tillage system confirmed the theory and showed the beneficial effects of the residue on soil surface with respect to water infiltration. It also showed that the no-tillage system is a more appropriate system to adopt in areas characterized by high intensity rainfall.

  5. Geostatistical regularization of inverse models for the retrieval of vegetation biophysical variables

    Science.gov (United States)

    Atzberger, C.; Richter, K.

    2009-09-01

    The robust and accurate retrieval of vegetation biophysical variables using radiative transfer models (RTM) is seriously hampered by the ill-posedness of the inverse problem. With this research we further develop our previously published (object-based) inversion approach [Atzberger (2004)]. The object-based RTM inversion takes advantage of the geostatistical fact that the biophysical characteristics of nearby pixel are generally more similar than those at a larger distance. A two-step inversion based on PROSPECT+SAIL generated look-up-tables is presented that can be easily implemented and adapted to other radiative transfer models. The approach takes into account the spectral signatures of neighboring pixel and optimizes a common value of the average leaf angle (ALA) for all pixel of a given image object, such as an agricultural field. Using a large set of leaf area index (LAI) measurements (n = 58) acquired over six different crops of the Barrax test site, Spain), we demonstrate that the proposed geostatistical regularization yields in most cases more accurate and spatially consistent results compared to the traditional (pixel-based) inversion. Pros and cons of the approach are discussed and possible future extensions presented.

  6. Non-invasive tools for measuring metabolism and biophysical analyte transport: self-referencing physiological sensing.

    Science.gov (United States)

    McLamore, Eric S; Porterfield, D Marshall

    2011-11-01

    Biophysical phenomena related to cellular biochemistry and transport are spatially and temporally dynamic, and are directly involved in the regulation of physiology at the sub-cellular to tissue spatial scale. Real time monitoring of transmembrane transport provides information about the physiology and viability of cells, tissues, and organisms. Combining information learned from real time transport studies with genomics and proteomics allows us to better understand the functional and mechanistic aspects of cellular and sub-cellular systems. To accomplish this, ultrasensitive sensing technologies are required to probe this functional realm of biological systems with high temporal and spatial resolution. In addition to ongoing research aimed at developing new and enhanced sensors (e.g., increased sensitivity, enhanced analyte selectivity, reduced response time, and novel microfabrication approaches), work over the last few decades has advanced sensor utility through new sensing modalities that extend and enhance the data recorded by sensors. A microsensor technique based on phase sensitive detection of real time biophysical transport is reviewed here. The self-referencing technique converts non-invasive extracellular concentration sensors into dynamic flux sensors for measuring transport from the membrane to the tissue scale. In this tutorial review, we discuss the use of self-referencing micro/nanosensors for measuring physiological activity of living cells/tissues in agricultural, environmental, and biomedical applications comprehensible to any scientist/engineer. PMID:21761069

  7. Extraction of Mangrove Biophysical Parameters Using Airborne LiDAR

    Directory of Open Access Journals (Sweden)

    Poonsak Miphokasap

    2013-04-01

    Full Text Available Tree parameter determinations using airborne Light Detection and Ranging (LiDAR have been conducted in many forest types, including coniferous, boreal, and deciduous. However, there are only a few scientific articles discussing the application of LiDAR to mangrove biophysical parameter extraction at an individual tree level. The main objective of this study was to investigate the potential of using LiDAR data to estimate the biophysical parameters of mangrove trees at an individual tree scale. The Variable Window Filtering (VWF and Inverse Watershed Segmentation (IWS methods were investigated by comparing their performance in individual tree detection and in deriving tree position, crown diameter, and tree height using the LiDAR-derived Canopy Height Model (CHM. The results demonstrated that each method performed well in mangrove forests with a low percentage of crown overlap conditions. The VWF method yielded a slightly higher accuracy for mangrove parameter extractions from LiDAR data compared with the IWS method. This is because the VWF method uses an adaptive circular filtering window size based on an allometric relationship. As a result of the VWF method, the position measurements of individual tree indicated a mean distance error value of 1.10 m. The individual tree detection showed a kappa coefficient of agreement (K value of 0.78. The estimation of crown diameter produced a coefficient of determination (R2 value of 0.75, a Root Mean Square Error of the Estimate (RMSE value of 1.65 m, and a Relative Error (RE value of 19.7%. Tree height determination from LiDAR yielded an R2 value of 0.80, an RMSE value of 1.42 m, and an RE value of 19.2%. However, there are some limitations in the mangrove parameters derived from LiDAR. The results indicated that an increase in the percentage of crown overlap (COL results in an accuracy decrease of the mangrove parameters extracted from the LiDAR-derived CHM, particularly for crown measurements. In this

  8. Evaluation of the biophysical limitations on photosynthesis of four varietals of Brassica rapa

    Science.gov (United States)

    Pleban, J. R.; Mackay, D. S.; Aston, T.; Ewers, B.; Weinig, C.

    2014-12-01

    Evaluating performance of agricultural varietals can support the identification of genotypes that will increase yield and can inform management practices. The biophysical limitations of photosynthesis are amongst the key factors that necessitate evaluation. This study evaluated how four biophysical limitations on photosynthesis, stomatal response to vapor pressure deficit, maximum carboxylation rate by Rubisco (Ac), rate of photosynthetic electron transport (Aj) and triose phosphate use (At) vary between four Brassica rapa genotypes. Leaf gas exchange data was used in an ecophysiological process model to conduct this evaluation. The Terrestrial Regional Ecosystem Exchange Simulator (TREES) integrates the carbon uptake and utilization rate limiting factors for plant growth. A Bayesian framework integrated in TREES here used net A as the target to estimate the four limiting factors for each genotype. As a first step the Bayesian framework was used for outlier detection, with data points outside the 95% confidence interval of model estimation eliminated. Next parameter estimation facilitated the evaluation of how the limiting factors on A different between genotypes. Parameters evaluated included maximum carboxylation rate (Vcmax), quantum yield (ϕJ), the ratio between Vc-max and electron transport rate (J), and trios phosphate utilization (TPU). Finally, as trios phosphate utilization has been shown to not play major role in the limiting A in many plants, the inclusion of At in models was evaluated using deviance information criteria (DIC). The outlier detection resulted in a narrowing in the estimated parameter distributions allowing for greater differentiation of genotypes. Results show genotypes vary in the how limitations shape assimilation. The range in Vc-max , a key parameter in Ac, was 203.2 - 223.9 umol m-2 s-1 while the range in ϕJ, a key parameter in AJ, was 0.463 - 0.497 umol m-2 s-1. The added complexity of the TPU limitation did not improve model

  9. Abstracts of the 9. Brazilian Congress of Biophysics, 2. Brazilian Congress of Pharmacology and Experimental Therapeutics and 19. Brazilian Congress of Physiology

    International Nuclear Information System (INIS)

    Abstracts about biophysics, pharmacology, experimental therapeutics and physiology are presented. The use of radioisotopes in radioassays involve topics like biophysics and renal physiology; central nervous system; endocrinology; animal and comparative physiology; general physiology, digestion and nutrition; general pharmacology. (M.A.C.)

  10. Exploring the biophysical option space for feeding the world without deforestation.

    Science.gov (United States)

    Erb, Karl-Heinz; Lauk, Christian; Kastner, Thomas; Mayer, Andreas; Theurl, Michaela C; Haberl, Helmut

    2016-01-01

    Safeguarding the world's remaining forests is a high-priority goal. We assess the biophysical option space for feeding the world in 2050 in a hypothetical zero-deforestation world. We systematically combine realistic assumptions on future yields, agricultural areas, livestock feed and human diets. For each scenario, we determine whether the supply of crop products meets the demand and whether the grazing intensity stays within plausible limits. We find that many options exist to meet the global food supply in 2050 without deforestation, even at low crop-yield levels. Within the option space, individual scenarios differ greatly in terms of biomass harvest, cropland demand and grazing intensity, depending primarily on the quantitative and qualitative aspects of human diets. Grazing constraints strongly limit the option space. Without the option to encroach into natural or semi-natural land, trade volumes will rise in scenarios with globally converging diets, thereby decreasing the food self-sufficiency of many developing regions. PMID:27092437

  11. Biophysical methods for assessing the radiation dose causing lesions in the skin and subcutaneous tissues

    International Nuclear Information System (INIS)

    Two main questions have to be solved from the clinical point of view: can irradiated tissues be distinguished from non-irradiated tissues and how conservative should be the surgery on those tissues which may be expected to proceed to late necrosis. The purpose of this paper is to show how a few new biophysical methods can help to answer these questions. With regard to early diagnosis, infra-red thermography for superficial damage, and X-ray computed tomography and magnetic resonance imaging, for lesions at a depth, are presently the most valuable methods. Vascular scintigraphy and microwave thermography can help with the diagnosis and provide a valuable contribution to prognosis. The earlier these methods are used, the better. (author)

  12. Construction of force measuring optical tweezers instrumentation and investigations of biophysical properties of bacterial adhesion organelles

    CERN Document Server

    Andersson, Magnus

    2015-01-01

    Optical tweezers are a technique in which microscopic-sized particles, including living cells and bacteria, can be non-intrusively trapped with high accuracy solely using focused light. The technique has therefore become a powerful tool in the field of biophysics. Optical tweezers thereby provide outstanding manipulation possibilities of cells as well as semi-transparent materials, both non-invasively and non-destructively, in biological systems. In addition, optical tweezers can measure minute forces (< 10-12 N), probe molecular interactions and their energy landscapes, and apply both static and dynamic forces in biological systems in a controlled manner. The assessment of intermolecular forces with force measuring optical tweezers, and thereby the biomechanical structure of biological objects, has therefore considerably facilitated our understanding of interactions and structures of biological systems. Adhesive bacterial organelles, so called pili, mediate adhesion to host cells and are therefore crucial...

  13. Simple biophysics underpins collective conformations of the intrinsically disordered proteins of the Nuclear Pore Complex.

    Science.gov (United States)

    Vovk, Andrei; Gu, Chad; Opferman, Michael G; Kapinos, Larisa E; Lim, Roderick Yh; Coalson, Rob D; Jasnow, David; Zilman, Anton

    2016-01-01

    Nuclear Pore Complexes (NPCs) are key cellular transporter that control nucleocytoplasmic transport in eukaryotic cells, but its transport mechanism is still not understood. The centerpiece of NPC transport is the assembly of intrinsically disordered polypeptides, known as FG nucleoporins, lining its passageway. Their conformations and collective dynamics during transport are difficult to assess in vivo. In vitro investigations provide partially conflicting results, lending support to different models of transport, which invoke various conformational transitions of the FG nucleoporins induced by the cargo-carrying transport proteins. We show that the spatial organization of FG nucleoporin assemblies with the transport proteins can be understood within a first principles biophysical model with a minimal number of key physical variables, such as the average protein interaction strengths and spatial densities. These results address some of the outstanding controversies and suggest how molecularly divergent NPCs in different species can perform essentially the same function. PMID:27198189

  14. Retrieval of canopy biophysical variables from remote sensing data using contextual information

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    In order to improve the accuracy of biophysical parameters retrieved from remotely sensing data,a new algorithm was presented by using spatial contextual to estimate canopy variables from high-resolution remote sensing images.The developed algorithm was used for inversion of leaf area index (LAI) from Enhanced Thematic Mapper Plus (ETM+) data by combining with optimization method to minimize cost functions.The results show that the distribution of LAI is spatially consistent with the false composition imagery from ETM+ and the accuracy of LAI is significantly improved over the results retrieved by the conventional pixelwise retrieval methods,demonstrating that this method can be reliably used to integrate spatial contextual information for inverting LAI from high-resolution remote sensing images.

  15. 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. PMID:24525076

  16. Computer Simulation and Data Analysis in Molecular Biology and Biophysics An Introduction Using R

    CERN Document Server

    Bloomfield, Victor

    2009-01-01

    This book provides an introduction, suitable for advanced undergraduates and beginning graduate students, to two important aspects of molecular biology and biophysics: computer simulation and data analysis. It introduces tools to enable readers to learn and use fundamental methods for constructing quantitative models of biological mechanisms, both deterministic and with some elements of randomness, including complex reaction equilibria and kinetics, population models, and regulation of metabolism and development; to understand how concepts of probability can help in explaining important features of DNA sequences; and to apply a useful set of statistical methods to analysis of experimental data from spectroscopic, genomic, and proteomic sources. These quantitative tools are implemented using the free, open source software program R. R provides an excellent environment for general numerical and statistical computing and graphics, with capabilities similar to Matlab®. Since R is increasingly used in bioinformat...

  17. Validation of Global EO Biophysical Products at JECAM Test Site in Ukraine

    Science.gov (United States)

    Skakun, Sergii; Kussul, Nataliia; Kravchenko, Oleksiy; Basarab, Ruslan; Ostapenko, Vadym; Yailymov, Bohdan; Shelestov, Andrii; Kolotii, Andrii; Mironov, Andrii

    Efficient global agriculture monitoring requires appropriate validation of Earth observation (EO) products for different regions and cropping system. This problem is addressed within the Joint Experiment of Crop Assessment and Monitoring (JECAM) initiative which aims to develop monitoring and reporting protocols and best practices for a variety of global agricultural systems. Ukraine is actively involved into JECAM, and a JECAM Ukraine test site was officially established in 2011. The following problems are being solved within JECAM Ukraine: (i) crop identification and crop area estimation [1]; (ii) crop yield forecasting [2]; (iii) EO products validation. The following case study regions were selected for these purposes: (i) the whole Kyiv oblast (28,000 sq. km) indented for crop mapping and acreage estimation; (ii) intensive observation sub-site in Pshenichne which is a research farm from the National University of Life and Environmental Sciences of Ukraine and indented for crop biophysical parameters estimation; (iii) Lviv region for rape-seed identification and crop rotation control; (iv) Crimea region for crop damage assessment due to droughts, and illegial field detection. In 2013, Ukrainian JECAM test site was selected as one of the “Champion User” for the ESA Sentinel-2 for Agriculture project. The test site was observed with SPOT-4 and RapidEye satellites every 5 days. The collected images are then used to simulate Sentinel-2 images for agriculture purposes. JECAM Ukraine is responsible for collecting ground observation data for validation purposes, and is involved in providing user requirements for Sentinel-2 agriculture related products. In particular, three field campaigns to characterize the vegetation biophysical parameters at the Pshenichne test site were carried out: First campaign - 14th to 17th of May 2013; second campaign - 12th to 15th of June 2013; third campaign - 14th to 17th of July 2013. Digital Hemispheric Photographs (DHP) images were

  18. Biophysical and biological factors determining the ability to achieve long-term cryobiological preservation

    Energy Technology Data Exchange (ETDEWEB)

    Mazur, P. [Oak Ridge National Lab., TN (United States). Life Sciences Div.

    1997-12-01

    The BESTCapsule will maintain appropriate biological specimens for decades or centuries at cryogenic temperatures in the living state. Maintenance at temperatures below {approximately} {minus}140 C is not a problem. No ordinary chemical reactions in aqueous solutions can occur. The only source of damage will be the slow accumulation of physical damage to DNA from background ionizing radiation. But this source of damage should not become serious in less than a millennium. Rather, the main problem in cryopreservation is to devise procedures for cooling the biological specimens to {minus}196 C and returning them to normal temperatures without inflicting lethal injury. Regardless of the cell type, there are certain encompassing biophysical factors and constraints that determine whether they will survive or die during freezing and thawing. Superimposed on these may be special biological factors that apply to specific cell types. This paper will emphasize the former and give illustrative examples of the latter.

  19. THE INFLUENCE OF THE NUTRITIONAL FACTORS ON SOME BIOPHYSICAL PARAMETERS OF THE RUMINAL FLUID

    Directory of Open Access Journals (Sweden)

    IULIANA CREłESCU

    2013-12-01

    Full Text Available At this hour, a large part of the products obtained through biotechnologies are used in animal fodder, thus contributing to the enhancement of the animal products obtained in economical conditions through optimising the nutrition. In the present study, we wanted to pursue the influence of a high level of cereal in fodder rations, as well as the effect of the yeast Saccharomyces cerevisiae, Yea Sacc1026 strain on some biophysical parameters of the ruminal fluid, such as: pH, density and superficial tension. It has been noted, that Yea Sacc1026 improves the pH and the superficial tension, which represents more stable ruminal fermentation when using fodder rations with a high level of barley.

  20. LMS Moodle in teaching biophysics and medical informatics at Faculty of Medicine, University of Ostrava

    Directory of Open Access Journals (Sweden)

    Hana Sochorová

    2013-12-01

    Full Text Available The paper deals with the assessment of the current state of use of LMS Moodle for teaching medical biophysics and informatics for students of the Faculty of Medicine, the University of Ostrava. The initial experience with the implementation of blended learning methods (combination of distance and full-time instruction in teaching students in the part-time form of study were used for education and for full-time students. A few survey questions given to first-year students, which are presented in the paper, confirm that this is a move in the positive direction. A well-structured e-learning course and experienced teachers support student´s attention, motivation and results in achieving educational goals.

  1. Chemical and Biophysical Modulation of Cas9 for Tunable Genome Engineering.

    Science.gov (United States)

    Nuñez, James K; Harrington, Lucas B; Doudna, Jennifer A

    2016-03-18

    The application of the CRISPR-Cas9 system for genome engineering has revolutionized the ability to interrogate genomes of mammalian cells. Programming the Cas9 endonuclease to induce DNA breaks at specified sites is achieved by simply modifying the sequence of its cognate guide RNA. Although Cas9-mediated genome editing has been shown to be highly specific, cleavage events at off-target sites have also been reported. Minimizing, and eventually abolishing, unwanted off-target cleavage remains a major goal of the CRISPR-Cas9 technology before its implementation for therapeutic use. Recent efforts have turned to chemical biology and biophysical approaches to engineer inducible genome editing systems for controlling Cas9 activity at the transcriptional and protein levels. Here, we review recent advancements to modulate Cas9-mediated genome editing by engineering split-Cas9 constructs, inteins, small molecules, protein-based dimerizing domains, and light-inducible systems. PMID:26857072

  2. The Physics of Proteins An Introduction to Biological Physics and Molecular Biophysics

    CERN Document Server

    Frauenfelder, Hans; Chan, Winnie S

    2010-01-01

    Physics and the life sciences have established new connections within the past few decades, resulting in biological physics as an established subfield with strong groups working in many physics departments. These interactions between physics and biology form a two-way street with physics providing new tools and concepts for understanding life, while biological systems can yield new insights into the physics of complex systems. To address the challenges of this interdisciplinary area, The Physics of Proteins: An Introduction to Biological Physics and Molecular Biophysics is divided into three interconnected sections. In Parts I and II, early chapters introduce the terminology and describe the main biological systems that physicists will encounter. Similarities between biomolecules, glasses, and solids are stressed with an emphasis on the fundamental concepts of living systems. The central section (Parts III and IV) delves into the dynamics of complex systems. A main theme is the realization that biological sys...

  3. The biophysical and biochemical properties of the autoimmune regulator (AIRE) protein.

    Science.gov (United States)

    Perniola, Roberto; Musco, Giovanna

    2014-02-01

    AIRE (for autoimmune regulator) is a multidomain protein that performs a fundamental function in the thymus and possibly in the secondary lymphoid organs: the regulation, especially in the sense of activation, of the process of gene transcription in cell lines deputed to the presentation of self-antigens to the maturing T lymphocytes. The apoptosis of the elements bearing T-cell receptors with critical affinity for the exhibited self-antigens prevents the escape of autoreactive clones and represents a simple and efficient mechanism of deletional self-tolerance. However, AIRE action relies on an articulated complex of biophysical and biochemical properties, in most cases attributable to single subspecialized domains. Here a thorough review of the matter is presented, with a privileged look at the pathogenic changes of AIRE that interfere with such properties and lead to the impairment in its chief function. PMID:24275490

  4. Diffusion-weighted MRI and quantitative biophysical modeling of hippocampal neurite loss in chronic stress.

    Directory of Open Access Journals (Sweden)

    Peter Vestergaard-Poulsen

    Full Text Available Chronic stress has detrimental effects on physiology, learning and memory and is involved in the development of anxiety and depressive disorders. Besides changes in synaptic formation and neurogenesis, chronic stress also induces dendritic remodeling in the hippocampus, amygdala and the prefrontal cortex. Investigations of dendritic remodeling during development and treatment of stress are currently limited by the invasive nature of histological and stereological methods. Here we show that high field diffusion-weighted MRI combined with quantitative biophysical modeling of the hippocampal dendritic loss in 21 day restraint stressed rats highly correlates with former histological findings. Our study strongly indicates that diffusion-weighted MRI is sensitive to regional dendritic loss and thus a promising candidate for non-invasive studies of dendritic plasticity in chronic stress and stress-related disorders.

  5. 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 ...... 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....... 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 into these...

  6. Quantification of Dance Movement by Simultaneous Measurement of Body Motion and Biophysical Information

    Institute of Scientific and Technical Information of China (English)

    Woong Choi; Tadao Isaka; Mamiko Sakata; Seiya Tsuruta; Kozaburo Hachimura

    2007-01-01

    The purpose of this research is a quantitative analysis of movement patterns of dance, which cannot be analyzed with a motion capture system alone, using simultaneous measurement of body motion and biophysical information. In this research, two kinds of same leg movement are captured by simultaneous measurement; one is a leg movement with given strength, the other is a leg movement without strength on condition of basic experiment using optical motion capture and electromyography (EMG) equipment in order to quantitatively analyze characteristics of leg movement. Also, we measured the motion of the traditional Japanese dance using the constructed system. We can visualize leg movement of Japanese dance by displaying a 3D CG character animation with motion data and EMG data. In addition, we expect that our research will help dancers and researchers on dance through giving new information on dance movement which cannot be analyzed with only motion capture.

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

    CERN Document Server

    Williams, Mark C

    2011-01-01

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

  8. Scaling properties of evolutionary paths in a biophysical model of protein adaptation

    Science.gov (United States)

    Manhart, Michael; Morozov, Alexandre V.

    2015-07-01

    The enormous size and complexity of genotypic sequence space frequently requires consideration of coarse-grained sequences in empirical models. We develop scaling relations to quantify the effect of this coarse-graining on properties of fitness landscapes and evolutionary paths. We first consider evolution on a simple Mount Fuji fitness landscape, focusing on how the length and predictability of evolutionary paths scale with the coarse-grained sequence length and alphabet. We obtain simple scaling relations for both the weak- and strong-selection limits, with a non-trivial crossover regime at intermediate selection strengths. We apply these results to evolution on a biophysical fitness landscape that describes how proteins evolve new binding interactions while maintaining their folding stability. We combine the scaling relations with numerical calculations for coarse-grained protein sequences to obtain quantitative properties of the model for realistic binding interfaces and a full amino acid alphabet.

  9. Modern nuclear medicine methods as a topic of biophysics in veterinary training at UVM in Kosice

    International Nuclear Information System (INIS)

    Diagnostic and therapeutic application of ionising radiation is very important in all of branches of medicine including veterinary medicine. In veterinary training at University of Veterinary Medicine in Kosice (UVM), biophysics is a basic subject and it grants physical basis necessary for understanding subsequent subjects such as veterinary surgery, roentgenology, orthopedics. In view of this, traditional methods of radiology such as fluoroscopy, skiagraphy and tomography are explaining. The appearance and application of the theory so called reconstruction of image and also computers led to qualitatively new solutions via the development of modern methods in radiology. Explaining of physical principles, advantages or disadvantages of these new methods is also important in veterinary training although some of them do not use in veterinary practice yet. Two modern methods of nuclear medicine using in diagnostic (SPECT and PET) are discussed bellow. (authors)

  10. A biophysical signature of network affiliation and sensory processing in mitral cells

    DEFF Research Database (Denmark)

    Angelo, Kamilla; Rancz, Ede A; Pimentel, Diogo;

    2012-01-01

    One defining characteristic of the mammalian brain is its neuronal diversity. For a given region, substructure, layer or even cell type, variability in neuronal morphology and connectivity persists. Although it is well known that such cellular properties vary considerably according to neuronal type......, the substantial biophysical diversity of neurons of the same morphological class is typically averaged out and ignored. Here we show that the amplitude of hyperpolarization-evoked sag of membrane potential recorded in olfactory bulb mitral cells is an emergent, homotypic property of local networks and sensory...... receptor is universally expressed. Population diversity in this intrinsic property therefore reflects differential expression between local mitral cell networks processing distinct odour-related information....

  11. Summaries of research projects for fiscal years 1996 and 1997, medical applications and biophysical research

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-02-01

    The Medical Applications and Biophysical Research Division of the Office of Biological and Environmental Research supports and manages research in several distinct areas of science and technology. The projects described in this book are grouped by the main budgetary areas: General Life Sciences (structural molecular biology), Medical Applications (primarily nuclear medicine) and Measurement Science (analytical chemistry instrumentation), Environmental Management Science Program, and the Small Business Innovation Research Program. The research funded by this division complements that of the other two divisions in the Office of Biological and Environmental Research (OBER): Health Effects and Life Sciences Research, and Environmental Sciences. Most of the OBER programs are planned and administered jointly by the staff of two or all three of the divisions. This summary book provides information on research supported in these program areas during Fiscal Years 1996 and 1997.

  12. Bioabsorbable Bypass Grafts Biofunctionalised with RGD Have Enhanced Biophysical Properties and Endothelialisation Tested In vivo.

    Science.gov (United States)

    Antonova, Larisa V; Seifalian, Alexander M; Kutikhin, Anton G; Sevostyanova, Victoria V; Krivkina, Evgeniya O; Mironov, Andrey V; Burago, Andrey Y; Velikanova, Elena A; Matveeva, Vera G; Glushkova, Tatiana V; Sergeeva, Evgeniya A; Vasyukov, Georgiy Y; Kudryavtseva, Yuliya A; Barbarash, Olga L; Barbarash, Leonid S

    2016-01-01

    Small diameter arterial bypass grafts are considered as unmet clinical need since the current grafts have poor patency of 25% within 5 years. We have developed a 3D scaffold manufactured from natural and synthetic biodegradable polymers, poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) and poly(-caprolactone) (PCL), respectively. Further to improve the biophysical properties as well as endothelialisation, the grafts were covalently conjugated with arginine-glycine-aspartic acid (RGD) bioactive peptides. The biophysical properties as well as endothelialisation of PHBV/PCL and PCL 2 mm diameter bypass grafts were assessed with and without biofunctionalisation with RGD peptides in vitro and in vivo. Morphology of the grafts was assessed by scanning electron microscopy, whereas physico-mechanical properties were evaluated using a physiological circulating system equipped with a state of art ultrasound vascular wall tracking system. Endothelialisation of the grafts in vitro and in vivo were assessed using a cell viability assay and rat abdominal aorta replacement model, respectively. The biofunctionalisation with RGD bioactive peptides decreased mean fiber diameter and mean pore area in PHBV/PCL grafts; however, this was not the case for PCL grafts. Both PHBV/PCL and PCL grafts with RGD peptides had lower durability compared to those without; these durability values were similar to those of internal mammary artery. Modification of PHBV/PCL and PCL grafts with RGD peptides increased endothelial cell viability in vitro by a factor of eight and enhanced the formation of an endothelial cell monolayer in vivo 1 month postimplantation. In conclusion, PHBV/PCL small-caliber graft can be a suitable 3D scaffold for the development of a tissue engineering arterial bypass graft. PMID:27252652

  13. Integrating socio-economic and biophysical data to enhance watershed management and planning

    Science.gov (United States)

    Pirani, Farshad Jalili; Mousavi, Seyed Alireza

    2016-09-01

    Sustainability has always been considered as one of the main aspects of watershed management plans. In many developing countries, watershed management practices and planning are usually performed by integrating biophysical layers, and other existing layers which cannot be identified as geographic layers are ignored. We introduce an approach to consider some socioeconomic parameters which are important for watershed management decisions. Ganj basin in Chaharmahal-Bakhtiari Province was selected as the case study area, which includes three traditional sanctums: Ganj, Shiremard and Gerdabe Olya. Socioeconomic data including net agricultural income, net ranching income, population and household number, literacy rate, unemployment rate, population growth rate and active population were mapped within traditional sanctums and then were integrated into other biophysical layers. After overlaying and processing these data to determine management units, different quantitative and qualitative approaches were adopted to achieve a practical framework for watershed management planning and relevant plans for homogeneous units were afterwards proposed. Comparing the results with current plans, the area of allocated lands to different proposed operations considering both qualitative and quantitative approaches were the same in many cases and there was a meaningful difference with current plans; e.g., 3820 ha of lands are currently managed under an enclosure plan, while qualitative and quantitative approaches in this study suggest 1388 and 1428 ha to be allocated to this operation type, respectively. Findings show that despite the ambiguities and complexities, different techniques could be adopted to incorporate socioeconomic conditions in watershed management plans. This introductory approach will help to enhance watershed management decisions with more attention to societal background and economic conditions, which will presumably motivate local communities to participate in

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

    International Nuclear Information System (INIS)

    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

  15. 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.

  16. Anthropogenic and biophysical contributions to increasing atmospheric CO2 growth rate and airborne fraction

    Directory of Open Access Journals (Sweden)

    C. Le Quéré

    2008-11-01

    Full Text Available We quantify the relative roles of natural and anthropogenic influences on the growth rate of atmospheric CO2 and the CO2 airborne fraction, considering both interdecadal trends and interannual variability. A combined ENSO-Volcanic Index (EVI relates most (~75% of the interannual variability in CO2 growth rate to the El-Niño-Southern-Oscillation (ENSO climate mode and volcanic activity. Analysis of several CO2 data sets with removal of the EVI-correlated component confirms a previous finding of a detectable increasing trend in CO2 airborne fraction (defined using total anthropogenic emissions including fossil fuels and land use change over the period 1959–2006, at a proportional growth rate 0.24% y−1 with probability ~0.9 of a positive trend. This implies that the atmospheric CO2 growth rate increased slightly faster than total anthropogenic CO2 emissions. To assess the combined roles of the biophysical and anthropogenic drivers of atmospheric CO2 growth, the increase in the CO2 growth rate (1.9% y−1 over 1959–2006 is expressed as the sum of the growth rates of four global driving factors: population (contributing +1.7% y−1; per capita income (+1.8% y−1; the total carbon intensity of the global economy (−1.7% y−1; and airborne fraction (averaging +0.2% y−1 with strong interannual variability. The first three of these factors, the anthropogenic drivers, have therefore dominated the last, biophysical driver as contributors to accelerating CO2 growth. Together, the recent (post-2000 increase in growth of per capita income and decline in the negative growth (improvement in the carbon intensity of the economy will drive a significant further acceleration in the CO2 growth rate over coming decades, unless these recent trends reverse.

  17. Across Space and Time: Social Responses to Large-Scale Biophysical Systems

    Science.gov (United States)

    Macmynowski, Dena P.

    2007-06-01

    The conceptual rubric of ecosystem management has been widely discussed and deliberated in conservation biology, environmental policy, and land/resource management. In this paper, I argue that two critical aspects of the ecosystem management concept require greater attention in policy and practice. First, although emphasis has been placed on the “space” of systems, the “time”—or rates of change—associated with biophysical and social systems has received much less consideration. Second, discussions of ecosystem management have often neglected the temporal disconnects between changes in biophysical systems and the response of social systems to management issues and challenges. The empirical basis of these points is a case study of the “Crown of the Continent Ecosystem,” an international transboundary area of the Rocky Mountains that surrounds Glacier National Park (USA) and Waterton Lakes National Park (Canada). This project assessed the experiences and perspectives of 1) middle- and upper-level government managers responsible for interjurisdictional cooperation, and 2) environmental nongovernment organizations with an international focus. I identify and describe 10 key challenges to increasing the extent and intensity of transboundary cooperation in land/resource management policy and practice. These issues are discussed in terms of their political, institutional, cultural, information-based, and perceptual elements. Analytic techniques include a combination of environmental history, semistructured interviews with 48 actors, and text analysis in a systematic qualitative framework. The central conclusion of this work is that the rates of response of human social systems must be better integrated with the rates of ecological change. This challenge is equal to or greater than the well-recognized need to adapt the spatial scale of human institutions to large-scale ecosystem processes and transboundary wildlife.

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

    Science.gov (United States)

    Melendy, Robert F.

    2015-12-01

    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.

  19. Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT

    International Nuclear Information System (INIS)

    Global multi-method analysis for protein interactions (GMMA) can increase the precision and complexity of binding studies for the determination of the stoichiometry, affinity and cooperativity of multi-site interactions. The principles and recent developments of biophysical solution methods implemented for GMMA in the software SEDPHAT are reviewed, their complementarity in GMMA is described and a new GMMA simulation tool set in SEDPHAT is presented. Reversible macromolecular interactions are ubiquitous in signal transduction pathways, often forming dynamic multi-protein complexes with three or more components. Multivalent binding and cooperativity in these complexes are often key motifs of their biological mechanisms. Traditional solution biophysical techniques for characterizing the binding and cooperativity are very limited in the number of states that can be resolved. A global multi-method analysis (GMMA) approach has recently been introduced that can leverage the strengths and the different observables of different techniques to improve the accuracy of the resulting binding parameters and to facilitate the study of multi-component systems and multi-site interactions. Here, GMMA is described in the software SEDPHAT for the analysis of data from isothermal titration calorimetry, surface plasmon resonance or other biosensing, analytical ultracentrifugation, fluorescence anisotropy and various other spectroscopic and thermodynamic techniques. The basic principles of these techniques are reviewed and recent advances in view of their particular strengths in the context of GMMA are described. Furthermore, a new feature in SEDPHAT is introduced for the simulation of multi-method data. In combination with specific statistical tools for GMMA in SEDPHAT, simulations can be a valuable step in the experimental design

  20. Biophysical Impacts of Tropical Land Transformation from Forest to Oil Palm and Rubber Plantations in Indonesia

    Science.gov (United States)

    Knohl, Alexander; Meijide, Ana; Fan, Yuanchao; Gunawan, Dodo; Hölscher, Dirk; June, Tania; Niu, Furong; Panferov, Oleg; Ringeler, Andre; Röll, Alexander; Sabajo, Clifton; Tiralla, Nina

    2016-04-01

    Indonesia currently experiences rapid and large-scale land-use changes resulting in forest loss and the expansion of cash crop plantations such as oil palm and rubber. Such land transformations are associated with changes in surface properties that affect biophysical processes influencing the atmosphere. Yet, the overall effect of such land transformations on the atmosphere at local and regional scale remains unclear. In our study, we combine measurements of microclimate, transpiration via sap-flux, surface energy fluxes via eddy covariance, surface temperature via remote sensing, land surface (CLM) and regional climate modeling (WRF) for Jambi Province in Indonesia. Our microclimatic measurements showed that air temperature within the canopy was on average 0.7-0.8°C higher in monoculture plantations (oil palm and rubber) compared to forest. Remote sensing analysis using MODIS and Landsat revealed a higher canopy surface temperature for oil palm plantations (+1.5°C) compared to forest, but only little differences for rubber plantations. Transpiration (T) and evapotranspiration (ET) as well as the contribution of T to ET of oil palm showed a strong age-dependent increase. The sensible to latent heat flux ratio decreased with age. Overall, rubber plantations showed the lowest transpirations rates (320 mm year-1), oil palm intermediate rates (414 mm year-1), and forest the highest rates (558 mm year-1) indicating substantial differences in water use. Despite the differences in water use and the higher within-canopy and surface temperatures of the plantations compared to the forest, there was only a minor effect of land transformation on the atmosphere at the regional scale (<0.2 °C), irrespectively of the large spatial extend of the transformation. In conclusion, our study shows a strong local scale biophysical impact affecting the conditions at the stand level, which is however mitigated in the atmosphere at the regional level.

  1. Micro-morphologic changes around biophysically-stimulated titanium implants in ovariectomized rats

    Directory of Open Access Journals (Sweden)

    Chang Ting-Ling

    2007-07-01

    Full Text Available Abstract Background Osteoporosis may present a risk factor in achievement of osseointegration because of its impact on bone remodeling properties of skeletal phsiology. The purpose of this study was to evaluate micro-morphological changes in bone around titanium implants exposed to mechanical and electrical-energy in osteoporotic rats. Methods Fifteen 12-week old sprague-dowley rats were ovariectomized to develop osteoporosis. After 8 weeks of healing period, two titanium implants were bilaterally placed in the proximal metaphyses of tibia. The animals were randomly divided into a control group and biophysically-stimulated two test groups with five animals in each group. In the first test group, a pulsed electromagnetic field (PEMF stimulation was administrated at a 0.2 mT 4 h/day, whereas the second group received low-magnitude high-frequency mechanical vibration (MECHVIB at 50 Hz 14 min/day. Following completion of two week treatment period, all animals were sacrificed. Bone sites including implants were sectioned, removed en bloc and analyzed using a microCT unit. Relative bone volume and bone micro-structural parameters were evaluated for 144 μm wide peri-implant volume of interest (VOI. Results Mean relative bone volume in the peri-implant VOI around implants PEMF and MECHVIB was significantly higher than of those in control (P P > .05 while the difference in trabecular-number among test and control groups was significant in all VOIs (P Conclusion Biophysical stimulation remarkably enhances bone volume around titanium implants placed in osteoporotic rats. Low-magnitude high-frequency MECHVIB is more effective than PEMF on bone healing in terms of relative bone volume.

  2. Colloquium: Biophysical principles of undulatory self-propulsion in granular media

    Science.gov (United States)

    Goldman, Daniel I.

    2014-07-01

    Biological locomotion, movement within environments through self-deformation, encompasses a range of time and length scales in an organism. These include the electrophysiology of the nervous system, the dynamics of muscle activation, the mechanics of the skeletal system, and the interaction mechanics of such structures within natural environments like water, air, sand, and mud. Unlike the many studies of cellular and molecular scale biophysical processes, movement of entire organisms (like flies, lizards, and snakes) is less explored. Further, while movement in fluids like air and water is also well studied, little is known in detail of the mechanics that organisms use to move on and within flowable terrestrial materials such as granular media, ensembles of small particles that collectively display solid, fluid, and gaslike behaviors. This Colloquium reviews recent progress to understand principles of biomechanics and granular physics responsible for locomotion of the sandfish, a small desert-dwelling lizard that "swims" within sand using undulation of its body. Kinematic and muscle activity measurements of sand swimming using high speed x-ray imaging and electromyography are discussed. This locomotion problem poses an interesting challenge: namely, that equations that govern the interaction of the lizard with its environment do not yet exist. Therefore, complementary modeling approaches are also described: resistive force theory for granular media, multiparticle simulation modeling, and robotic physical modeling. The models reproduce biomechanical and neuromechanical aspects of sand swimming and give insight into how effective locomotion arises from the coupling of the body movement and flow of the granular medium. The argument is given that biophysical study of movement provides exciting opportunities to investigate emergent aspects of living systems that might not depend sensitively on biological details.

  3. The biophysical property of A549 cells transferred by VEGF-D.

    Science.gov (United States)

    Wang, Zhen; Wu, Xiu-Li; Wang, Xu; Tian, Hong-Xia; Chen, Zhi-Hong; Li, Yang-Qiu

    2014-01-01

    Vascular endothelial growth factor-D (VEGF-D) together with VEGF-C is considered to be associated with lymphangiogenesis and angiogenesis and involve in tumorization. This study aims to investigate the influence of exogenous VEGF-D gene on the biophysical property of cell surface of lung adenocarcinoma cell line. A panel of lung adenocarcinoma cell lines were examined the expression of VEGF-D and VEGF-C by real-time PCR. The VEGF-D recombinant plasmid containing enhanced green fluorescence protein (EGFP) was constructed and transfected to the cell line with no expression of VEGF-D and confirmed by real-time PCR and Western blot analysis. Topographic images of cells were obtained by using atomic force microscope (AFM) in contact mode. Unlike VEGF-C, VEGF-D was found to have a very low expression or undetectable expression in lung adenocarcinoma cell lines. The VEGF-D recombinant plasmid had been constructed successfully and was transferred into the human lung adenocarcinoma cell line A549 cells which had no endogenous expression of VEGF-D, and exogenous VEGF-D could be detected in mRNA and protein expression levels in the gene modified cells, while the VEGF-C gene expression had no change after VEGF-D transfection. After transfection, the irregular microspikes or nano clusters could observe on the surface of A549 cells, and VEGF-D transfected A549 cells became more rigid. The exogenous VEGF-D gene might cause the remarkable biophysical architectural changes in the A549 cells, which might as a novel biomarker for evaluation of its biological function. PMID:23526563

  4. Impacts on the biophysical economy and environment of a transition to 100% renewable electricity in Australia

    International Nuclear Information System (INIS)

    We investigate the impacts on the biophysical economy, employment and environment of a transition scenario to an energy-efficient, 100% renewable electricity (RE) system by 2060, based on wind, solar and biomass technologies, and an introduction of electric vehicles. We employ a CSIRO process-based model of the physical activity of Australia’s economy and environmental resources, the Australian Stocks and Flows Framework. The RE systems are assumed to be manufactured in Australia to identify possible employment benefits. In comparison with the business-as-usual (BAU) scenario, on a national scale, the RE scenario has much lower economy-wide net emissions, remaining below contemporary levels and becoming zero in the electricity sector by 2060. Compared with BAU, the RE scenario also has significantly lower industrial water use, somewhat higher materials use, slightly lower unemployment, lower net foreign debt (relative to a GDP proxy) and, resulting from the growth in electric vehicles, reduced oil imports. The GDP per capita growth, based on the physical stocks of capital and labour, is virtually the same in both scenarios. Hence, from the viewpoint of the biophysical economy, there are no major barriers to implementing policies to facilitate the transition to a 100% renewable electricity system for Australia. - Highlights: ► Simulation of a 100% renewable electricity (RE) system in a process-based model. ► The RE scenario achieves zero GHG emissions in the electricity sector by 2060. ► Consumption of secondary materials is higher and more variable in the RE scenario. ► The RE scenario has lower water use, unemployment, foreign debt and oil imports

  5. Quantifying the thermal heat requirement of Brassica in assessing biophysical parameters under semi-arid microenvironments

    Science.gov (United States)

    Adak, Tarun; Chakravarty, N. V. K.

    2010-07-01

    Evaluation of the thermal heat requirement of Brassica spp. across agro-ecological regions is required in order to understand the further effects of climate change. Spatio-temporal changes in hydrothermal regimes are likely to affect the physiological growth pattern of the crop, which in turn will affect economic yields and crop quality. Such information is helpful in developing crop simulation models to describe the differential thermal regimes that prevail at different phenophases of the crop. Thus, the current lack of quantitative information on the thermal heat requirement of Brassica crops under debranched microenvironments prompted the present study, which set out to examine the response of biophysical parameters [leaf area index (LAI), dry biomass production, seed yield and oil content] to modified microenvironments. Following 2 years of field experiments on Typic Ustocrepts soils under semi-arid climatic conditions, it was concluded that the Brassica crop is significantly responsive to microenvironment modification. A highly significant and curvilinear relationship was observed between LAI and dry biomass production with accumulated heat units, with thermal accumulation explaining ≥80% of the variation in LAI and dry biomass production. It was further observed that the economic seed yield and oil content, which are a function of the prevailing weather conditions, were significantly responsive to the heat units accumulated from sowing to 50% physiological maturity. Linear regression analysis showed that growing degree days (GDD) could indicate 60-70% variation in seed yield and oil content, probably because of the significant response to differential thermal microenvironments. The present study illustrates the statistically strong and significant response of biophysical parameters of Brassica spp. to microenvironment modification in semi-arid regions of northern India.

  6. Testing the Simple Biosphere Model (SiB) Using Point Micrometeorological and Biophysical Data.

    Science.gov (United States)

    Sellers, P. J.; Dorman, J. L.

    1987-05-01

    The Simple Biosphere model (SiB) of Sellers et al. (1986) was designed for use within General Circulation Models (GCMs) of the earth's atmosphere. The main objective of SiB is to provide a biophysically realistic description of those processes which control the transfer of radiation, sensible heat, latent heat and momentum between the terrestrial surface and the atmosphere. As a result, SiB is more complex and has a larger input parameter set than most equivalent formulations used in GCMs. Prior to implementing SiB in a GCM, it is essential that its components and its functioning as a whole, be thoroughly tested. Additionally, it is highly desirable that the model's response to errors or uncertainties in the input parameter set be explored. This paper discusses investigations that were directed at addressing then two issues.Micrometeorological and biophysical measurements from surface experiments conducted over arable crops in West Germany and the United States and a forested site in the United Kingdom were used to test the operation of SiB. Observed values of the downward radiative fluxes, wind speed, air temperature and water vapor pressure recorded above the surface were used as the boundary forcing for the SiB model. The predicted partitioning of the absorbed radiation into the sensible and latent heat fluxes compares well with observations and the various subcomponents of the model appear to operate realistically. The sensitivity of the model's energy balance calculations to changes in the various model parameters and the soil moisture initialization is examined. It is estimated that the model will generate uncertainties of the order of ±7% in the calculated net radiation, and up to ±25% in the calculated evapotranspiration rate, with typical values of ±15%.

  7. Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Huaying, E-mail: zhaoh3@mail.nih.gov; Schuck, Peter, E-mail: zhaoh3@mail.nih.gov [National Institutes of Health, Bethesda, MD 20892 (United States)

    2015-01-01

    Global multi-method analysis for protein interactions (GMMA) can increase the precision and complexity of binding studies for the determination of the stoichiometry, affinity and cooperativity of multi-site interactions. The principles and recent developments of biophysical solution methods implemented for GMMA in the software SEDPHAT are reviewed, their complementarity in GMMA is described and a new GMMA simulation tool set in SEDPHAT is presented. Reversible macromolecular interactions are ubiquitous in signal transduction pathways, often forming dynamic multi-protein complexes with three or more components. Multivalent binding and cooperativity in these complexes are often key motifs of their biological mechanisms. Traditional solution biophysical techniques for characterizing the binding and cooperativity are very limited in the number of states that can be resolved. A global multi-method analysis (GMMA) approach has recently been introduced that can leverage the strengths and the different observables of different techniques to improve the accuracy of the resulting binding parameters and to facilitate the study of multi-component systems and multi-site interactions. Here, GMMA is described in the software SEDPHAT for the analysis of data from isothermal titration calorimetry, surface plasmon resonance or other biosensing, analytical ultracentrifugation, fluorescence anisotropy and various other spectroscopic and thermodynamic techniques. The basic principles of these techniques are reviewed and recent advances in view of their particular strengths in the context of GMMA are described. Furthermore, a new feature in SEDPHAT is introduced for the simulation of multi-method data. In combination with specific statistical tools for GMMA in SEDPHAT, simulations can be a valuable step in the experimental design.

  8. Radiation physics, biophysics, and radiation biology. Progress report, December 1, 1985-November 30, 1986

    International Nuclear Information System (INIS)

    This is the annual report of the Radiological Research Laboratory of the Department of Radiation Oncology, Columbia University. The bulk of the research of the Laboratory involves basic and fundamental aims, not confined to radiotherapy. Research carried out in the Laboratory covers the determination of microdosimetry quantities, computer simulation of particle tracks, determination of oncogenic transformation, and the transfection of DNA into cells. The Hallmark of the Laboratory is the interaction between physics and biology

  9. Biophysical characterization of the complex between human papillomavirus E6 protein and synapse-associated protein 97

    DEFF Research Database (Denmark)

    Chi, Celestine Ngang; Bach, Anders; Engström, Åke;

    2011-01-01

    The E6 protein of human papillomavirus exhibits complex interaction patterns with several host proteins and their roles in HPV mediated oncogenesis have proved challenging to study. Here we use several biophysical techniques to explore the binding of E6 to the three PDZ domains of the tumor suppr...

  10. Biogeochemical and biophysical climate regulation services from converting native grassland to bioenergy production in the US Midwest

    Science.gov (United States)

    Zhang, X.; Zhao, K.; Abraha, M.; Gelfand, I.; Izaurralde, R. C.; Thomson, A. M.; Hamilton, S. K.; Chen, J.; Robertson, P.; Xu, M.; Liang, X. Z.

    2015-12-01

    Land use conversion to bioenergy crops production not only alters biogeochemical cycles, but also modifies surface biophysics, such as albedo and and leaf area. These biophysical perturbations subsequently change radiation budget at land surface and land-atmosphere exchange in water and energy, and ultimately influence local/regional climate. Here, we combine long-term in situ field measurements, remote sensing observations, and regional earth system modeling to improve our understanding of changes in biophysical climate regulation services from converting native grassland to perennial bioenergy crops. In the US Midwest, albedo change as a result of cultivating native grassland for cellulosic bioenergy feedstocks could enhance the net greenhouse gases (GHGs) mitigation benefit of cellulosic bioenergy production (116.5 MgCO2 ha-1) by 20% over a time horizon of 50 years. With an integrated climate-agroecosystem model, parameterized with in situ and remote sensing data, we further demonstrate that cultivating native grassland may result in noticeable difference in simulated regional climate (e.g. precipitation, temperature, and radiation budget), highlighting the importance of additionally including biophysical climate services in evaluating land-based climate mitigation activities, such as bioenergy production.

  11. A Case Study of Cognitive and Biophysical Models of Education as Linked to Anxiety and Obsessive Compulsive Disorders

    Science.gov (United States)

    Maye, Kelly M.

    2012-01-01

    Cognitive and biophysical factors have been considered contributors linked to identifiable markers of obsessive compulsive and anxiety disorders. Research demonstrates multiple causes and mixed results for the short-term success of educational programs designed to ameliorate problems that children with obsessive compulsive and anxiety disorders…

  12. Forster Resonance Energy Transfer and Conformational Stability of Proteins: An Advanced Biophysical Module for Physical Chemistry Students

    Science.gov (United States)

    Sanchez, Katheryn M.; Schlamadinger, Diana E.; Gable, Jonathan E.; Kim, Judy E.

    2008-01-01

    Protein folding is an exploding area of research in biophysics and physical chemistry. Here, we describe the integration of several techniques, including absorption spectroscopy, fluorescence spectroscopy, and Forster resonance energy transfer (FRET) measurements, to probe important topics in protein folding. Cytochrome c is used as a model…

  13. NASA Space Radiation Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The NASA Space Radiation Laboratory (NSRL) at Brookhaven National Laboratory is a NASA funded facility, delivering heavy ion beams to a target area where scientists...

  14. Lincoln Laboratory Grid

    Data.gov (United States)

    Federal Laboratory Consortium — The Lincoln Laboratory Grid (LLGrid) is an interactive, on-demand parallel computing system that uses a large computing cluster to enable Laboratory researchers to...

  15. Synthesis and characterization of mixed-ligand diimine-piperonal thiosemicarbazone complexes of ruthenium(II): Biophysical investigations and biological evaluation as anticancer and antibacterial agents

    Science.gov (United States)

    Beckford, Floyd A.; Thessing, Jeffrey; Shaloski, Michael, Jr.; Canisius Mbarushimana, P.; Brock, Alyssa; Didion, Jacob; Woods, Jason; Gonzalez-Sarrías, Antonio; Seeram, Navindra P.

    2011-04-01

    We have used a novel microwave-assisted method developed in our laboratories to synthesize a series of ruthenium-thiosemicarbazone complexes. The new thiosemicarbazone ligands are derived from benzo[ d][1,3]dioxole-5-carbaldehyde (piperonal) and the complexes are formulated as [(diimine) 2Ru(TSC)](PF 6) 2 (where the TSC is the bidentate thiosemicarbazone ligand). The diimine in the complexes is either 2,2'-bipyridine or 1,10-phenanthroline. The complexes have been characterized by spectroscopic means (NMR, IR and UV-Vis) as well as by elemental analysis. We have studied the biophysical characteristics of the complexes by investigating their anti-oxidant ability as well as their ability to disrupt the function of the human topoisomerase II enzyme. The complexes are moderately strong binders of DNA with binding constants of 10 4 M -1. They are also strong binders of human serum albumin having binding constants on the order of 10 4 M -1. The complexes show good in vitro anticancer activity against human colon cancer cells, Caco-2 and HCT-116 and indeed show some cytotoxic selectivity for cancer cells. The IC 50 values range from 7 to 159 μM (after 72 h drug incubation). They also have antibacterial activity against Gram-positive strains of pathogenic bacteria with IC 50 values as low as 10 μM; little activity was seen against Gram-negative strains. It has been established that all the compounds are catalytic inhibitors of human topoisomerase II.

  16. Laboratory-acquired brucellosis

    DEFF Research Database (Denmark)

    Fabiansen, C.; Knudsen, J.D.; Lebech, A.M.

    2008-01-01

    Brucellosis is a rare disease in Denmark. We describe one case of laboratory-acquired brucellosis from an index patient to a laboratory technician following exposure to an infected blood culture in a clinical microbiology laboratory Udgivelsesdato: 2008/6/9......Brucellosis is a rare disease in Denmark. We describe one case of laboratory-acquired brucellosis from an index patient to a laboratory technician following exposure to an infected blood culture in a clinical microbiology laboratory Udgivelsesdato: 2008/6/9...

  17. Neural Systems Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — As part of the Electrical and Computer Engineering Department and The Institute for System Research, the Neural Systems Laboratory studies the functionality of the...

  18. Optical Remote Sensing Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Optical Remote Sensing Laboratory deploys rugged, cutting-edge electro-optical instrumentation for the collection of various event signatures, with expertise in...

  19. Central Laboratories Services

    Data.gov (United States)

    Federal Laboratory Consortium — The TVA Central Laboratories Services is a comprehensive technical support center, offering you a complete range of scientific, engineering, and technical services....

  20. ANALYTICAL MICROBIOLOGY LABORATORY

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory contains equipment that performs a broad array of microbiological analyses for pathogenic and spoilage microorganisms. It performs challenge studies...

  1. Environmental Microbiology Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Environmental Microbiology Laboratory, located in Bldg. 644 provides a dual-gas respirometer for measurement of oxygen consumption and carbon dioxide evolution...

  2. Vehicle Development Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Supports the development of prototype deployment platform vehicles for offboard countermeasure systems. DESCRIPTION: The Vehicle Development Laboratory is...

  3. Intelligent Optics Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Intelligent Optics Laboratory supports sophisticated investigations on adaptive and nonlinear optics; advancedimaging and image processing; ground-to-ground and...

  4. Laboratory of Chemical Physics

    Data.gov (United States)

    Federal Laboratory Consortium — Current research in the Laboratory of Chemical Physics is primarily concerned with experimental, theoretical, and computational problems in the structure, dynamics,...

  5. Rapid Prototyping Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The ARDEC Rapid Prototyping (RP) Laboratory was established in December 1992 to provide low cost RP capabilities to the ARDEC engineering community. The Stratasys,...

  6. Fuels Processing Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — NETL’s Fuels Processing Laboratory in Morgantown, WV, provides researchers with the equipment they need to thoroughly explore the catalytic issues associated with...

  7. Space Weather Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Space Weather Computational Laboratory is a Unix and PC based modeling and simulation facility devoted to research analysis of naturally occurring electrically...

  8. Embedded Processor Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Embedded Processor Laboratory provides the means to design, develop, fabricate, and test embedded computers for missile guidance electronics systems in support...

  9. Thermogravimetric Analysis Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — At NETL’s Thermogravimetric Analysis Laboratory in Morgantown, WV, researchers study how chemical looping combustion (CLC) can be applied to fossil energy systems....

  10. FOOD SAFETY TESTING LABORATORY

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory develops screening assays, tests and modifies biosensor equipment, and optimizes food safety testing protocols for the military and civilian sector...

  11. COGNITIVE PERFORMANCE LABORATORY

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory conducts basic and applied human research studies to characterize cognitive performance as influenced by militarily-relevant contextual and physical...

  12. Atmospheric Measurements Laboratory (AML)

    Data.gov (United States)

    Federal Laboratory Consortium — The Atmospheric Measurements Laboratory (AML) is one of the nation's leading research facilities for understanding aerosols, clouds, and their interactions. The AML...

  13. Virtual Training Devices Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Virtual Training Devices (VTD) Laboratory at the Life Cycle Software Engineering Center, Picatinny Arsenal, provides a software testing and support environment...

  14. Engineered Natural Systems Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — With its pressure vessels that simulate the pressures and temperatures found deep underground, NETL’s Engineered Natural Systems Laboratory in Pittsburgh, PA, gives...

  15. Tactical Systems Integration Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Tactical Systems Integration Laboratory is used to design and integrate computer hardware and software and related electronic subsystems for tactical vehicles....

  16. [Theme: Using Laboratories.

    Science.gov (United States)

    Pritchard, Jack; Braker, Clifton

    1982-01-01

    Pritchard discusses the opportunities for applied learning afforded by laboratories. Braker describes the evaluation of cognitive, affective, and psychomotor skills in the agricultural mechanics laboratory. (SK)

  17. Estimating Biophysical Crop Properties by a Machine Learning Model Inversion using Hyperspectral Imagery of Different Resolution

    Science.gov (United States)

    Preidl, S.; Doktor, D.

    2013-12-01

    This study investigates how image resolution and phenology affects the quality of biophysical variable estimation of different crop types. Hence, several hyperspectral at-sensor radiance images (400-2500 nm) of 1, 2 and 3 meter resolution were acquired by an AISA dual airborne system to estimate leaf chlorophyll content and leaf area index (LAI) of different crop types. The study area describes a climatic gradient that ranges from the Magdeburg Börde (130 meter a.s.l.) to the northeast of the Harz Mountain (450 meter a.s.l.), Germany. The 35 kilometer long flight strip is recorded on the same day at all three resolutions. Ground measurements were conducted simultaneously to the flight campaigns on selected crop fields. The SLC model was coupled with the atmospheric model MODTRAN4 to build up a look-up table (LUT) of simulated at-sensor radiances. To support a fast and more accurate inversion process, LUT-spectra were selected for model inversion which location in the PCA space (spanned by the first three principal components) is similar to the one of the measured spectra. A support vector regression (SVR) was trained on the reduced LUT to perform a pixel-based inversion of the hyperspectral images, subsequently. A multi-parameter sensitivity analysis was recently developed to define the most influential parameters for a reasonable model setup in the first place. This completes the development of an automated inversion process chain to estimate leaf and canopy biophysical properties. To achieve reasonable inversion results each pixel should be radiatively independent from its surrounding pixels. Image texture is used to calculate the second-order statistical variance between pixel pairs quantifying spatial heterogeneity throughout the spectral domain. The texture measurement can be employed as an uncertainty assessment of the biophysical variable estimation map. Results show that vegetated areas within the field are representing spectrally homogeneous systems. In

  18. Effects of graphene oxide nanosheets on the ultrastructure and biophysical properties of the pulmonary surfactant film

    Science.gov (United States)

    Hu, Qinglin; Jiao, Bao; Shi, Xinghua; Valle, Russell P.; Zuo, Yi Y.; Hu, Guoqing

    2015-10-01

    Graphene oxide (GO) is the most common derivative of graphene and has been used in a large range of biomedical applications. Despite considerable progress in understanding its cytotoxicity, its potential inhalation toxicity is still largely unknown. As the pulmonary surfactant (PS) film is the first line of host defense, interaction with the PS film determines the fate of the inhaled nanomaterials and their potential toxicity. Using a coarse-grained molecular dynamics model, we reported, for the first time, a novel mechanism of toxicity caused by the inhaled GO nanosheets. Upon deposition, the GO nanosheets induce pores in the PS film and thus have adverse effects on the ultrastructure and biophysical properties of the PS film. Notably, the pores induced by GO nanosheets result in increasing the compressibility of the PS film, which is an important indication of surfactant inhibition. In vitro experiments have also been conducted to study the interactions between GO and animal-derived natural PS films, qualitatively confirming the simulation results.Graphene oxide (GO) is the most common derivative of graphene and has been used in a large range of biomedical applications. Despite considerable progress in understanding its cytotoxicity, its potential inhalation toxicity is still largely unknown. As the pulmonary surfactant (PS) film is the first line of host defense, interaction with the PS film determines the fate of the inhaled nanomaterials and their potential toxicity. Using a coarse-grained molecular dynamics model, we reported, for the first time, a novel mechanism of toxicity caused by the inhaled GO nanosheets. Upon deposition, the GO nanosheets induce pores in the PS film and thus have adverse effects on the ultrastructure and biophysical properties of the PS film. Notably, the pores induced by GO nanosheets result in increasing the compressibility of the PS film, which is an important indication of surfactant inhibition. In vitro experiments have also been

  19. Statistical and Biophysical Models for Predicting Total and Outdoor Water Use in Los Angeles

    Science.gov (United States)

    Mini, C.; Hogue, T. S.; Pincetl, S.

    2012-04-01

    Modeling water demand is a complex exercise in the choice of the functional form, techniques and variables to integrate in the model. The goal of the current research is to identify the determinants that control total and outdoor residential water use in semi-arid cities and to utilize that information in the development of statistical and biophysical models that can forecast spatial and temporal urban water use. The City of Los Angeles is unique in its highly diverse socio-demographic, economic and cultural characteristics across neighborhoods, which introduces significant challenges in modeling water use. Increasing climate variability also contributes to uncertainties in water use predictions in urban areas. Monthly individual water use records were acquired from the Los Angeles Department of Water and Power (LADWP) for the 2000 to 2010 period. Study predictors of residential water use include socio-demographic, economic, climate and landscaping variables at the zip code level collected from US Census database. Climate variables are estimated from ground-based observations and calculated at the centroid of each zip code by inverse-distance weighting method. Remotely-sensed products of vegetation biomass and landscape land cover are also utilized. Two linear regression models were developed based on the panel data and variables described: a pooled-OLS regression model and a linear mixed effects model. Both models show income per capita and the percentage of landscape areas in each zip code as being statistically significant predictors. The pooled-OLS model tends to over-estimate higher water use zip codes and both models provide similar RMSE values.Outdoor water use was estimated at the census tract level as the residual between total water use and indoor use. This residual is being compared with the output from a biophysical model including tree and grass cover areas, climate variables and estimates of evapotranspiration at very high spatial resolution. A

  20. Senegalese land surface change analysis and biophysical parameter estimation using NOAA AVHRR spectral data

    Science.gov (United States)

    Vukovich, Fred M.; Toll, David L.; Kennard, Ruth L.

    1989-01-01

    Surface biophysical estimates were derived from analysis of NOAA Advanced Very High Spectral Resolution (AVHRR) spectral data of the Senegalese area of west Africa. The parameters derived were of solar albedo, spectral visible and near-infrared band reflectance, spectral vegetative index, and ground temperature. Wet and dry linked AVHRR scenes from 1981 through 1985 in Senegal were analyzed for a semi-wet southerly site near Tambacounda and a predominantly dry northerly site near Podor. Related problems were studied to convert satellite derived radiance to biophysical estimates of the land surface. Problems studied were associated with sensor miscalibration, atmospheric and aerosol spatial variability, surface anisotropy of reflected radiation, narrow satellite band reflectance to broad solar band conversion, and ground emissivity correction. The middle-infrared reflectance was approximated with a visible AVHRR reflectance for improving solar albedo estimates. In addition, the spectral composition of solar irradiance (direct and diffuse radiation) between major spectral regions (i.e., ultraviolet, visible, near-infrared, and middle-infrared) was found to be insensitive to changes in the clear sky atmospheric optical depth in the narrow band to solar band conversion procedure. Solar albedo derived estimates for both sites were not found to change markedly with significant antecedent precipitation events or correspondingly from increases in green leaf vegetation density. The bright soil/substrate contributed to a high albedo for the dry related scenes, whereas the high internal leaf reflectance in green vegetation canopies in the near-infrared contributed to high solar albedo for the wet related scenes. The relationship between solar albedo and ground temperature was poor, indicating the solar albedo has little control of the ground temperature. The normalized difference vegetation index (NDVI) and the derived visible reflectance were more sensitive to antecedent

  1. Integrating Economic Models with Biophysical Models in the Willamette Water 2100 Project

    Science.gov (United States)

    Jaeger, W. K.; Plantinga, A.

    2013-12-01

    This paper highlights the human system modeling components for Willamette Water 2100, a comprehensive, highly integrated study of hydrological, ecological, and human factors affecting water scarcity in the Willamette River Basin (WRB). The project is developing a spatiotemporal simulation model to predict future trajectories of water scarcity, and to evaluate mitigation policies. Economic models of land use and water use are the main human system models in WW2100. Water scarcity depends on both supply and demand for water, and varies greatly across time and space (Jaeger et al., 2013). Thus, the locations of human water use can have enormous influence on where and when water is used, and hence where water scarcity may arise. Modeling the locations of human uses of water (e.g., urban versus agricultural) as well as human values and choices, are the principal quantitative ways that social science can contribute to research of this kind. Our models are empirically-based models of human resource allocation. Each model reflects private behavior (choices by households, farms, firms), institutions (property rights, laws, markets, regulations), public infrastructure (dams, canals, highways), and also 'external drivers' that influence the local economy (migration, population growth, national markets and policies). This paper describes the main model components, emphasizing similarities between human and biophysical components of the overall project, and the model's linkages and feedbacks relevant to our predictions of changes in water scarcity between now and 2100. Results presented include new insights from individual model components as well as available results from the integrated system model. Issues include water scarcity and water quality (temperature) for out-of-stream and instream uses, the impact of urban expansion on water use and potential flood damage. Changes in timing and variability of spring discharge with climate change, as well as changes in human uses of

  2. Remote Sensing of Boreal Forest Biophysical and Inventory Parameters: A Review

    Science.gov (United States)

    Lutz, D. A.; Washington-Allen, R. A.

    2007-12-01

    Vegetation makes up nearly 70 % of the Earth's terrestrial surface and products from vegetated systems are vitally important for human populations. The growing need to manage vegetation resources at regional and global spatial scales has led to the increased use of remote sensing technologies among forestry scientists and managers for use in their investigation and supervision of forested landscapes. With a panoply of extant and developing airborne and satellite sensors, as well as multiple analysis techniques, there is a need to discern the most acceptable methods in which to examine remotely sensed imagery for forest ecosystem parameters. This includes both biophysical and inventory indicators. This study investigates the methods used to examine plant parameters in the boreal forest, and attempts to derive the most appropriate methods for extracting information regarding plant structure and stand information. A suggested methodology is constructed for use by remote sensors and forest managers. Specifically, we reviewed the literature on the remote sensing of boreal forests that featured airborne and satellite optical, passive and active radar, and lidar systems in order to determine if common frameworks for monitoring and assessing change in forest biophysical and inventory parameters could be developed. Other important remote sensing techniques such as change detection and land cover identification were also examined. Our review considered the purpose of each study, the type of sensor(s) used [e.g., Landsat or Lidar], where the study occurred, the methods used, including what vegetation and soil parameters or processes were considered, and the remote sensing indicator developed to measure this parameter [e.g., the normalized difference vegetation index (NDVI) is a surrogate for phytomass, LAI, land cover type, and other plant parameters]. We also investigated how the measured indicators were calibrated and validated as well as the limitations of the sensors that

  3. Multi-scale modeling of biophysical phenomena: ionic transport, biomineralization, and force spectroscopy

    Science.gov (United States)

    Kelly, Mark A.

    2011-07-01

    Biophysics is the study of the complex physical processes occurring in biological systems that are responsible for life. This dissertation addresses three important topics in biophysics: ionic transport, biomineralization, and force spectroscopy. Ionic transport involves the passage of ions through a special class of hollow, transmembrane proteins called ion channels which regulate the movement of charged species across nearly all biological membranes with varying degrees of specificity. Despite the fundamental importance of these channels to many physiological processes little is known about how channel structure and composition couple to determine its function. Deriving inspiration from these systems, a simple computational platform is developed to study the salient features of these channels in order to better understand the fundamental physics of these systems. The results of this work indicate that a converging-diverging region formed within the pore to create a single constriction is the most effective method to regulate the passage of ions through the pore. By controlling the geometry of the constriction the local potential and chemical gradients can be manipulated to tailor the channel for specific applications. The process of selective extraction and incorporation of local elements from the surrounding environment into functional structures under strict biological control is known as biomineralization. As an initial step to gain a more fundamental understanding of directed crystallization of zinc oxide molecular dynamics simulations were performed to study the conformational behavior of two experimentally derived biomimetic peptides in a precursor solution. Substantial differences in the conformational properties and affinity for zinc and hydroxide ions in solution were observed. These findings are in qualitative agreement with experimental observations. The mechanical response of biopolymers such as RNA and DNA to externally applied forces is a topic that

  4. Laboratory Information Systems.

    Science.gov (United States)

    Henricks, Walter H

    2016-03-01

    Laboratory information systems (LISs) supply mission-critical capabilities for the vast array of information-processing needs of modern laboratories. LIS architectures include mainframe, client-server, and thin client configurations. The LIS database software manages a laboratory's data. LIS dictionaries are database tables that a laboratory uses to tailor an LIS to the unique needs of that laboratory. Anatomic pathology LIS (APLIS) functions play key roles throughout the pathology workflow, and laboratories rely on LIS management reports to monitor operations. This article describes the structure and functions of APLISs, with emphasis on their roles in laboratory operations and their relevance to pathologists. PMID:26851660

  5. Key importance of compression properties in the biophysical characteristics of hyaluronic acid soft-tissue fillers.

    Science.gov (United States)

    Gavard Molliard, Samuel; Albert, Séverine; Mondon, Karine

    2016-08-01

    Hyaluronic acid (HA) soft-tissue fillers are the most popular degradable injectable products used for correcting skin depressions and restoring facial volume loss. From a rheological perspective, HA fillers are commonly characterised through their viscoelastic properties under shear-stress. However, despite the continuous mechanical pressure that the skin applies on the fillers, compression properties in static and dynamic modes are rarely considered. In this article, three different rheological tests (shear-stress test and compression tests in static and dynamic mode) were carried out on nine CE-marked cross-linked HA fillers. Corresponding shear-stress (G', tanδ) and compression (E', tanδc, normal force FN) parameters were measured. We show here that the tested products behave differently under shear-stress and under compression even though they are used for the same indications. G' showed the expected influence on the tissue volumising capacity, and the same influence was also observed for the compression parameters E'. In conclusion, HA soft-tissue fillers exhibit widely different biophysical characteristics and many variables contribute to their overall performance. The elastic modulus G' is not the only critical parameter to consider amongst the rheological properties: the compression parameters E' and FN also provide key information, which should be taken into account for a better prediction of clinical outcomes, especially for predicting the volumising capacity and probably the ability to stimulate collagen production by fibroblasts. PMID:27093589

  6. ``Microclimatic Impacts of Green Spaces: Sociological and Biophysical Scale Considerations for Municipal Site Developments''

    Science.gov (United States)

    Heinse, R.; Vanhoozer, A. D.; Microclimatic Impacts Of Green Spaces

    2010-12-01

    Local government participation in greenhouse gas inventory and action planning within the context of climate change science is a growing national practice. Effective municipal policy-making and community action depends on accurate predictions of economic, socio-cultural and managerial implications for site and species selection in green developments. Our objective was to test if and how quantitative biophysical data combined with qualitative socio-economic data at the community scale can be utilized to characterize comparative advantages of potential green application sites via a comparative study of scales. The considered scales include the NASA Ames Research Center Sustainability Base site and the City of Moscow, Idaho Sustainability program for municipal Greenhouse Gas Inventory. First, qualitative study of economic, socio-cultural and managerial implications for each site was utilized via modeling and survey data analyses to characterize comparative advantages of potential applications. Second, microclimate conditions within each site will be analyzed through field experimentation to test for optimal green development sites in terms of carbon sequestration, water conservation and energy efficiency gains potentials. This study will provide metrics adaptable to multiple scales of application for the purposes of addressing and responding to climate change and energy efficiency issues. Methodologies developed from this and other studies can be used to enhance optimization of site and species selection for investment in green space developments.

  7. Biochemical and Biophysical Characterization of Recombinant Yeast Proteasome Maturation Factor UMP1

    Directory of Open Access Journals (Sweden)

    Bebiana Sá-Moura

    2013-04-01

    Full Text Available Protein degradation is essential for maintaining cellular homeostasis. The proteasome is the central enzyme responsible for non-lysosomal protein degradation in eukaryotic cells. Although proteasome assembly is not yet completely understood, a number of cofactors required for proper assembly and maturation have been identified. Ump1 is a short-lived maturation factor required for the efficient biogenesis of the 20S proteasome. Upon the association of the two precursor complexes, Ump1 is encased and is rapidly degraded after the proteolytic sites in the interior of the nascent proteasome are activated. In order to further understand the mechanisms behind proteasomal maturation, we expressed and purified yeast Ump1 in E. coli for biophysical and structural analysis.We show that recombinant Ump1 is purified as a mixture of different oligomeric species and that oligomerization is mediated by intermolecular disulfide bond formation involving the only cysteine residue present in the protein. Furthermore, a combination of bioinformatics tools, biochemical and structural analysis revealed that Ump1 shows characteristics of an intrinsically disordered protein, which might become structured only upon interaction with the proteasome subunits.

  8. Functional imaging in oncology. Biophysical basis and technical approaches. Vol. 1

    Energy Technology Data Exchange (ETDEWEB)

    Luna, Antonio [Health Time Group, Jaen (Spain); University Hospitals, Case Western Reserve Univ., Cleveland, OH (United States). Dept. of Radiology; Vilanova, Joan C. [Clinica Girona - Hospital Sta. Caterina, Girona (Spain); Hygino da Cruz, L. Celso Jr. [CDPI and IRM, Rio de Janeiro, RJ (Brazil). Dept. of Radiology; Rossi, Santiago E. (ed.) [Centro de Diagnostico, Buenos Aires (Argentina)

    2014-07-01

    Easy-to-read manual on new functional imaging techniques in oncology. Explains current clinical applications and outlines future avenues. Includes numerous high-quality illustrations to highlight the major teaching points. In the new era of functional and molecular imaging, both currently available imaging biomarkers and biomarkers under development are expected to lead to major changes in the management of oncological patients. This well-illustrated two-volume book is a practical manual on the various imaging techniques capable of delivering functional information on cancer, including preclinical and clinical imaging techniques, based on US, CT, MRI, PET and hybrid modalities. This first volume explains the biophysical basis for these functional imaging techniques and describes the techniques themselves. Detailed information is provided on the imaging of cancer hallmarks, including angiogenesis, tumor metabolism, and hypoxia. The techniques and their roles are then discussed individually, covering the full range of modalities in clinical use as well as new molecular and functional techniques. The value of a multiparametric approach is also carefully considered.

  9. Indigenous community health and climate change: integrating biophysical and social science indicators

    Science.gov (United States)

    Donatuto, Jamie; Grossman, Eric E.; Konovsky, John; Grossman, Sarah; Campbell, Larry W.

    2014-01-01

    This article describes a pilot study evaluating the sensitivity of Indigenous community health to climate change impacts on Salish Sea shorelines (Washington State, United States and British Columbia, Canada). Current climate change assessments omit key community health concerns, which are vital to successful adaptation plans, particularly for Indigenous communities. Descriptive scaling techniques, employed in facilitated workshops with two Indigenous communities, tested the efficacy of ranking six key indicators of community health in relation to projected impacts to shellfish habitat and shoreline archaeological sites stemming from changes in the biophysical environment. Findings demonstrate that: when shellfish habitat and archaeological resources are impacted, so is Indigenous community health; not all community health indicators are equally impacted; and, the community health indicators of highest concern are not necessarily the same indicators most likely to be impacted. Based on the findings and feedback from community participants, exploratory trials were successful; Indigenous-specific health indicators may be useful to Indigenous communities who are assessing climate change sensitivities and creating adaptation plans.

  10. Modeling the effects of noninvasive transcranial brain stimulation at the biophysical, network, and cognitive Level

    DEFF Research Database (Denmark)

    Hartwigsen, Gesa; Bergmann, Til Ole; Herz, Damian Marc;

    2015-01-01

    Noninvasive transcranial brain stimulation (NTBS) is widely used to elucidate the contribution of different brain regions to various cognitive functions. Here we present three modeling approaches that are informed by functional or structural brain mapping or behavior profiling and discuss how the...... emerge in the context of rapid automatic responses or in the context of slow deliberate responses. We argue that these complementary modeling approaches facilitate the use of NTBS as a means of dissecting the causal architecture of cognitive systems of the human brain.......Noninvasive transcranial brain stimulation (NTBS) is widely used to elucidate the contribution of different brain regions to various cognitive functions. Here we present three modeling approaches that are informed by functional or structural brain mapping or behavior profiling and discuss how these...... approaches advance the scientific potential of NTBS as an interventional tool in cognitive neuroscience. (i) Leveraging the anatomical information provided by structural imaging, the electric field distribution in the brain can be modeled and simulated. Biophysical modeling approaches generate testable...

  11. Optimized expression and purification of biophysical quantities of Lac repressor and Lac repressor regulatory domain.

    Science.gov (United States)

    Stetz, Matthew A; Carter, Marie V; Wand, A Joshua

    2016-07-01

    The recombinant production of Lac repressor (LacI) in Escherichia coli is complicated by its ubiquitous use as a regulatory element in commercially-available expression vectors and host strains. While LacI-regulated expression systems are often used to produce recombinant LacI, the product can be heterogeneous and unsuitable for some studies. Alternative approaches include using unregulated vectors which typically suffer from low yield or vectors with promoters induced by metabolically active sugars which can dilute isotope labels necessary for certain biophysical studies. Here, an optimized expression system and isolation protocol for producing various constructs of LacI is introduced which eliminates these complications. The expression vector is an adaptation of the pASK backbone wherein expression of the lacI gene is regulated by an anhydrotetracyline inducible tetA promoter and the host strain lacks the lacI gene. Typical yields in highly deuterated minimal medium are nearly 2-fold greater than those previously reported. Notably, the new expression system is also able to produce the isolated regulatory domain of LacI without co-expression of the full-length protein and without any defects in cell viability, eliminating the inconvenient requirement for strict monitoring of cell densities during pre-culturing. Typical yields in highly deuterated minimal medium are significantly greater than those previously reported. Characterization by solution NMR shows that LacI constructs produced using this expression system are highly homogenous and functionally active. PMID:27064119

  12. Discrimination And Biophysical Characterization Of Brazilian Cerrado Physiognomies With Eo-1 Hyperspectral Hyperion

    Science.gov (United States)

    Miura, Tomoaki; Huete, Alfredo R.; Ferreira, Laerte G.; Sano, Edson E.

    2004-01-01

    The savanna, typically found in the sub-tropics and seasonal tropics, are the dominant vegetation biome type in the southern hemisphere, covering approximately 45% of the South America. In Brazil, the savanna, locally known as "cerrado," is the most intensely stressed biome with both natural environmental pressures (e.g., the strong seasonality in weather, extreme soil nutrient impoverishment, and widespread fire occurrences) and rapid/aggressive land conversions (Skole et al., 1994; Ratter et al., 1997). Better characterization and discrimination of cerrado physiognomies are needed in order to improve understanding of cerrado dynamics and its impact on carbon storage, nutrient dynamics, and the prospect for sustainable land use in the Brazilian cerrado biome. Satellite remote sensing have been known to be a useful tool for land cover and land use mapping (Rougharden et al., 1991; Hansen et al., 2000). However, attempts to discriminate and classify Brazilian cerrado using multi-spectral sensors (e.g., Landsat TM) and/or moderate resolution sensors (e.g., NOAA AVHRR NDVI) have often resulted in a limited success due partly to small contrasts depicted in their multiband, spectral reflectance or vegetation index values among cerrado classes (Seyler et al., 2002; Fran a and Setzer, 1998). In this study, we aimed to improve discrimination as well as biophysical characterization of the Brazilian cerrado physiognomies with hyperspectral remote sensing. We used Hyperion, the first satellite-based hyperspectral imager, onboard the Earth Observing-1 (EO-1) platform.

  13. Biophysical characterization of V3-lipopeptide liposomes influencing HIV-1 infectivity

    International Nuclear Information System (INIS)

    The V3-loop of the HIV-1 gp120 alters host cell immune function and modulates infectivity. We investigated biophysical parameters of liposome constructs with embedded lipopeptides from the principle neutralizing domain of the V3-loop and their influence on viral infectivity. Dynamic light scattering measurements showed liposome supramolecular structures with hydrodynamic radius of the order of 900 and 1300 nm for plain and V3-lipopeptide liposomes. Electron paramagnetic resonance measurements showed almost identical local microenvironment. The difference in liposome hydrodynamic radius was attributed to the fluctuating ionic environment of the V3-lipopeptide liposomes. In vitro HIV-1 infectivity assays showed that plain liposomes reduced virus production in all cell cultures, probably due to the hydrophobic nature of the aggregates. Liposomes carrying V3-lipopeptides with different cationic potentials restored and even enhanced infectivity (p < 0.05). These results highlight the need for elucidation of the involvement of lipid bilayers as dynamic components in supramolecular structures and in HIV-1 fusion mechanisms

  14. Investigating Irregularly Patterned Deep Brain Stimulation Signal Design Using Biophysical Models

    Directory of Open Access Journals (Sweden)

    Samantha Rose Summerson

    2015-06-01

    Full Text Available Parkinson’s disease (PD is a neurodegenerative disorder which follows from cell loss of dopaminergic neurons in the substantia nigra pars compacta (SNc, a nucleus in the basal ganglia (BG. Deep brain stimulation (DBS is an electrical therapy that modulates the pathological activity to treat the motor symptoms of PD. Although this therapy is currently used in clinical practice, the sufficient conditions for therapeutic efficacy are unknown. In this work we develop a model of critical motor circuit structures in the brain using biophysical cell models as the base components and then evaluate performance of different DBS signals in this model to perform comparative studies of their efficacy. Biological models are an important tool for gaining insights into neural function and, in this case, serve as effective tools for investigating innovative new DBS paradigms. Experiments were performed using the hemi-parkinsonian rodent model to test the same set of signals, verifying the obedience of the model to physiological trends. We show that antidromic spiking from DBS of the subthalamic nucleus (STN has a significant impact on cortical neural activity, which is frequency dependent and additionally modulated by the regularity of the stimulus pulse train used. Irregular spacing between stimulus pulses, where the amount of variability added is bounded, is shown to increase diversification of response of basal ganglia neurons and reduce entropic noise in cortical neurons, which may be fundamentally important to restoration of information flow in the motor circuit.

  15. Biophysical analysis of water filtration phenomenon in the roots of halophytes

    Science.gov (United States)

    Kim, Kiwoong; Lee, Sang Joon

    2015-11-01

    The water management systems of plants, such as water collection and water filtration have been optimized through a long history. In this point of view, new bio-inspired technologies can be developed by mimicking the nature's strategies for the survival of the fittest. In this study, the biophysical characteristics of water filtration process in the roots of halophytes are experimentally investigated in the plant hydrodynamic point of view. To understand the functional features of the halophytes 3D morphological structure of their roots are analyzed using advanced bioimaging techniques. The surface properties of the roots of halophytes are also examined Based on the quantitatively analyzed information, water filtration phenomenon in the roots is examined. Sodium treated mangroves are soaked in sodium acting fluorescent dye solution to trace sodium ions in the roots. In addition, in vitroexperiment is carried out by using the roots. As a result, the outermost layer of the roots filters out continuously most of sodium ions. This study on developing halophytes would be helpful for understanding the water filtration mechanism of the roots of halophytes and developing a new bio inspired desalination system. This research was financially supported by the National Research Foundation (NRF) of Korea (Contract grant number: 2008-0061991).

  16. Oxidized phosphatidylcholines in membrane-level cellular signaling: from biophysics to physiology and molecular pathology.

    Science.gov (United States)

    Volinsky, Roman; Kinnunen, Paavo K J

    2013-06-01

    The oxidation of lipids has been shown to impact virtually all cellular processes. The paradigm has been that this involvement is due to interference with the functions of membrane-associated proteins. It is only recently that methodological advances in molecular-level detection and identification have begun to provide insights into oxidative lipid modification and its involvement in cell signaling as well as in major diseases and inflammation. Extensive evidence suggests a correlation between lipid peroxidation and degenerative neurological diseases such as Parkinson's and Alzheimer's, as well as type 2 diabetes and cancer. Despite the obvious relevance of understanding the molecular basis of the above ailments, the exact modes of action of oxidized lipids have remained elusive. In this minireview, we summarize recent findings on the biophysical characteristics of biomembranes following oxidative derivatization of their lipids, and how these altered properties are involved in both physiological processes and major pathological conditions. Lipid-bearing, oxidatively truncated and functionalized acyl chains are known to modify membrane bulk physical properties, such as thermal phase behavior, bilayer thickness, hydration and polarity profiles, as manifest in the altered structural dynamics of lipid bilayers, leading to augmented membrane permeability, fast lipid transbilayer diffusion (flip-flop), loss of lipid asymmetry (scrambling) and phase segregation (the formation of 'rafts'). These changes, together with the generated reactive lipid derivatives, can be further expected to interfere with lipid-protein interactions, influencing metabolic pathways, causing inflammation, the execution phase in apoptosis and initiating pathological processes. PMID:23506295

  17. A biophysically-based neuromorphic model of spike rate- and timing-dependent plasticity.

    Science.gov (United States)

    Rachmuth, Guy; Shouval, Harel Z; Bear, Mark F; Poon, Chi-Sang

    2011-12-01

    Current advances in neuromorphic engineering have made it possible to emulate complex neuronal ion channel and intracellular ionic dynamics in real time using highly compact and power-efficient complementary metal-oxide-semiconductor (CMOS) analog very-large-scale-integrated circuit technology. Recently, there has been growing interest in the neuromorphic emulation of the spike-timing-dependent plasticity (STDP) Hebbian learning rule by phenomenological modeling using CMOS, memristor or other analog devices. Here, we propose a CMOS circuit implementation of a biophysically grounded neuromorphic (iono-neuromorphic) model of synaptic plasticity that is capable of capturing both the spike rate-dependent plasticity (SRDP, of the Bienenstock-Cooper-Munro or BCM type) and STDP rules. The iono-neuromorphic model reproduces bidirectional synaptic changes with NMDA receptor-dependent and intracellular calcium-mediated long-term potentiation or long-term depression assuming retrograde endocannabinoid signaling as a second coincidence detector. Changes in excitatory or inhibitory synaptic weights are registered and stored in a nonvolatile and compact digital format analogous to the discrete insertion and removal of AMPA or GABA receptor channels. The versatile Hebbian synapse device is applicable to a variety of neuroprosthesis, brain-machine interface, neurorobotics, neuromimetic computation, machine learning, and neural-inspired adaptive control problems. PMID:22089232

  18. Biophysical bases of keratorefractive surgical techniques applicable to myopic human eyes

    International Nuclear Information System (INIS)

    In this study, we have shown that: (a) the refractive power of the optical system of the myopic human eye could be decreased either by increasing the radius of curvature of its anterior corneal surface or decreasing that of its posterior corneal one, (b) a certain increase in the radius of curvature of the anterior corneal surface of the myopic eye results in a much greater decrease in the refractive power of its cornea than an equal decrease in that of its posterior corneal surface can do, and, (C) the decision that the surgical operation which aims at decreasing the refractive power of the optical system of the myopic eye is performed on its anterior corneal surface in the keratorefractive surgical techniques is a reasonable one from the physical and biophysical points of view in that the increase in the radius of curvature of the anterior corneal corneal surface of the myopic eyes provides a wider range for the correction of the refractive errors in the optical systems of these eyes than a decrease in that of their posterior corneal surface can do

  19. Biophysically inspired rational design of structured chimeric substrates for DNAzyme cascade engineering.

    Directory of Open Access Journals (Sweden)

    Matthew R Lakin

    Full Text Available The development of large-scale molecular computational networks is a promising approach to implementing logical decision making at the nanoscale, analogous to cellular signaling and regulatory cascades. DNA strands with catalytic activity (DNAzymes are one means of systematically constructing molecular computation networks with inherent signal amplification. Linking multiple DNAzymes into a computational circuit requires the design of substrate molecules that allow a signal to be passed from one DNAzyme to another through programmed biochemical interactions. In this paper, we chronicle an iterative design process guided by biophysical and kinetic constraints on the desired reaction pathways and use the resulting substrate design to implement heterogeneous DNAzyme signaling cascades. A key aspect of our design process is the use of secondary structure in the substrate molecule to sequester a downstream effector sequence prior to cleavage by an upstream DNAzyme. Our goal was to develop a concrete substrate molecule design to achieve efficient signal propagation with maximal activation and minimal leakage. We have previously employed the resulting design to develop high-performance DNAzyme-based signaling systems with applications in pathogen detection and autonomous theranostics.

  20. FIACH: A biophysical model for automatic retrospective noise control in fMRI.

    Science.gov (United States)

    Tierney, Tim M; Weiss-Croft, Louise J; Centeno, Maria; Shamshiri, Elhum A; Perani, Suejen; Baldeweg, Torsten; Clark, Christopher A; Carmichael, David W

    2016-01-01

    Different noise sources in fMRI acquisition can lead to spurious false positives and reduced sensitivity. We have developed a biophysically-based model (named FIACH: Functional Image Artefact Correction Heuristic) which extends current retrospective noise control methods in fMRI. FIACH can be applied to both General Linear Model (GLM) and resting state functional connectivity MRI (rs-fcMRI) studies. FIACH is a two-step procedure involving the identification and correction of non-physiological large amplitude temporal signal changes and spatial regions of high temporal instability. We have demonstrated its efficacy in a sample of 42 healthy children while performing language tasks that include overt speech with known activations. We demonstrate large improvements in sensitivity when FIACH is compared with current methods of retrospective correction. FIACH reduces the confounding effects of noise and increases the study's power by explaining significant variance that is not contained within the commonly used motion parameters. The method is particularly useful in detecting activations in inferior temporal regions which have proven problematic for fMRI. We have shown greater reproducibility and robustness of fMRI responses using FIACH in the context of task induced motion. In a clinical setting this will translate to increasing the reliability and sensitivity of fMRI used for the identification of language lateralisation and eloquent cortex. FIACH can benefit studies of cognitive development in young children, patient populations and older adults. PMID:26416652

  1. Understanding the distribution of fitness effects of mutations by a biophysical-organismal approach

    Science.gov (United States)

    Bershtein, Shimon

    2011-03-01

    The distribution of fitness effects of mutations is central to many questions in evolutionary biology. However, it remains poorly understood, primarily due to the fact that a fundamental connection that exists between the fitness of organisms and molecular properties of proteins encoded by their genomes is largely overlooked by traditional research approaches. Past efforts to breach this gap followed the ``evolution first'' paradigm, whereby populations were subjected to selection under certain conditions, and mutations which emerged in adapted populations were analyzed using genomic approaches. The results obtained in the framework of this approach, while often useful, are not easily interpretable because mutations get fixed due to a convolution of multiple causes. We have undertaken a conceptually opposite strategy: Mutations with known biophysical and biochemical effects on E. coli's essential proteins (based on computational analysis and in vitro measurements) were introduced into the organism's chromosome and the resulted fitness effects were monitored. Studying the distribution of fitness effects of such fully controlled replacements revealed a very complex fitness landscape, where impact of the microscopic properties of the mutated proteins (folding, stability, and function) is modulated on a macroscopic, whole genome level. Furthermore, the magnitude of the cellular response to the introduced mutations seems to depend on the thermodynamic status of the mutant.

  2. More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature.

    Science.gov (United States)

    Ladunga, Istvan

    2007-01-01

    Highly accurate knockdown functional analyses based on RNA interference (RNAi) require the possible most complete hydrolysis of the targeted mRNA while avoiding the degradation of untargeted genes (off-target effects). This in turn requires significant improvements to target selection for two reasons. First, the average silencing activity of randomly selected siRNAs is as low as 62%. Second, applying more than five different siRNAs may lead to saturation of the RNA-induced silencing complex (RISC) and to the degradation of untargeted genes. Therefore, selecting a small number of highly active siRNAs is critical for maximizing knockdown and minimizing off-target effects. To satisfy these needs, a publicly available and transparent machine learning tool is presented that ranks all possible siRNAs for each targeted gene. Support vector machines (SVMs) with polynomial kernels and constrained optimization models select and utilize the most predictive effective combinations from 572 sequence, thermodynamic, accessibility and self-hairpin features over 2200 published siRNAs. This tool reaches an accuracy of 92.3% in cross-validation experiments. We fully present the underlying biophysical signature that involves free energy, accessibility and dinucleotide characteristics. We show that while complete silencing is possible at certain structured target sites, accessibility information improves the prediction of the 90% active siRNA target sites. Fast siRNA activity predictions can be performed on our web server at http://optirna.unl.edu/. PMID:17169992

  3. Biophysical stability of hyFc fusion protein with regards to buffers and various excipients.

    Science.gov (United States)

    Lim, Jun Yeul; Kim, Nam Ah; Lim, Dae Gon; Eun, Chang-yong; Choi, Donghoon; Jeong, Seong Hoon

    2016-05-01

    A novel non-cytolytic hybrid Fc (hyFc) with an intact Ig structure without any mutation in the hyFc region, was developed to construct a long-acting agonistic protein. The stability of interleukin-7 (IL-7) fused with the hyFc (GXN-04) was evaluated to develop early formulations. Various biophysical methods were utilized and three different buffer systems with various pH ranges were investigated including histidine-acetate, sodium citrate, and tris buffers. Various excipients were incorporated into the systems to obtain optimum protein stability. Two evident thermal transitions were observed with the unfolding of IL-7 and hyFc. The Tm and ΔH increased with pH, suggesting increased conformational stability. Increased Z-average size with PDI and decreased zeta potential with pH increase, with the exception of tris buffer, showed aggregation issues. Moreover, tris buffer at higher pH showed aggregation peaks from DLS. Non-ionic surfactants were effective against agitation by outcompeting protein molecules for hydrophobic surfaces. Sucrose and sorbitol accelerated protein aggregation during agitation, but exhibited a protective effect against oxidation, with preferential exclusion favoring the compact states of GXN-04. The stability of GXN-04 was varied by basal buffers and excipients, hence the buffers and excipients need to be evaluated carefully to achieve the maximum stability of proteins. PMID:26851357

  4. Biochemical and biophysical characterization of the transmissible gastroenteritis coronavirus fusion core

    International Nuclear Information System (INIS)

    Transmissible gastroenteritis coronavirus (TGEV) is one of the most destructive agents, responsible for the enteric infections that are lethal for suckling piglets, causing enormous economic loss to the porcine fostering industry every year. Although it has been known that TGEV spiker protein is essential for the viral entry for many years, the detail knowledge of the TGEV fusion protein core is still very limited. Here, we report that TGEV fusion core (HR1-SGGRGG-HR2), in vitro expressed in GST prokaryotic expression system, shares the typical properties of the trimer of coiled-coil heterodimer (six α-helix bundle), which has been confirmed by a combined series of biochemical and biophysical evidences including size exclusion chromatography (gel-filtration), chemical crossing, and circular diagram. The 3D homologous structure model presents its most likely structure, extremely similar to those of the coronaviruses documented. Taken together, TGEV spiker protein belongs to the class I fusion protein, characterized by the existence of two heptad-repeat (HR) regions, HR1 and HR2, and the present knowledge about the truncated TGEV fusion protein core may facilitate in the design of the small molecule or polypeptide drugs targeting the membrane fusion between TGEV and its host

  5. A multivariate analysis of biophysical parameters of tallgrass prairie among land management practices and years

    Science.gov (United States)

    Griffith, J.A.; Price, K.P.; Martinko, E.A.

    2001-01-01

    Six treatments of eastern Kansas tallgrass prairie - native prairie, hayed, mowed, grazed, burned and untreated - were studied to examine the biophysical effects of land management practices on grasslands. On each treatment, measurements of plant biomass, leaf area index, plant cover, leaf moisture and soil moisture were collected. In addition, measurements were taken of the Normalized Difference Vegetation Index (NDVI), which is derived from spectral reflectance measurements. Measurements were taken in mid-June, mid-July and late summer of 1990 and 1991. Multivariate analysis of variance was used to determine whether there were differences in the set of variables among treatments and years. Follow-up tests included univariate t-tests to determine which variables were contributing to any significant difference. Results showed a significant difference (p < 0.0005) among treatments in the composite of parameters during each of the months sampled. In most treatment types, there was a significant difference between years within each month. The univariate tests showed, however, that only some variables, primarily soil moisture, were contributing to this difference. We conclude that biomass and % plant cover show the best potential to serve as long-term indicators of grassland condition as they generally were sensitive to effects of different land management practices but not to yearly change in weather conditions. NDVI was insensitive to precipitation differences between years in July for most treatments, but was not in the native prairie. Choice of sampling time is important for these parameters to serve effectively as indicators.

  6. The Principle of Stationary Action in Biophysics: Stability in Protein Folding

    CERN Document Server

    Simmons, Walter

    2013-01-01

    Processes that proceed reliably from a variety of initial conditions to a unique final form, regardless of moderately changing conditions, are of obvious importance in biophysics. Protein folding is a case in point. We show that the action principle can be applied directly to study the stability of biological processes. The action principle in classical physics starts with the first variation of the action and leads immediately to the equations of motion. The second variation of the action leads in a natural way to powerful theorems that provide quantitative treatment of stability and focusing and also explain how some very complex processes can behave as though some seemingly important forces drop out. We first apply these ideas to the non-equilibrium states involved in two-state folding. We treat torsional waves and use the action principle to talk about critical points in the dynamics. For some proteins the theory resembles TST. We reach several quantitative and qualitative conclusions. Besides giving an e...

  7. Effects of vegetable oils on biochemical and biophysical properties of membrane retinal pigment epithelium cells.

    Science.gov (United States)

    Said, Toihiri; Tremblay-Mercier, Jennifer; Berrougui, Hicham; Rat, Patrice; Khalil, Abdelouahed

    2013-10-01

    The aim of this study was to investigate the effect of vegetable oil enrichment of retinal pigment epithelial (RPE) cells on their biochemical and biophysical properties. For this, RPE cells were incubated with 4 different vegetables oils (olive oil, corn oil, argan oil, and camelina oil). The cytotoxicity of these vegetable oils was assessed in vivo on 8-week-old mice and in vitro by using the neutral red and YO-PRO-1 tests. Membrane fluidity was evaluated by fluorescence anisotropy using the fluorescent probe diphenylhexatriene, and membrane fatty acid composition was assessed by gas chromatography. None of the oils tested displayed cytotoxic effects. In vitro, omega-3 rich oils improved membrane fluidity by 47% compared with the control cells. The omega-3 PUFA content within membranes decreased by 38% to 55% when cells were incubated separately with olive oil, corn oil, or argan oil, and increased when cells were incubated with a mixture of those oils, or with camelina oil alone (50% and 103% increase, respectively). Our results show that the fatty acids in vegetable oil incorporate into retinal cells and increase the plasma membrane fluidity. PMID:24144052

  8. Simple biophysics underpins collective conformations of the intrinsically disordered proteins of the Nuclear Pore Complex

    Science.gov (United States)

    Vovk, Andrei; Gu, Chad; Opferman, Michael G; Kapinos, Larisa E; Lim, Roderick YH; Coalson, Rob D; Jasnow, David; Zilman, Anton

    2016-01-01

    Nuclear Pore Complexes (NPCs) are key cellular transporter that control nucleocytoplasmic transport in eukaryotic cells, but its transport mechanism is still not understood. The centerpiece of NPC transport is the assembly of intrinsically disordered polypeptides, known as FG nucleoporins, lining its passageway. Their conformations and collective dynamics during transport are difficult to assess in vivo. In vitro investigations provide partially conflicting results, lending support to different models of transport, which invoke various conformational transitions of the FG nucleoporins induced by the cargo-carrying transport proteins. We show that the spatial organization of FG nucleoporin assemblies with the transport proteins can be understood within a first principles biophysical model with a minimal number of key physical variables, such as the average protein interaction strengths and spatial densities. These results address some of the outstanding controversies and suggest how molecularly divergent NPCs in different species can perform essentially the same function. DOI: http://dx.doi.org/10.7554/eLife.10785.001 PMID:27198189

  9. Stability, biophysical properties and effect of ultracentrifugation and diafiltration on measles virus and mumps virus.

    Science.gov (United States)

    Sviben, Dora; Forčić, Dubravko; Kurtović, Tihana; Halassy, Beata; Brgles, Marija

    2016-06-01

    Measles virus and mumps virus (MeV and MuV) are enveloped RNA viruses used for production of live attenuated vaccines for prophylaxis of measles and mumps disease, respectively. For biotechnological production of and basic research on these viruses, the preparation of highly purified and infectious viruses is a prerequisite, and to meet that aim, knowledge of their stability and biophysical properties is crucial. Our goal was to carry out a detailed investigation of the stability of MeV and MuV under various pH, temperature, shear stress, filtration and storage conditions, as well as to evaluate two commonly used purification techniques, ultracentrifugation and diafiltration, with regard to their efficiency and effect on virus properties. Virus titers were estimated by CCID50 assay, particle size and concentration were measured by Nanoparticle tracking analysis (NTA) measurements, and the host cell protein content was determined by ELISA. The results demonstrated the stability of MuV and MeV at pH 9. Storage without stabilizer did not result in structural changes, but the reduction in infectivity after 24 hours was significant at +37 °C. Vortexing of the viruses resulted in significant particle degradation, leading to lower virus titers, whereas pipetting had much less impact on virus viability. Diafiltration resulted in higher recovery of both total and infectious virus particles than ultracentrifugation. These results provide important data for research on all upstream and downstream processes on these two viruses regarding biotechnological production and basic research. PMID:26935920

  10. Effects of graphene oxide nanosheets on the ultrastructure and biophysical properties of the pulmonary surfactant film†

    Science.gov (United States)

    Hu, Qinglin; Jiao, Bao; Shi, Xinghua; Valle, Russell P.

    2016-01-01

    Graphene oxide (GO) is the most common derivative of graphene and has been used in a large range of biomedical applications. Despite considerable progress in understanding its cytotoxicity, its potential inhalation toxicity is still largely unknown. As the pulmonary surfactant (PS) film is the first line of host defense, interaction with the PS film determines the fate of the inhaled nanomaterials and their potential toxicity. Using a coarse-grained molecular dynamics model, we reported, for the first time, a novel mechanism of toxicity caused by the inhaled GO nanosheets. Upon deposition, the GO nanosheets induce pores in the PS film and thus have adverse effects on the ultrastructure and biophysical properties of the PS film. Notably, the pores induced by GO nanosheets result in increasing the compressibility of the PS film, which is an important indication of surfactant inhibition. In vitro experiments have also been conducted to study the interactions between GO and animal-derived natural PS films, qualitatively confirming the simulation results. PMID:26482703

  11. Biophysical and biological characterisation of collagen/resilin-like protein composite fibres.

    Science.gov (United States)

    Sanami, M; Shtein, Z; Sweeney, I; Sorushanova, A; Rivkin, A; Miraftab, M; Shoseyov, O; O'Dowd, C; Mullen, A M; Pandit, A; Zeugolis, D I

    2015-12-01

    Collagen type I, in various physical forms, is widely used in tissue engineering and regenerative medicine. To control the mechanical properties and biodegradability of collagen-based devices, exogenous cross-links are introduced into the 3D supramolecular structure. However, potent cross-linking methods are associated with cytotoxicity, whilst mild cross-linking methods are associated with suboptimal mechanical resilience. Herein, we assessed the influence of resilin, a super-elastic and highly stretchable protein found within structures in arthropods where energy storage and long-range elasticity are needed, on the biophysical and biological properties of mildly cross-linked extruded collagen fibres. The addition of resilin-like protein in the 4-arm poly(ethylene glycol) ether tetrasuccinimidyl glutarate cross-linked collagen fibres resulted in a significant increase of stress and strain at break values and a significant decrease of modulus values. The addition of resilin-like protein did not compromise cell metabolic activity and DNA concentration. All groups are supported parallel to the longitudinal fibre axis cell orientation. Herein we provide evidence that the addition of resilin-like protein in mildly cross-linked collagen fibres improves their biomechanical properties, without jeopardising their biological properties. PMID:26541078

  12. The biophysical perspective of a middle income economy. Material flows in Mexico

    International Nuclear Information System (INIS)

    We analyse natural resource use dynamics in the Mexican economy during the last three decades. Despite low and uneven economic growth, the extraction and use of materials in the Mexican economy has continuously increased during the last 30 years. In this period, population growth rather than economic growth was the main driving force for biophysical growth. In addition, fundamental changes have taken place in the primary sectors, in manufacturing, and in household consumption and these are reflected in an increasing emphasis on the use of fossil fuels and construction materials. Mexico's economy has been strongly influenced by international trade since the country commenced competing in international markets. In the 1970s, Mexico mainly exported primary resources. This pattern has changed and manufactured goods now have a much greater importance due to a boom in assembling industries. In contrast with other Latin American countries, Mexico has achieved a diversification of production, moving towards technology-intensive products and a better mix in its export portfolio. However, crude oil exports still represent the single most important export good. Mexico's material consumption is still well below the OECD average but is growing fast and the current resource use patterns may well present serious social and environmental problems to the medium and long-term sustainability of Mexico's economy and community. Information on natural resource use and resource productivity could provide valuable guidance for economic policy planning in Mexico. (author)

  13. Biophysical Methods to Investigate Intrinsically Disordered Proteins: Avoiding an "Elephant and Blind Men" Situation.

    Science.gov (United States)

    Uversky, Vladimir N

    2015-01-01

    Intrinsically disordered proteins (IDPs) and hybrid proteins possessing ordered domains and intrinsically disordered protein regions (IDPRs) are highly abundant in various proteomes. They are different from ordered proteins at many levels, and an unambiguous representation of an IDP structure is a difficult task. In fact, IDPs show an extremely wide diversity in their structural properties, being able to attain extended conformations (random coil-like) or to remain globally collapsed (molten globule-like). Disorder can differently affect different parts of a protein, with some regions being more ordered than others. IDPs and IDPRs exist as dynamic ensembles, resembling "protein-clouds". IDP structures are best presented as conformational ensembles that contain highly dynamic structures interconverting on a number of timescales. The determination of a unique high-resolution structure is not possible for an isolated IDP, and a detailed structural and dynamic characterization of IDPs cannot typically be provided by a single tool. Therefore, accurate descriptions of IDPs/IDPRs rely on a multiparametric approach that includes a host of biophysical methods that can provide information on the overall compactness of IDPs and their conformational stability, shape, residual secondary structure, transient long-range contacts, regions of restricted or enhanced mobility, etc. The goal of this chapter is to provide a brief overview of some of the components of this multiparametric approach. PMID:26387104

  14. Biophysical consequences of linker chemistry and polymer size on stealth erythrocytes: size does matter.

    Science.gov (United States)

    Bradley, Amanda J; Murad, Kari L; Regan, Katy L; Scott, Mark D

    2002-04-12

    Immunocamouflaged red blood cells (RBC) are produced by cell surface derivatization with methoxypolyethylene glycol (mPEG). These immunologically attenuated cells may reduce the risk of allosensitization in chronically transfused patients. To characterize the effects of differing linker chemistries and polymer lengths, RBC were modified with cyanuric chloride activated mPEG (C-mPEG 5 kDa), benzotriazole carbonate methoxyPEG (BTC-mPEG; 5 or 20 kDa) or N-hydroxysuccinimidyl ester of mPEG propionic acid (SPA-mPEG; 2, 5 or 20 kDa). Biophysical methods including particle electrophoresis and aqueous two-phase polymer partitioning were employed to compare the PEG derivatives. While C-mPEG was faster reacting, both BTC-mPEG and SPA-mPEG gave comparable findings after 1 h. Both PEG surface density and molecular mass had a large effect on RBC surface properties. Proportional changes in electrophoretic mobility and preferential phase partitioning were achieved by increasing either the quantity of surface PEG or the PEG molecular mass. In addition, two-phase partitioning may provide a means for efficiently removing unmodified or lightly modified (hence potentially immunogenic) RBC in the clinical setting. Furthermore, mPEG modification significantly inhibits cell-cell interaction as evidenced by loss of Rouleaux formation and, consequently, sedimentation rate. Importantly, BTC-mPEG 20 kDa RBC showed normal in vivo survival in mice at immunoprotective concentrations (up to 2 mM). PMID:11997115

  15. Magnetic nanoparticles for biophysical applications synthesized by high-power physical dispersion

    International Nuclear Information System (INIS)

    The low cost and high output methods of high-power physical dispersion: the electrical explosion of wire and the laser target evaporation were elaborated for the production of iron oxide magnetic nanoparticles (MNPs) with controlled dispersion parameters and highly reproducible functional properties. The synthesized MNPs were spherical in shape with mean diameter 10 nm and lognormal particle size distribution. The phase composition, shape, particle size and functional properties of MNPs were cross-examined by a variety of contemporary experimental techniques. The phase structure of MNPs corresponds to the inverse spinel of magnetite. Meanwhile, due to the non-equilibrium conditions of the dispersion chemical composition of MNPs is close to maghemite—γ-Fe2O3. Their magnetic properties are reproducible and very close to the single domain superparamagnetic behavior. The stability of the suspensions of these MNPs and their applicability in the biophysical purposes such as magneto-induced heating have been demonstrated. - Highlights: • We present two methods of low-cost and high output production of iron oxide nanoparticles. • We obtained 10 nm spherical maghemite nanoparticles with close to superparamagnetic behavior. • The suspensions of obtained nanoparticles are stable to salt in physiological concentration. • Magneto-induced heating of suspensions fits well with the theoretical predictions

  16. Energy Materials Research Laboratory (EMRL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Energy Materials Research Laboratory at the Savannah River National Laboratory (SRNL) creates a cross-disciplinary laboratory facility that lends itself to the...

  17. Biophysical characterization data on Aβ soluble oligomers produced through a method enabling prolonged oligomer stability and biological buffer conditions

    Directory of Open Access Journals (Sweden)

    Amanda C. Crisostomo

    2015-09-01

    Aβ1-40 soluble oligomers are produced that are suitable for biophysical studies requiring sufficient transient stability to exist in their “native” conformation in biological phosphate-saline buffers for extended periods of time. The production involves an initial preparation of highly monomeric Aβ in a phosphate saline buffer that transitions to fibrils and oligomers through time incubation alone, without added detergents or non-aqueous chemicals. This criteria ensures that the only difference between initial monomeric Aβ reactant and subsequent Aβ oligomer products is their degree of peptide assembly. A number of chemical and biophysical methods were used to characterize the monomeric reactants and soluble oligomer and amyloid fibril products, including chemical cross-linking, Western blots, fraction solubility, thioflvain T binding, size exclusion chromatography, transmission electron micrscopy, circular dichroism spectroscopy, and fluorescence resonance energy transfer.

  18. A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation

    OpenAIRE

    Farasat, Iman; Salis, Howard M.

    2016-01-01

    The ability to precisely modify genomes and regulate specific genes will greatly accelerate several medical and engineering applications. The CRISPR/Cas9 (Type II) system binds and cuts DNA using guide RNAs, though the variables that control its on-target and off-target activity remain poorly characterized. Here, we develop and parameterize a system-wide biophysical model of Cas9-based genome editing and gene regulation to predict how changing guide RNA sequences, DNA superhelical densities, ...

  19. A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation.

    OpenAIRE

    Iman Farasat; Salis, Howard M.

    2016-01-01

    The ability to precisely modify genomes and regulate specific genes will greatly accelerate several medical and engineering applications. The CRISPR/Cas9 (Type II) system binds and cuts DNA using guide RNAs, though the variables that control its on-target and off-target activity remain poorly characterized. Here, we develop and parameterize a system-wide biophysical model of Cas9-based genome editing and gene regulation to predict how changing guide RNA sequences, DNA superhelical densities, ...

  20. A biophysical model of brain deformation to simulate and analyze longitudinal MRIs of patients with Alzheimer's disease

    OpenAIRE

    Khanal, Bishesh; Lorenzi, Marco; Ayache, Nicholas; Pennec, Xavier

    2016-01-01

    We propose a framework for developing a comprehensive biophysical model that could predict and simulate realistic longitudinal MRIs of patients with Alzheimer's Disease (AD). The framework includes three major building blocks: i) Atrophy generation ii) Brain deformation iii) Realistic MRI generation. Within this framework, this paper focuses on a detailed implementation of the brain deformation block with a carefully designed biomechanics-based tissue loss model. For a given baseline brain MR...

  1. In vitro inhibition of biophysical surface properties and change in ultrastructures of exogenous pulmonary surfactant by albumin or fibrinogen.

    OpenAIRE

    Park, J.; Bae, C. W.; Choi, Y. M.

    1998-01-01

    In order to observe the effects of serum albumin and fibrinogen on biophysical surface properties and the morphology of pulmonary surfactant in vitro, we measured the surface adsorption rate, dynamic minimum and maximum surface tension (min-, max-ST) by Pulsating Bubble Surfactometer, and demonstrated ultrastructures on a series of mixtures with varying concentrations of albumin or fibrinogen and Surfactant-TA. The albumin and fibrinogen significantly inhibited the adsorption rate and ST-lowe...

  2. Fundamental principles of data assimilation underlying the Verdandi library: applications to biophysical model personalization within euHeart

    OpenAIRE

    Chapelle, Dominique; Fragu, Marc; Mallet, Vivien; Moireau, Philippe

    2013-01-01

    We present the fundamental principles of data assimilation underlying the Verdandi library, and how they are articulated with the modular architecture of the library. This translates -- in particular -- into the definition of standardized interfaces through which the data assimilation library interoperates with the model simulation software and the so-called observation manager. We also survey various examples of data assimilation applied to the personalization of biophysical models, in parti...

  3. The conformational stability and biophysical properties of the eukaryotic thioredoxins of Pisum sativum are not family-conserved.

    Directory of Open Access Journals (Sweden)

    David Aguado-Llera

    Full Text Available Thioredoxins (TRXs are ubiquitous proteins involved in redox processes. About forty genes encode TRX or TRX-related proteins in plants, grouped in different families according to their subcellular localization. For instance, the h-type TRXs are located in cytoplasm or mitochondria, whereas f-type TRXs have a plastidial origin, although both types of proteins have an eukaryotic origin as opposed to other TRXs. Herein, we study the conformational and the biophysical features of TRXh1, TRXh2 and TRXf from Pisum sativum. The modelled structures of the three proteins show the well-known TRX fold. While sharing similar pH-denaturations features, the chemical and thermal stabilities are different, being PsTRXh1 (Pisum sativum thioredoxin h1 the most stable isoform; moreover, the three proteins follow a three-state denaturation model, during the chemical-denaturations. These differences in the thermal- and chemical-denaturations result from changes, in a broad sense, of the several ASAs (accessible surface areas of the proteins. Thus, although a strong relationship can be found between the primary amino acid sequence and the structure among TRXs, that between the residue sequence and the conformational stability and biophysical properties is not. We discuss how these differences in the biophysical properties of TRXs determine their unique functions in pea, and we show how residues involved in the biophysical features described (pH-titrations, dimerizations and chemical-denaturations belong to regions involved in interaction with other proteins. Our results suggest that the sequence demands of protein-protein function are relatively rigid, with different protein-binding pockets (some in common for each of the three proteins, but the demands of structure and conformational stability per se (as long as there is a maintained core, are less so.

  4. Effect of GnRH antagonist on follicular development and uterine biophysical profile in controlled ovarian stimulation

    Directory of Open Access Journals (Sweden)

    Bhawana Tiwary

    2015-02-01

    Full Text Available Background: Objective of current study was to assess the effect of GnRH antagonist on follicular development, premature luteinization, uterine biophysical profile and pregnancy rate in controlled ovarian stimulation with clomiphene and gonadotropins for intrauterine insemination in women with unexplained infertility. Methods: Randomised controlled trial. Minimal stimulation protocol with or without GnRH antagonist was compared. Setting: Infertility clinic, PGIMER, Chandigarh. Patients: Couples with unexplained infertility, age of female partner between 20-39 years. Intervention: GnRH antagonist 0.25 mg since follicle size 14 mm till hCG administration. Main outcome measures: Follicle characteristics, premature luteinisation, uterine biophysical profile and pregnancy rate. Results: The mean number of follicles recruited in group A was 2.32 +/- 1.01 while that in group B (receiving GnRH antagonist it was 4.10 +/- 1.69. Statistically significant increase in total biophysical profile score was observed in periovulatory phase in the antagonist group. 40% women in group A had premature luteinization whereas only 4% women in group B suffered from premature luteinization. 20% women who received GnRH antagonist conceived against only 6% in group A, this difference however was not statistically significant Conclusions: GnRH antagonist has a role in increasing the number of follicles recruited. Furthermore, GnRH antagonist can improve the total uterine biophysical profile score by improving the endometrial thickness, endometrial pattern, blood flow and decreasing the impedance to the blood flow in uterine artery. The drug can potentially help in improving pregnancy rates by decreasing the rate of premature luteinisation. [Int J Reprod Contracept Obstet Gynecol 2015; 4(1.000: 157-163

  5. Statistical Distances and Their Applications to Biophysical Parameter Estimation: Information Measures, M-Estimates, and Minimum Contrast Methods

    Directory of Open Access Journals (Sweden)

    Peter R. J. North

    2013-03-01

    Full Text Available Radiative transfer models predicting the bidirectional reflectance factor (BRF of leaf canopies are powerful tools that relate biophysical parameters such as leaf area index (LAI, fractional vegetation cover fV and the fraction of photosynthetically active radiation absorbed by the green parts of the vegetation canopy (fAPAR to remotely sensed reflectance data. One of the most successful approaches to biophysical parameter estimation is the inversion of detailed radiative transfer models through the construction of Look-Up Tables (LUTs. The solution of the inverse problem requires additional information on canopy structure, soil background and leaf properties, and the relationships between these parameters and the measured reflectance data are often nonlinear. The commonly used approach for optimization of a solution is based on minimization of the least squares estimate between model and observations (referred to as cost function or distance; here we will also use the terms “statistical distance” or “divergence” or “metric”, which are common in the statistical literature. This paper investigates how least-squares minimization and alternative distances affect the solution to the inverse problem. The paper provides a comprehensive list of different cost functions from the statistical literature, which can be divided into three major classes: information measures, M-estimates and minimum contrast methods. We found that, for the conditions investigated, Least Square Estimation (LSE is not an optimal statistical distance for the estimation of biophysical parameters. Our results indicate that other statistical distances, such as the two power measures, Hellinger, Pearson chi-squared measure, Arimoto and Koenker–Basset distances result in better estimates of biophysical parameters than LSE; in some cases the parameter estimation was improved by 15%.

  6. Planning for sustainable tourism in southern Pulau Banggi: an assessment of biophysical conditions and their implications for future tourism development.

    Science.gov (United States)

    Teh, Lydia; Cabanban, Annadel S

    2007-12-01

    A priori assessments of a site's biophysical and socio-economic capacity for accommodating tourism are less common than tourism impact studies. A priori evaluations can provide a contextual understanding of ecological, economic and socio-cultural forces, which shape the prospects for sustainable tourism development at the host destination, and can avert adverse impacts of tourism. We conduct an a priori assessment of the biophysical environment of Pulau Banggi, in the Malaysian state of Sabah for sustainable tourism development. We characterise baseline conditions of the island's marine biodiversity, seasonality, and infrastructure. We then evaluate how existing biophysical conditions will influence options for sustainable tourism development. In particular, we suggest conditions, if there are any, which constitute a limit to future tourism development in terms of compatibility for recreation and resilience to visitor impacts. We find that the biggest constraint is the lack of adequate water and sanitation infrastructure. Blast fishing, although occurring less than once per hour, can potentially destroy the major attraction for tourists. We conclude that while Pulau Banggi possesses natural qualities that are attractive for ecotourism, financial and institutional support must be made available to provide facilities and services that will enable local participation in environmental protection and enhance prospects for future sustainable tourism. PMID:17204361

  7. Some behavioral aspects of energy descent: How a biophysical psychology might help people transition through the lean times ahead

    Directory of Open Access Journals (Sweden)

    Raymond eDe Young

    2014-11-01

    Full Text Available We may soon face biophysical limits to perpetual growth. Energy supplies may tighten and then begin a long slow descent while defensive expenditures rise to address problems caused by past resource consumption. The outcome may be significant changes in daily routines at the individual and community level. It is difficult to know when this scenario might begin to unfold but it clearly would constitute a new behavioral context, one that the behavioral sciences least attends to. Even if one posits a less dramatic scenario, people may still need to make many urgent and perhaps unsettling transitions. And while a robust response would be needed, it is not at all clear what should be the details of that response. Since it is likely that no single response will fix things everywhere, for all people or for all time it would be useful to conduct many social experiments. Indeed, a culture of small experiments should be fostered which, at the individual and small group level, can be described as behavioral entrepreneurship. This may have begun, hidden in plain sight, but more social experiments are needed. To be of help, it may be useful to both package behavioral insights in a way that is practitioner-oriented and grounded in biophysical trends and to propose a few key questions that need attention. This paper begins the process of developing a biophysical psychology, incomplete as it is at this early stage.

  8. Some behavioral aspects of energy descent: how a biophysical psychology might help people transition through the lean times ahead.

    Science.gov (United States)

    De Young, Raymond

    2014-01-01

    We may soon face biophysical limits to perpetual growth. Energy supplies may tighten and then begin a long slow descent while defensive expenditures rise to address problems caused by past resource consumption. The outcome may be significant changes in daily routines at the individual and community level. It is difficult to know when this scenario might begin to unfold but it clearly would constitute a new behavioral context, one that the behavioral sciences least attends to. Even if one posits a less dramatic scenario, people may still need to make many urgent and perhaps unsettling transitions. And while a robust response would be needed, it is not at all clear what should be the details of that response. Since it is likely that no single response will fix things everywhere, for all people or for all time, it would be useful to conduct many social experiments. Indeed, a culture of small experiments should be fostered which, at the individual and small group level, can be described as behavioral entrepreneurship. This may have begun, hidden in plain sight, but more social experiments are needed. To be of help, it may be useful to both package behavioral insights in a way that is practitioner-oriented and grounded in biophysical trends and to propose a few key questions that need attention. This paper begins the process of developing a biophysical psychology, incomplete as it is at this early stage. PMID:25404926

  9. Unveiling soil degradation and desertification risk in the Mediterranean basin: a data mining analysis of the relationships between biophysical and socioeconomic factors in agro-forest landscapes

    NARCIS (Netherlands)

    Salvati, L.; Kosmas, C.; Kairis, O.; Karavitis, C.; Hessel, R.; Ritsema, C.J.

    2015-01-01

    Soil degradation and desertification processes in the Mediterranean basin reflect the interplay between environmental and socioeconomic drivers. An approach to evaluate comparatively the multiple relationships between biophysical variables and socioeconomic factors is illustrated in the present stud

  10. Biophysical analysis of natural, double-helical DNA modified by dinuclear platinum(II) organometallic compound in a cell-free medium

    Czech Academy of Sciences Publication Activity Database

    Marini, Victoria; Kašpárková, Jana; Nováková, Olga; Scolaro, L. M.; Romeo, R.; Brabec, Viktor

    Florence, 2001, s. 9. [COST Action: D20 Metal Compounds in the Treatment of Cancer . Florence (IT), 29.08.2001] Institutional research plan: CEZ:AV0Z5004920 Keywords : DNA * platinum * cross-link Subject RIV: BO - Biophysics

  11. QTL for shelf life in lettuce co-locate with those for leaf biophysical properties but not for leaf developmental traits

    OpenAIRE

    Zhang, Fang Z.; Wagstaff, Carol; Rae, Anne M; Sihota, Arinder K.; Keevil, C. William; Rothwell, Steve D.; Clarkson, Graham J. J.; Michelmore, Richard W; Truco, Maria Jose; Dixon, Mark S.; Taylor, Gail

    2007-01-01

    Developmental and biophysical leaf characteristics that influence post-harvest shelf life in lettuce, an important leafy crop, have been examined. The traits were studied using 60 informative F9 recombinant inbreed lines (RILs) derived from a cross between cultivated lettuce (Lactuca sativa cv. Salinas) and wild lettuce (L. serriola acc. UC96US23). Quantitative Trait Loci (QTL) for shelf life co-located most closely with those for leaf biophysical properties such as plasticity, elasticity and...

  12. Early integration of the individual student in academic activities: a novel classroom concept for graduate education in molecular biophysics and structural biology

    OpenAIRE

    Leuba, Sanford H.; Carney, Sean M; Dahlburg, Elizabeth M; Eells, Rebecca J; Ghodke, Harshad; Yanamala, Naveena; Schauer, Grant; Klein-Seetharaman, Judith

    2014-01-01

    Background A key challenge in interdisciplinary research is choosing the best approach from a large number of techniques derived from different disciplines and their interfaces. Results To address this challenge in the area of Biophysics and Structural Biology, we have designed a graduate level course to teach students insightful use of experimental biophysical approaches in relationship to addressing biological questions related to biomolecular interactions and dynamics. A weekly seminar and...

  13. Program Review Challenges and Opportunities for Training the Next Generation of Biophysicists: Perspectives of the Directors of the Molecular Biophysics Training Program at Northwestern University

    OpenAIRE

    Neuhaus, Francis; Widom, Jonathan; MacDonald, Robert; Jardetzky, Theodore; Radhakrishnan, Ishwar

    2008-01-01

    Molecular biophysics is a broad, diverse, and dynamic field that has presented a variety of unique challenges and opportunities for training future generations of investigators. Having been or currently being intimately associated with the Molecular Biophysics Training Program at Northwestern, we present our perspectives on various issues that we have encountered over the years. We propose no cookie-cutter solutions, as there is no consensus on what constitutes the “ideal” program. However, t...

  14. Use of passive UAS imaging to measure biophysical parameters in a southern Rocky Mountain subalpine forest

    Science.gov (United States)

    Caldwell, M. K.; Sloan, J.; Mladinich, C. S.; Wessman, C. A.

    2013-12-01

    Unmanned Aerial Systems (UAS) can provide detailed, fine spatial resolution imagery for ecological uses not otherwise obtainable through standard methods. The use of UAS imagery for ecology is a rapidly -evolving field, where the study of forest landscape ecology can be augmented using UAS imagery to scale and validate biophysical data from field measurements to spaceborne observations. High resolution imagery provided by UAS (30 cm2 pixels) offers detailed canopy cover and forest structure data in a time efficient and inexpensive manner. Using a GoPro Hero2 (2 mm focal length) camera mounted in the nose cone of a Raven unmanned system, we collected aerial and thermal data monthly during the summer 2013, over two subalpine forests in the Southern Rocky Mountains in Colorado. These forests are dominated by lodgepole pine (Pinus ponderosae) and have experienced insect-driven (primarily mountain pine beetle; MPB, Dendroctonus ponderosae) mortality. Objectives of this study include observations of forest health variables such as canopy water content (CWC) from thermal imagery and leaf area index (LAI), biomass and forest productivity from the Normalized Difference Vegetation Index (NDVI) from UAS imagery. Observations were, validated with ground measurements. Images were processed using a combination of AgiSoft Photoscan professional software and ENVI remote imaging software. We utilized the software Leaf Area Index Calculator (LAIC) developed by Córcoles et al. (2013) for calculating LAI from digital images and modified to conform to leaf area of needle-leaf trees as in Chen and Cihlar (1996) . LAIC uses a K-means cluster analysis to decipher the RGB levels for each pixel and distinguish between green aboveground vegetation and other materials, and project leaf area per unit of ground surface area (i.e. half total needle surface area per unit area). Preliminary LAIC UAS data shows summer average LAI was 3.8 in the most dense forest stands and 2.95 in less dense

  15. Interaction of biocompatible natural rosin-based surfactants with human serum albumin: A biophysical study

    International Nuclear Information System (INIS)

    Biophysical insight into interaction of biocompatible rosin-based surfactants with human serum albumin (HSA) was studied at physiological conditions using various spectroscopic, calorimetric and molecular docking approaches. The binding constant (Kb), enthalpy (ΔH0), entropy (ΔS0) and Gibbs free energy change (ΔG0) were calculated by spectroscopic and calorimetric method. We have also calculated the probability of energy transfer by FRET analysis. The circular dichroism study showed that the cationic surfactant QRMAE significantly altered the secondary structure of HSA as compared to the nonionic rosin surfactants. The thermodynamic study was performed by ITC to determine binding constant as well as change in enthalpy of HSA in presence of rosin surfactants. It clearly showed that hydrogen binding and hydrophobic interaction play an important role in the binding of HSA to rosin surfactants. We have also performed molecular docking studies to locate the binding site on HSA and to visualize the mode of interaction. The present study provides a significant insight into HSA–rosin surfactants interaction, which also improves our understanding of the possible effect of rosin surfactants on human health. - Highlights: • RMPEG 750 has the highest Kb, Kq and Ksv value as compared to other rosin surfactants. • The probability of energy transfer from HSA to rosin surfactants was maximum in the case of RMPEG 750. • Cationic surfactant QRMAE significantly altered the secondary structure of the HSA as compared to other rosin surfactants. • Molecular docking and ITC experiment studies, to locate the binding site on HSA and to investigate the mode of interaction

  16. Laser therapy of the lung: biophysical background; Lasertherapie in der Lunge: Biophysikalischer Hintergrund

    Energy Technology Data Exchange (ETDEWEB)

    Knappe, V. [Laser- und Medizin-Technologie GmbH Berlin, Berlin (Germany); Mols, A. [Campus Benjamin Franklin, Charite - Universitaetsmedizin Berlin (Germany)

    2004-07-01

    The laser is a well established surgical instrument in lung therapy. This report provides information on the biophysical basics of the laser-induced thermotherapy (LITT) of lung metastases. Optical properties like absorption and scattering determine the penetration depth of laser radiation in tissue. These parameters vary dynamically during the application and define in combination with thermal tissue properties the achievable destruction volume. Parenchyma behaves very differently compared to more dense tissues due to local inhomogenities and the large amount cavaties filled with air. Beside an account of the affecting parameters an overview of therapy options is given. Therapeutic results depend not only on the tissue properties but also on the technical equipment, e.g. the applicator design and the energy applied. Complex dosimetric models allow for a calculation of the lesion's size in advance. (orig.) [German] Der Laser ist in der Lungenchirurgie ein bereits etabliertes Instrument. In diesem Beitrag werden speziell die biophysikalischen Hintergruende der laserinduzierten Thermotherapie (LITT) von Lungenmetastasen beschrieben. In der Gewebeoptik determinieren Absorption und Streuung die Eindringtiefe von Laserlicht. Diese Parameter veraendern sich dynamisch waehrend der Anwendung und bestimmen in Verbindung mit den thermischen Gewebeeigenschaften die maximal erzielbaren Destruktionsvolumina. Lokale Inhomogenitaeten und der hohe Anteil luftgefuellter Hohlraeume unterscheiden das Parenchym in dieser Hinsicht signifikant von dichteren Geweben. Neben einer Darstellung der beeinflussenden Parameter wird ein Ueberblick ueber die Therapieoptionen gegeben. Der Therapieerfolg haengt neben den genannten gewebeseitigen Parametern von Anzahl und Geometrie der Applikatoren und der applizierten Energie ab und kann mit komplexen Dosimetriemodellen im voraus kalkuliert werden. (orig.)

  17. Biophysical Mechanisms Underlying Hearing Loss Associated with a Shortened Tectorial Membrane

    Science.gov (United States)

    Oghalai, John S.; Xia, Anping; Liu, Christopher C.; Gao, Simon S.; Applegate, Brian E.; Puria, Sunil; Rousso, Itay; Steele, Charles

    2011-11-01

    The tectorial membrane (TM) connects to the stereociliary bundles of outer hair cells (OHCs). Herein, we summarize key experimental data and modeling analyses that describe how biophysical alterations to these connections underlie hearing loss. The heterozygous C1509G mutation in alpha tectorin produces partial congenital hearing loss that progresses in humans. We engineered this mutation in mice, and histology revealed that the TM was shortened. DIC imaging of freshly-dissected cochlea as well as imaging with optical coherence tomography indicated that the TM is malformed and only stimulates the first row of OHCs. Noise exposure produced acute threshold shifts that fully recovered in Tecta+/+ mice although there was some OHC loss within all three rows at the cochlear base. In contrast, threshold shifts only partially recovered in TectaC1509G/+ mice. This was associated with OHC loss more apically and nearly entirely within the first row. Young's modulus of the TM, measured using atomic force microscopy, was substantially reduced at the middle and basal regions. Both the wild-type and heterozygous conditions were simulated in a computational model. This demonstrated that the normalized stress distribution levels between the TM and the tall cilia were significantly elevated in the middle region of the heterozygous cochlea. Another feature of the TectaC1509G/+ mutation is higher prestin expression within all three rows of OHCs. This increased electricallyevoked movements of the reticular lamina and otoacoustic emissions. Furthermore, electrical stimulation was associated with an increased risk of OHC death as measured by vital dye staining. Together, these findings indicate that uncoupling of the TM from some OHCs not only leads to partial hearing loss, but also puts the OHCs that remain coupled at higher risk. Both the mechanics of the malformed TM and increased electromotility contribute to this higher risk profile.

  18. Interaction of biocompatible natural rosin-based surfactants with human serum albumin: A biophysical study

    Energy Technology Data Exchange (ETDEWEB)

    Ishtikhar, Mohd [Protein Biophysics Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002 (India); Ali, Mohd Sajid [Surfactant Research Chair, Department of Chemistry, King Saud University, P.O. Box-2455, Riyadh 11451 (Saudi Arabia); Atta, Ayman M. [Surfactant Research Chair, Department of Chemistry, King Saud University, P.O. Box-2455, Riyadh 11451 (Saudi Arabia); Petroleum Application department, Egyptian Petroleum Research Institute, Ahmad Elzomor St., Nasr city, Cairo-11727 (Egypt); Al-Lohedan, H.A. [Surfactant Research Chair, Department of Chemistry, King Saud University, P.O. Box-2455, Riyadh 11451 (Saudi Arabia); Nigam, Lokesh; Subbarao, Naidu [Centre for Computational Biology and Bioinformatics, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067 (India); Hasan Khan, Rizwan, E-mail: rizwanhkhan@hotmail.com [Protein Biophysics Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002 (India)

    2015-11-15

    Biophysical insight into interaction of biocompatible rosin-based surfactants with human serum albumin (HSA) was studied at physiological conditions using various spectroscopic, calorimetric and molecular docking approaches. The binding constant (K{sub b}), enthalpy (ΔH{sup 0}), entropy (ΔS{sup 0}) and Gibbs free energy change (ΔG{sup 0}) were calculated by spectroscopic and calorimetric method. We have also calculated the probability of energy transfer by FRET analysis. The circular dichroism study showed that the cationic surfactant QRMAE significantly altered the secondary structure of HSA as compared to the nonionic rosin surfactants. The thermodynamic study was performed by ITC to determine binding constant as well as change in enthalpy of HSA in presence of rosin surfactants. It clearly showed that hydrogen binding and hydrophobic interaction play an important role in the binding of HSA to rosin surfactants. We have also performed molecular docking studies to locate the binding site on HSA and to visualize the mode of interaction. The present study provides a significant insight into HSA–rosin surfactants interaction, which also improves our understanding of the possible effect of rosin surfactants on human health. - Highlights: • RMPEG 750 has the highest Kb, Kq and Ksv value as compared to other rosin surfactants. • The probability of energy transfer from HSA to rosin surfactants was maximum in the case of RMPEG 750. • Cationic surfactant QRMAE significantly altered the secondary structure of the HSA as compared to other rosin surfactants. • Molecular docking and ITC experiment studies, to locate the binding site on HSA and to investigate the mode of interaction.

  19. Biophysical perspective of the binding of ester-functionalized gemini surfactants with catalase.

    Science.gov (United States)

    Akram, Mohd; Bhat, Imtiyaz Ahmad; Anwar, Sana; Ahmad, Ajaz; Kabir-Ud-Din

    2016-07-01

    Interaction of surfactants with biomacromolecules is an essential subject of biophysical chemistry to address their diverse applications in industry, biomedical, and cosmetic domains. In this context, we have examined the binding interactions of three ester-functionalized surfactants (m-E2-m) with bovine liver catalase (BLC, 10μM) by employing a multi-technique approach. The m-E2-m geminis quench fluorescence intensity of BLC through static procedure. The binding ability of concerned gemini surfactants was found to be in the order 12-E2-12 (Kb=2.3×10(2))>16-E2-16 (Kb=1.1×10(2))>14-E2-14 (Kb=1.0×10(2)). Quenching efficacy, as determined by Ksv values, were observed as 12-E2-12 (3.0×10(2))>16-E2-16 (1.4×10(2))>14-E2-14 (1.0×10(2)). The negative ΔG°b values (12-E2-12 (-13.48kJ/mol)>16-E2-16 (-11.65kJ/mol)>14-E2-14 (-11.41kJ/mol)) indicate spontaneous nature of m-E2-m-BLC interactions. UV-vis spectroscopy, circular dichroism (CD) and micropolarity (F1/F3) assessments indicate conformational changes in BLC upon m-E2-m combination. ITC confirms the stability of BLC upon gemini combination. Docking provides support to fluorescence results by presenting the localization site of m-E2-m surfactants near to aromatic residues (mainly Tyr, Trp and Phe). Moreover, since surfactant-protein interactions have essential miscellaneous implications, therefore, this study can be significant for industrial and biomedical realms. PMID:27060016

  20. Specificity and affinity of phenosafranine protein adduct: Insights from biophysical aspects

    Energy Technology Data Exchange (ETDEWEB)

    Ding Fei [Department of Chemistry, China Agricultural University, Beijing 100193 (China); Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Zhang Li; Sun Ye [Department of Chemistry, China Agricultural University, Beijing 100193 (China); Diao Jianxiong [College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193 (China); Yang Xinling [Department of Chemistry, China Agricultural University, Beijing 100193 (China); Sun Ying, E-mail: sunying@cau.edu.cn [College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193 (China); Zhang Li, E-mail: zhli.work@gmail.com [Key Laboratory of Pesticide Chemistry and Application Technology, Ministry of Agriculture, Department of Applied Chemistry, China Agricultural University, Beijing 100193 (China)

    2012-03-15

    Phenosafranine is a toxic and recalcitrant compound, whose capacity to intercalate with double stranded DNA has been shown. In this contribution, a biophysical discuss on the conjugation of phenosafranine with two model proteins human serum albumin (HSA) and lysozyme (Lys) has been identified utilizing a combination of molecular modeling, steady state and time-resolved fluorescence and circular dichroism (CD) approaches. The accurate binding domain of phenosafranine in protein has been characterized from molecular modeling, subdomain IIIA of HSA and Trp-62, Trp-63 and Trp-108 residues of Lys was designated to possess high-affinity for this compound, the dominant forces in the protein-phenosafranine adduct are hydrogen bonds and {pi}-{pi} interactions, but hydrophobic interactions between dye and Lys are also not exclude. The data of fluorescence displayed that the complex of phenosafranine with protein produces quenching through static property, this corroborates the time-resolved fluorescence results that the ground state complex formation with a moderate affinity of 10{sup 4} M{sup -1}. Moreover, via synchronous fluorescence, CD and three-dimensional fluorescence we indicated some extent of polypeptide chain of protein partially unfolding upon conjugation with phenosafranine. Through this work, we anticipate it can supply salient clues on the toxicological action of phenosafranine and other azines, which have analogous configuration with phenosafranine. - Highlights: Black-Right-Pointing-Pointer Our study supply salient clues on the toxicological action of toxic phenosafranine. Black-Right-Pointing-Pointer Phenosafranine is situated within subdomain IIIA, Sudlow's site II on HSA. Black-Right-Pointing-Pointer Trp-62, Trp-63 and Trp-108 residues on the Lys molecule are all close to dye. Black-Right-Pointing-Pointer Static property of the phenosafranine induced quenching of protein Trp fluorescence. Black-Right-Pointing-Pointer Protein spatial structure proved

  1. A biophysical model of endocannabinoid-mediated short term depression in hippocampal inhibition.

    Directory of Open Access Journals (Sweden)

    Margarita Zachariou

    Full Text Available Memories are believed to be represented in the synaptic pathways of vastly interconnected networks of neurons. The plasticity of synapses, that is, their strengthening and weakening depending on neuronal activity, is believed to be the basis of learning and establishing memories. An increasing number of studies indicate that endocannabinoids have a widespread action on brain function through modulation of synaptic transmission and plasticity. Recent experimental studies have characterised the role of endocannabinoids in mediating both short- and long-term synaptic plasticity in various brain regions including the hippocampus, a brain region strongly associated with cognitive functions, such as learning and memory. Here, we present a biophysically plausible model of cannabinoid retrograde signalling at the synaptic level and investigate how this signalling mediates depolarisation induced suppression of inhibition (DSI, a prominent form of short-term synaptic depression in inhibitory transmission in hippocampus. The model successfully captures many of the key characteristics of DSI in the hippocampus, as observed experimentally, with a minimal yet sufficient mathematical description of the major signalling molecules and cascades involved. More specifically, this model serves as a framework to test hypotheses on the factors determining the variability of DSI and investigate under which conditions it can be evoked. The model reveals the frequency and duration bands in which the post-synaptic cell can be sufficiently stimulated to elicit DSI. Moreover, the model provides key insights on how the state of the inhibitory cell modulates DSI according to its firing rate and relative timing to the post-synaptic activation. Thus, it provides concrete suggestions to further investigate experimentally how DSI modulates and is modulated by neuronal activity in the brain. Importantly, this model serves as a stepping stone for future deciphering of the role of

  2. Human and biophysical influences on fire occurrence in the United States.

    Science.gov (United States)

    Hawbaker, Todd J; Radeloff, Volker C; Stewart, Susan I; Hammer, Roger B; Keuler, Nicholas S; Clayton, Murray K

    2013-04-01

    National-scale analyses of fire occurrence are needed to prioritize fire policy and management activities across the United States. However, the drivers of national-scale patterns of fire occurrence are not well understood, and how the relative importance of human or biophysical factors varies across the country is unclear. Our research goal was to model the drivers of fire occurrence within ecoregions across the conterminous United States. We used generalized linear models to compare the relative influence of human, vegetation, climate, and topographic variables on fire occurrence in the United States, as measured by MODIS active fire detections collected between 2000 and 2006. We constructed models for all fires and for large fires only and generated predictive maps to quantify fire occurrence probabilities. Areas with high fire occurrence probabilities were widespread in the Southeast, and localized in the Mountain West, particularly in southern California, Arizona, and New Mexico. Probabilities for large-fire occurrence were generally lower, but hot spots existed in the western and south-central United States The probability of fire occurrence is a critical component of fire risk assessments, in addition to vegetation type, fire behavior, and the values at risk. Many of the hot spots we identified have extensive development in the wildland--urban interface and are near large metropolitan areas. Our results demonstrated that human variables were important predictors of both all fires and large fires and frequently exhibited nonlinear relationships. However, vegetation, climate, and topography were also significant variables in most ecoregions. If recent housing growth trends and fire occurrence patterns continue, these areas will continue to challenge policies and management efforts seeking to balance the risks generated by wildfires with the ecological benefits of fire. PMID:23734486

  3. REMOTE-SENSING-BASED BIOPHYSICAL MODELS FOR ESTIMATING LAI OF IRRIGATED CROPS IN MURRY DARLING BASIN

    Directory of Open Access Journals (Sweden)

    I. Wittamperuma

    2012-07-01

    Full Text Available Remote sensing is a rapid and reliable method for estimating crop growth data from individual plant to crops in irrigated agriculture ecosystem. The LAI is one of the important biophysical parameter for determining vegetation health, biomass, photosynthesis and evapotranspiration (ET for the modelling of crop yield and water productivity. Ground measurement of this parameter is tedious and time-consuming due to heterogeneity across the landscape over time and space. This study deals with the development of remote-sensing based empirical relationships for the estimation of ground-based LAI (LAIG using NDVI, modelled with and without atmospheric correction models for three irrigated crops (corn, wheat and rice grown in irrigated farms within Coleambally Irrigation Area (CIA which is located in southern Murray Darling basin, NSW in Australia. Extensive ground truthing campaigns were carried out to measure crop growth and to collect field samples of LAI using LAI- 2000 Plant Canopy Analyser and reflectance using CROPSCAN Multi Spectral Radiometer at several farms within the CIA. A Set of 12 cloud free Landsat 5 TM satellite images for the period of 2010-11 were downloaded and regression analysis was carried out to analyse the co-relationships between satellite and ground measured reflectance and to check the reliability of data sets for the crops. Among all the developed regression relationships between LAI and NDVI, the atmospheric correction process has significantly improved the relationship between LAI and NDVI for Landsat 5 TM images. The regression analysis also shows strong correlations for corn and wheat but weak correlations for rice which is currently being investigated.

  4. Human and biophysical drivers of fires in Semiarid Chaco mountains of Central Argentina.

    Science.gov (United States)

    Argañaraz, Juan P; Gavier Pizarro, Gregorio; Zak, Marcelo; Landi, Marcos A; Bellis, Laura M

    2015-07-01

    Fires are a recurrent disturbance in Semiarid Chaco mountains of central Argentina. The interaction of multiple factors generates variable patterns of fire occurrence in space and time. Understanding the dominant fire drivers at different spatial scales is a fundamental goal to minimize the negative impacts of fires. Our aim was to identify the biophysical and human drivers of fires in the Semiarid Chaco mountains of Central Argentina and their individual effects on fire activity, in order to determine the thresholds and/or ranges of the drivers at which fire occurrence is favored or disfavored. We used fire frequency as the response variable and a set of 28 potential predictor variables, which included climatic, human, topographic, biological and hydrological factors. Data were analyzed using Boosted Regression Trees, using data from near 10,500 sampling points. Our model identified the fire drivers accurately (75.6% of deviance explained). Although humans are responsible for most ignitions, climatic variables, such as annual precipitation, annual potential evapotranspiration and temperature seasonality were the most important determiners of fire frequency, followed by human (population density and distance to waste disposals) and biological (NDVI) predictors. In general, fire activity was higher at intermediate levels of precipitation and primary productivity and in the proximity of urban solid waste disposals. Fires were also more prone to occur in areas with greater variability in temperature and productivity. Boosted Regression Trees proved to be a useful and accurate tool to determine fire controls and the ranges at which drivers favor fire activity. Our approach provides a valuable insight into the ecology of fires in our study area and in other landscapes with similar characteristics, and the results will be helpful to develop management policies and predict changes in fire activity in response to different climate changes and development scenarios. PMID

  5. Biophysical determinants of alveolar epithelial plasma membrane wounding associated with mechanical ventilation.

    Science.gov (United States)

    Hussein, Omar; Walters, Bruce; Stroetz, Randolph; Valencia, Paul; McCall, Deborah; Hubmayr, Rolf D

    2013-10-01

    Mechanical ventilation may cause harm by straining lungs at a time they are particularly prone to injury from deforming stress. The objective of this study was to define the relative contributions of alveolar overdistension and cyclic recruitment and "collapse" of unstable lung units to membrane wounding of alveolar epithelial cells. We measured the interactive effects of tidal volume (VT), transpulmonary pressure (PTP), and of airspace liquid on the number of alveolar epithelial cells with plasma membrane wounds in ex vivo mechanically ventilated rat lungs. Plasma membrane integrity was assessed by propidium iodide (PI) exclusion in confocal images of subpleural alveoli. Cyclic inflations of normal lungs from zero end-expiratory pressure to 40 cmH2O produced VT values of 56.9 ± 3.1 ml/kg and were associated with 0.12 ± 0.12 PI-positive cells/alveolus. A preceding tracheal instillation of normal saline (3 ml) reduced VT to 49.1 ± 6 ml/kg but was associated with a significantly greater number of wounded alveolar epithelial cells (0.52 ± 0.16 cells/alveolus; P < 0.01). Mechanical ventilation of completely saline-filled lungs with saline (VT = 52 ml/kg) to pressures between 10 and 15 cmH2O was associated with the least number of wounded epithelial cells (0.02 ± 0.02 cells/alveolus; P < 0.01). In mechanically ventilated, partially saline-filled lungs, the number of wounded cells increased substantially with VT, but, once VT was accounted for, wounding was independent of maximal PTP. We found that interfacial stress associated with the generation and destruction of liquid bridges in airspaces is the primary biophysical cell injury mechanism in mechanically ventilated lungs. PMID:23997173

  6. NMR Solution Structure and Biophysical Characterization of Vibrio harveyi Acyl Carrier Protein A75H

    Science.gov (United States)

    Chan, David I.; Chu, Byron C. H.; Lau, Cheryl K. Y.; Hunter, Howard N.; Byers, David M.; Vogel, Hans J.

    2010-01-01

    Bacterial acyl carrier protein (ACP) is a highly anionic, 9 kDa protein that functions as a cofactor protein in fatty acid biosynthesis. Escherichia coli ACP is folded at neutral pH and in the absence of divalent cations, while Vibrio harveyi ACP, which is very similar at 86% sequence identity, is unfolded under the same conditions. V. harveyi ACP adopts a folded conformation upon the addition of divalent cations such as Ca2+ and Mg2+ and a mutant, A75H, was previously identified that restores the folded conformation at pH 7 in the absence of divalent cations. In this study we sought to understand the unique folding behavior of V. harveyi ACP using NMR spectroscopy and biophysical methods. The NMR solution structure of V. harveyi ACP A75H displays the canonical ACP structure with four helices surrounding a hydrophobic core, with a narrow pocket closed off from the solvent to house the acyl chain. His-75, which is charged at neutral pH, participates in a stacking interaction with Tyr-71 in the far C-terminal end of helix IV. pH titrations and the electrostatic profile of ACP suggest that V. harveyi ACP is destabilized by anionic charge repulsion around helix II that can be partially neutralized by His-75 and is further reduced by divalent cation binding. This is supported by differential scanning calorimetry data which indicate that calcium binding further increases the melting temperature of V. harveyi ACP A75H by ∼20 °C. Divalent cation binding does not alter ACP dynamics on the ps-ns timescale as determined by 15N NMR relaxation experiments, however, it clearly stabilizes the protein fold as observed by hydrogen-deuterium exchange studies. Finally, we demonstrate that the E. coli ACP H75A mutant is similarly unfolded as wild-type V. harveyi ACP, further stressing the importance of this particular residue for proper protein folding. PMID:20659901

  7. Cystic fibrosis transmembrane conductance regulator chloride channel blockers: Pharmacological, biophysical and physiological relevance

    Institute of Scientific and Technical Information of China (English)

    Paul; Linsdell

    2014-01-01

    Dysfunction of the cystic fibrosis transmembrane con-ductance regulator(CFTR) chloride channel causes cys-tic fibrosis, while inappropriate activity of this channeloccurs in secretory diarrhea and polycystic kidney dis-ease. Drugs that interact directly with CFTR are there-fore of interest in the treatment of a number of diseasestates. This review focuses on one class of small mol-ecules that interacts directly with CFTR, namely inhibi-tors that act by directly blocking chloride movementthrough the open channel pore. In theory such com-pounds could be of use in the treatment of diarrheaand polycystic kidney disease, however in practice allknown substances acting by this mechanism to inhibitCFTR function lack either the potency or specificity forin vivo use. Nevertheless, this theoretical pharmaco-logical usefulness set the scene for the developmentof more potent, specific CFTR inhibitors. Biophysically,open channel blockers have proven most useful as ex-perimental probes of the structure and function of theCFTR chloride channel pore. Most importantly, the useof these blockers has been fundamental in developing afunctional model of the pore that includes a wide innervestibule that uses positively charged amino acid sidechains to attract both permeant and blocking anionsfrom the cell cytoplasm. CFTR channels are also subjectto this kind of blocking action by endogenous anionspresent in the cell cytoplasm, and recently this blocking effect has been suggested to play a role in the physio-logical control of CFTR channel function, in particular as a novel mechanism linking CFTR function dynamically to the composition of epithelial cell secretions. It has also been suggested that future drugs could target this same pathway as a way of pharmacologically increasing CFTR activity in cystic fibrosis. Studying open channel blockers and their mechanisms of action has resulted in significant advances in our understanding of CFTR as a pharmacological target in disease states, of

  8. High-field 1H NMR microscopy for fundamental biophysical research

    International Nuclear Information System (INIS)

    This work has a biophysical background and uses different examples to demonstrate the practical applicability of NMR-Microscopy in the medical and biological sector. Therefore, the different projects are feasibility studies which are used to compare the possibilities and advantages of NMR-Microscopy with other, established examination techniques. In detail, using MR-Microscopy, different living and fixed biological samples have been visualized non-invasively with high spatial resolution. The specific purpose of the studies ranged from the visualization of the invasion of tumor-spheroids into cell aggregates using T2 parameter maps (time constant of the spin-spin relaxation) to the three-dimensional display of the honey bee brain in the intact head capsule and the non-invasive visualization of the anatomy of prenatal dolphins. For all these projects, the non-invasive character of MR-experiments was of utmost importance. The tumor invasion was not to be disturbed by the measurements, the bee brain should be visualized as close to its true natural shape as possible and the examined dolphins represent rare museum specimens which should not be destroyed. The different samples were all imaged with the best possible spatial resolution which was either limited by the necessary signal-to-noise ratio (SNR) or the available scan time. In order to resolve single details and fine structures in the images, it was necessary to optimize the SNR as well as the contrast-to-noise ratio. To guarantee the necessary SNR, the measurements were performed on high field MR-spectrometers with resonance frequencies of 500 and 750 MHz

  9. Potential influences of climate and nest structure on spotted owl reproductive success: a biophysical approach.

    Directory of Open Access Journals (Sweden)

    Jeremy T Rockweit

    Full Text Available Many bird species do not make their own nests; therefore, selection of existing sites that provide adequate microclimates is critical. This is particularly true for owls in north temperate climates that often nest early in the year when inclement weather is common. Spotted owls use three main types of nest structures, each of which are structurally distinct and may provide varying levels of protection to the eggs or young. We tested the hypothesis that spotted owl nest configuration influences nest microclimate using both experimental and observational data. We used a wind tunnel to estimate the convective heat transfer coefficient (h(c of eggs in 25 potential nest configurations that mimicked 2 nest types (top-cavity and platform nests, at 3 different wind speeds. We then used the estimates of h(c in a biophysical heat transfer model to estimate how long it would take unattended eggs to cool from incubation temperature (~36 °C to physiological zero temperature (PZT; ~26 °C under natural environmental conditions. Our results indicated that the structural configuration of nests influences the cooling time of the eggs inside those nests, and hence, influences the nest microclimate. Estimates of time to PZT ranged from 10.6 minutes to 33.3 minutes. Nest configurations that were most similar to platform nests always had the fastest egg cooling times, suggesting that platform nests were the least protective of those nests we tested. Our field data coupled with our experimental results suggested that nest choice is important for the reproductive success of owls during years of inclement weather or in regions characterized by inclement weather during the nesting season.

  10. Regulations of evapotranspiration and ecosystem productivity from biophysical and human drivers in drylands Northern Eurasia

    Science.gov (United States)

    Chen, J.; Ouyang, Z.; John, R.; Henebry, G. M.; Xie, Y.; de Beurs, K.; Fan, Y.; Shao, C.; Qi, J.; Wu, J.; Liu, Y.

    2015-12-01

    The concept of coupled human and environmental systems (CHES) has been a dominant framework in the past decade for understanding the cohesive connections between natural and human systems. Here we focus on how socio-ecological services may be regulated by the regional and local water cycles and by ecosystem production in the drylands of Northern Asia (>40 degree N), which includes Inner Mongolia of China, Kazakhstan, Kyrgyzstan, Mongolia, Tajikistan, Turkmenistan, and Uzbekistan. Total precipitation and evapotranspiration are used as the primary drivers to explain ecosystem production (e.g., GPP) and indicators of social function and structure (e.g., GDP, population) using the data collected from 1980 through 2010 of these seven areas. We hypothesize that the changes in the regional and local water cycles in these contrasting regions and socioeconomic settings significantly affect CHES functioning. Institutional changes, including shifts in policy, can play a much stronger role than those caused by the physical changes in determining the relationships between water cycle and CHES functioning. The complex connections among the biophysical and socioeconomic variables are analyzed through structural equation modeling (SEM) at country and regional scales. The highest water use efficiency (GPP:PET=0.57) was found for Uzbekistan, which also had the highest GDP:GPP (0.66) among the seven areas. In contrast, Mongolia exhibited the lowest values during the study period despite its very high GPP:Population value (45.8). The low population in Mongolia appeared responsible for its rank within the dryland region. Regional institutional changes with global ramifications, such as the collapse of Soviet Union and China joining the World Trade Organization, appears to have affected the CHES of the study areas.

  11. Lessons from the biophysics of interfaces: lung surfactant and tear fluid.

    Science.gov (United States)

    Rantamäki, Antti H; Telenius, Jelena; Koivuniemi, Artturi; Vattulainen, Ilpo; Holopainen, Juha M

    2011-05-01

    The purpose of this review is to provide insight into the biophysical properties and functions of tear fluid and lung surfactant--two similar fluids covering the epithelium of two distinctive organs. Both fluids form a layer-like structure that essentially comprise of an aqueous layer next to the epithelium and an anterior lipid layer at the air-water interface. The aqueous layers contain soluble proteins and metabolites, and they are responsible for the host defence system and nutrition of the organ. However, many proteins also interact with the lipid layer and are important for the surface-active function of the fluid film. The lipid layer of lung surfactant comprises mainly of phospholipids, especially phosphatidylcholines, and only small amounts of non-polar lipids, mainly cholesterol. In contrast, tear fluid lipid layer comprises of a mixture of polar and non-polar lipids. However, the relative proportion and the spectrum of different polar and non-polar lipids seem to be more extensive in tear fluid than in lung surfactant. The differing lipid compositions generate distinctive lipid layer structures. Despite the structural differences, these lipid layers decrease the surface tension of the air-water interface. The structure of the tear film lipid layer also minimises the evaporation of the tear fluid. In lung surfactant surface activity is crucial for the function of the organ, as the lipid layer prevents the collapse of the lung alveoli during the compression-expansion cycle of breathing. Similarly the tear film experiences a compression-expansion cycle during blinking. The dynamics of this cycle have been studied to a lesser extent and are not as clear as those of lung surfactant. The common structure and properties suggest a similar behaviour under rapid compression-expansion for both fluids. PMID:21352946

  12. Seasonal variability in the biophysical properties of stratum corneum from different anatomical sites.

    Science.gov (United States)

    Black, D.; Del Pozo, A.; Lagarde, J. M.; Gall, Y.

    2000-05-01

    BACKGROUND/PURPOSE: A 10-month-long study on a panel of 24 young female subjects was carried out to determine whether various biophysical aspects of the stratum corneum (SC) varied with season. METHODS: Three different anatomical sites (calf, inner forearm and crow's foot wrinkle area of the face) were assessed in February, April, July and December of the same year. The assessments made were skin surface hydration using an electrical capacitance technique, transepidermal water loss by evaporimetry, number of corneocytes released using a turbine stimulation method, and skin surface topography using optical profilometry. RESULTS: The results showed significant anatomical differences: with the crow's foot site > forearm > calf, for skin surface hydration and corneocyte numbers; and the crow's foot site > forearm and calf, with no difference between the latter two sites, for TEWL measurements. With these techniques, seasonal differences were observed mainly in the calf, to a lesser extent in the forearm, but not in the crow's foot area. These mainly involved increases in these three parameters in July, as opposed to the other time-points. Parameters of skin surface topography however, showed no consistent seasonal pattern, but markedly higher values were observed for the forearm in comparison to the calf and crow's foot sites, which were similar. From meteorological data obtained, the average daily maximum temperature and hours of sunshine increased to peak values in July, as did the absolute humidity derived from relative humidity data. CONCLUSION: We conclude that the results are most likely to represent changes in the SC due to climatic factors, with the calf and forearm sites being most affected in comparison to the face (crow's foot wrinkle area), which seems unaffected. The reasons for this latter site remaining unchanged may be due to its greater UV exposure, sebum content, and that the use of facial cosmetics was allowed. PMID:11428945

  13. Geospatial approach for assessment of biophysical vulnerability to agricultural drought and its intra-seasonal variations.

    Science.gov (United States)

    Sehgal, Vinay Kumar; Dhakar, Rajkumar

    2016-03-01

    The study presents a methodology to assess and map agricultural drought vulnerability during main kharif crop season at local scale and compare its intra-seasonal variations. A conceptual model of vulnerability based on variables of exposure, sensitivity, and adaptive capacity was adopted, and spatial datasets of key biophysical factors contributing to vulnerability were generated using remote sensing and GIS for Rajasthan State of India. Hazard exposure was based on frequency and intensity of gridded standardized precipitation index (SPI). Agricultural sensitivity was based on soil water holding capacity as well as on frequency and intensity of normalized difference vegetation index (NDVI)-derived trend adjusted vegetation condition index (VCITadj). Percent irrigated area was used as a measure of adaptive capacity. Agricultural drought vulnerability was derived separately for early, mid, late, and whole kharif seasons by composting rating of factors using linear weighting scheme and pairwise comparison of multi-criteria evaluation. The regions showing very low to extreme rating of hazard exposure, drought sensitivity, and agricultural vulnerability were identified at all four time scales. The results indicate that high to extreme vulnerability occurs in more than 50% of net sown area in the state and such areas mostly occur in western, central, and southern parts. The higher vulnerability is on account of non-irrigated croplands, moderate to low water holding capacity of sandy soils, resulting in higher sensitivity, and located in regions with high probability of rainfall deficiency. The mid and late season vulnerability has been found to be much higher than that during early and whole season. Significant correlation of vulnerability rating with food grain productivity, drought recurrence period, crop area damaged in year 2009 and socioeconomic indicator of human development index (HDI) proves the general soundness of methodology. Replication of this methodology

  14. Irrigation Management with Remote Sensing Techniques. Crop Water Requirements and Biophysical Indicators

    Science.gov (United States)

    Toureiro, Célia; Serralheiro, Ricardo

    2013-04-01

    Saving water in irrigated agriculture is increasingly relevant, as the irrigation sector is in many regions the biggest water consumer, but must be a sustainable activity. Therefore, the need urges for water use control methods and water resources planning. In irrigated agriculture, the right way for saving water is constituted by the increase of efficiency in water management. This work validates procedures and methodologies with remote sensing to determine the water availability in the soil at each moment and therefore the opportunity for the application of the water volume strictly necessary to optimize crop growth (irrigation opportunity and irrigation amount). The analysis applied to the Irrigation District of Divor, Évora, having used 7 experiment plots, which are areas watered by center-pivot systems, cultivated to corn. Data were determined from multispectral and infrared images of the cultivated surface obtained by satellite or by flying unmanned platform and integrated with parameters of the atmosphere and of the crops for calculating biophysical indicators and indices of water stress in the vegetation (NDVI, Kc, Kcb, CWSI). Therefore, evapotranspiration (ETc) was estimated, with which crop water requirement was calculated, with the opportunity and the amount of irrigation water to allocate. As this information is geographic referenced, maps can be prepared with GIS technology, describing water situation and the opportunity for watering crops. If the remote images are available with enough high spatial and temporal resolution, the frequent availability of maps can serve as a basis for a farmers irrigation advice system and for the regional irrigation authority to make decisions on the irrigation management at the regional scale. This can be a significant contribute to an efficient water management technology and a sustainable irrigated agriculture. Key-Words: Remote Sensing, Vegetation Index, Crop Coefficients, Water Balance

  15. Association, intrinsic shape, and molecular recognition: Elucidating DNA biophysics through coarse-grained simulation

    Science.gov (United States)

    Freeman, Gordon Samuel

    DNA is of central importance in biology as it is responsible for carrying, copying, and translating the genetic code into the building blocks that comprise life. In order to accomplish these tasks, the DNA molecule must be versatile and robust. Indeed, the underlying molecular interactions that allow DNA to execute these tasks are complex and their origins are only beginning to be understood. While experiments are able to elucidate many key biophysical phenomena, there remain many unanswered questions. Molecular simulation is able to shed light on phenomena at the molecular scale and provide information that is missing from experimental views of DNA behavior. In this dissertation I use state-of-the-art coarse-grained DNA models to address two key problems. In the first, metadynamics calculations are employed to uncover the free energy surface of two complimentary DNA strands. This free energy surface takes on the appearance of a hybridization funnel and reveals candidates for intermediate states in the hybridization of short DNA oligomers. Such short oligomers are important building blocks for DNA-driven self-assembly and the mechanism of hybridization in this regime is not well understood. The second problem is that of nucleosome formation. Nucleosomes are the fundamental subunit of genome compaction in the nucleus of a cell. As such, nucleosomes are a key epigenetic factor and affect gene expression and the ability of DNA-binding proteins to locate and bind to the appropriate position in the genome. However, the factors that drive nucleosome positioning are not well understood. While DNA sequence is known to affect nucleosome formation, the mechanism by which it does so has not been established and a number of hypotheses explaining this sequence-dependence exist in the literature. I demonstrate that DNA shape dominates this process with contributions arising from both intrinsic DNA curvature as well as DNA-protein interactions driven by sequence

  16. Biophysical Characterization and Activity of Lymphostatin, a Multifunctional Virulence Factor of Attaching and Effacing Escherichia coli.

    Science.gov (United States)

    Cassady-Cain, Robin L; Blackburn, Elizabeth A; Alsarraf, Husam; Dedic, Emil; Bease, Andrew G; Böttcher, Bettina; Jørgensen, René; Wear, Martin; Stevens, Mark P

    2016-03-11

    Attaching and effacing Escherichia coli cause diarrhea and typically produce lymphostatin (LifA), an inhibitor of mitogen-activated proliferation of lymphocytes and pro-inflammatory cytokine synthesis. A near-identical factor (Efa1) has been reported to mediate adherence of E. coli to epithelial cells. An amino-terminal region of LifA shares homology with the catalytic domain of the large clostridial toxins, which are retaining glycosyltransferases with a DXD motif involved in binding of a metal ion. Understanding the mode(s) of action of lymphostatin has been constrained by difficulties obtaining a stably transformed plasmid expression clone. We constructed a tightly inducible clone of enteropathogenic E. coli O127:H6 lifA for affinity purification of lymphostatin. The purified protein inhibited mitogen-activated proliferation of bovine T lymphocytes in the femtomolar range. It is a monomer in solution and the molecular envelope was determined using both transmission electron microscopy and small-angle x-ray scattering. Domain architecture was further studied by limited proteolysis. The largest proteolytic fragment containing the putative glycosyltransferase domain was tested in isolation for activity against T cells, and was not sufficient for activity. Tryptophan fluorescence studies indicated thatlymphostatin binds uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc) but not UDP-glucose (UDP-Glc). Substitution of the predicted DXD glycosyltransferase motif with alanine residues abolished UDP-GlcNAc binding and lymphostatin activity, although other biophysical properties were unchanged. The data indicate that lymphostatin has UDP-sugar binding potential that is critical for activity, and is a major leap toward identifying the nature and consequences of modifications of host cell factors. PMID:26786100

  17. Geological Services Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — Researchers use computed tomography (CT) scanners at NETL’s Geological Services Laboratory in Morgantown, WV, to peer into geologic core samples to determine how...

  18. High Bay Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory is a specially constructed facility with elevated (37 feet) ceilings and an overhead catwalk, and which is dedicated to research efforts in reducing...

  19. Clinical Laboratory Fee Schedule

    Data.gov (United States)

    U.S. Department of Health & Human Services — Outpatient clinical laboratory services are paid based on a fee schedule in accordance with Section 1833(h) of the Social Security Act. The clinical laboratory fee...

  20. Building the Korogwe Laboratory

    DEFF Research Database (Denmark)

    Knudsen, Jakob; von Seidlein, Lorenz; Richard, Jean Pierre

    2011-01-01

    An illustrated description of the building of a biomedical research laboratory in Korogwe, Tanzania.......An illustrated description of the building of a biomedical research laboratory in Korogwe, Tanzania....

  1. Space Systems Laboratory (SSL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Space Systems Laboratory (SSL) is part of the Aerospace Engineering Department and A. James Clark School of Engineering at the University of Maryland in College...

  2. Moriah Wind System Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — Purpose: The Moriah Wind System Laboratory provides in-service support for the more than 50 U.S. Navy, U.S. Coast Guard and Military Sealift Command ships on which...

  3. FLEXIBLE FOOD PACKAGING LABORATORY

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory contains equipment to fabricate and test prototype packages of many types and sizes (e.g., bags, pouches, trays, cartons, etc.). This equipment can...

  4. Electro-Deposition Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The electro-deposition laboratory can electro-deposit various coatings onto small test samples and bench level prototypes. This facility provides the foundation for...

  5. Aquatic Research Laboratory (ARL)

    Data.gov (United States)

    Federal Laboratory Consortium — Columbia River and groundwater well water sources are delivered to the Aquatic Research Laboratory (ARL), where these resources are used to conduct research on fish...

  6. Laboratory of Biological Modeling

    Data.gov (United States)

    Federal Laboratory Consortium — The Laboratory of Biological Modeling is defined by both its methodologies and its areas of application. We use mathematical modeling in many forms and apply it to...

  7. Aircraft Fire Protection Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Navy Aircraft Protection Laboratory provides complete test support for all Navy air vehicle fire protection systems. The facility allows for the simulation of a...

  8. Energetics Laboratory Facilities

    Data.gov (United States)

    Federal Laboratory Consortium — These energetic materials laboratories are equipped with explosion proof hoods with blow out walls for added safety, that are certified for safe handling of primary...

  9. Laboratory Demographics Lookup Tool

    Data.gov (United States)

    U.S. Department of Health & Human Services — This website provides demographic information about laboratories, including CLIA number, facility name and address, where the laboratory testing is performed, the...

  10. Protective Systems Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory is a 40 by 28 by 9 foot facility that is equipped with tools for the development of various items of control technology related to the transmission...

  11. Mechanical Testing Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — NETL’s Mechanical Testing Laboratory in Albany, OR, helps researchers investigate materials that can withstand the heat and pressure commonly found in fossil energy...

  12. EPA Environmental Chemistry Laboratory

    Science.gov (United States)

    1993-01-01

    The Environmental Protection Agency's (EPA) Chemistry Laboratory (ECL) is a national program laboratory specializing in residue chemistry analysis under the jurisdiction of the EPA's Office of Pesticide Programs in Washington, D.C. At Stennis Space Center, the laboratory's work supports many federal anti-pollution laws. The laboratory analyzes environmental and human samples to determine the presence and amount of agricultural chemicals and related substances. Pictured, ECL chemists analyze environmental and human samples for the presence of pesticides and other pollutants.

  13. Laboratory Activities in Israel

    Science.gov (United States)

    Mamlok-Naaman, Rachel; Barnea, Nitza

    2012-01-01

    Laboratory activities have long had a distinctive and central role in the science curriculum, and science educators have suggested that many benefits accrue from engaging students in science laboratory activities. Many research studies have been conducted to investigate the educational effectiveness of laboratory work in science education in…

  14. Skylab mobile laboratory

    Science.gov (United States)

    Primeaux, G. R.; Larue, M. A.

    1975-01-01

    The Skylab mobile laboratory was designed to provide the capability to obtain necessary data on the Skylab crewmen 30 days before lift-off, within 1 hour after recovery, and until preflight physiological baselines were reattained. The mobile laboratory complex consisted of six laboratories that supported cardiovascular, metabolic, nutrition and endocrinology, operational medicine, blood, and microbiology experiments; a utility package; and two shipping containers. The objectives and equipment requirements of the Skylab mobile laboratory and the data acquisition systems are discussed along with processes such as permanently mounting equipment in the individual laboratories and methods of testing and transporting the units. The operational performance, in terms of amounts of data collected, and the concept of mobile laboratories for medical and scientific experiments are evaluated. The Skylab mobile laboratory succeeded in facilitating the data collection and sample preservation associated with the three Skylab manned flights.

  15. Personalized laboratory medicine

    DEFF Research Database (Denmark)

    Pazzagli, M.; Malentacchi, F.; Mancini, I.;

    2015-01-01

    Developments in "omics" are creating a paradigm shift in Laboratory Medicine leading to Personalised Medicine. This allows the increasing in diagnostics and therapeutics focused on individuals rather than populations. In order to investigate whether Laboratory Medicine is able to implement new...... diagnostic tools and expertise and commands proper state-of-the-art knowledge about Personalized Medicine and Laboratory Medicine in Europe, the joint Working Group "Personalized Laboratory Medicine" of the EFLM and ESPT societies compiled and conducted the Questionnaire "Is Laboratory Medicine ready...... for the era of Personalized Medicine?". 48 laboratories from 18 European countries participated at this survey. The answers of the participating Laboratory Medicine professionals indicate that they are aware that Personalized Medicine can represent a new and promising health model. Whereas they are aware...

  16. Biophysical analysis of apolipoprotein E3 variants linked with development of type III hyperlipoproteinemia.

    Directory of Open Access Journals (Sweden)

    Dimitra Georgiadou

    Full Text Available BACKGROUND: Apolipoprotein E (apoE is a major protein of the lipoprotein transport system that plays important roles in lipid homeostasis and protection from atherosclerosis. ApoE is characterized by structural plasticity and thermodynamic instability and can undergo significant structural rearrangements as part of its biological function. Mutations in the 136-150 region of the N-terminal domain of apoE, reduce its low density lipoprotein (LDL receptor binding capacity and have been linked with lipoprotein disorders, such as type III hyperlipoproteinemia (HLP in humans. However, the LDL-receptor binding defects for these apoE variants do not correlate well with the severity of dyslipidemia, indicating that these variants may carry additional properties that contribute to their pathogenic potential. METHODOLOGY/PRINCIPAL FINDINGS: In this study we examined whether three type III HLP predisposing apoE3 variants, namely R136S, R145C and K146E affect the biophysical properties of the protein. Circular dichroism (CD spectroscopy revealed that these mutations do not significantly alter the secondary structure of the protein. Thermal and chemical unfolding analysis revealed small thermodynamic alterations in each variant compared to wild-type apoE3, as well as effects in the reversibility of the unfolding transition. All variants were able to remodel multillamelar 1,2-Dimyristoyl-sn-glycero-3-phosphocholine (DMPC vesicles, but R136S and R145C had reduced kinetics. Dynamic light scattering analysis indicated that the variant R136S exists in a higher-order oligomerization state in solution. Finally, 1-anilinonaphthalene-8-sulfonic acid (ANS binding suggested that the variant R145C exposes a larger amount of hydrophobic surface to the solvent. CONCLUSIONS/SIGNIFICANCE: Overall, our findings suggest that single amino acid changes in the functionally important region 136-150 of apoE3 can affect the molecule's stability and conformation in solution and may

  17. Living cardiac tissue slices: an organotypic pseudo two-dimensional model for cardiac biophysics research.

    Science.gov (United States)

    Wang, Ken; Terrar, Derek; Gavaghan, David J; Mu-U-Min, Razik; Kohl, Peter; Bollensdorff, Christian

    2014-08-01

    Living cardiac tissue slices, a pseudo two-dimensional (2D) preparation, have received less attention than isolated single cells, cell cultures, or Langendorff-perfused hearts in cardiac biophysics research. This is, in part, due to difficulties associated with sectioning cardiac tissue to obtain live slices. With moderate complexity, native cell-types, and well-preserved cell-cell electrical and mechanical interconnections, cardiac tissue slices have several advantages for studying cardiac electrophysiology. The trans-membrane potential (Vm) has, thus far, mainly been explored using multi-electrode arrays. Here, we combine tissue slices with optical mapping to monitor Vm and intracellular Ca(2+) concentration ([Ca(2+)]i). This combination opens up the possibility of studying the effects of experimental interventions upon action potential (AP) and calcium transient (CaT) dynamics in 2D, and with relatively high spatio-temporal resolution. As an intervention, we conducted proof-of-principle application of stretch. Mechanical stimulation of cardiac preparations is well-established for membrane patches, single cells and whole heart preparations. For cardiac tissue slices, it is possible to apply stretch perpendicular or parallel to the dominant orientation of cells, while keeping the preparation in a constant focal plane for fluorescent imaging of in-slice functional dynamics. Slice-to-slice comparison furthermore allows one to assess transmural differences in ventricular tissue responses to mechanical challenges. We developed and tested application of axial stretch to cardiac tissue slices, using a manually-controlled stretching device, and recorded Vm and [Ca(2+)]i by optical mapping before, during, and after application of stretch. Living cardiac tissue slices, exposed to axial stretch, show an initial shortening in both AP and CaT duration upon stretch application, followed in most cases by a gradual prolongation of AP and CaT duration during stretch maintained

  18. Reciprocal inhibitory coupling: Measure and control of chaos on a biophysically motivated model of bursting

    Science.gov (United States)

    Duarte, Jorge; Januário, Cristina; Martins, Nuno

    2009-06-01

    Bursting activity is an interesting feature of the temporal organization in many cell firing patterns. This complex behavior is characterized by clusters of spikes (action potentials) interspersed with phases of quiescence. As shown in experimental recordings, concerning the electrical activity of real neurons, the analysis of bursting models reveals not only patterned periodic activity but also irregular behavior 1,2]. The interpretation of experimental results, particularly the study of the influence of coupling on chaotic bursting oscillations, is of great interest from physiological and physical perspectives. The inability to predict the behavior of dynamical systems in presence of chaos suggests the application of chaos control methods, when we are more interested in obtaining regular behavior. In the present article, we focus our attention on a specific class of biophysically motivated maps, proposed in the literature to describe the chaotic activity of spiking-bursting cells [Cazelles B, Courbage M, Rabinovich M. Anti-phase regularization of coupled chaotic maps modelling bursting neurons. Europhys Lett 2001;56:504-9]. More precisely, we study a map that reproduces the behavior of a single cell and a map used to examine the role of reciprocal inhibitory coupling, specially on two symmetrically coupled bursting neurons. Firstly, using results of symbolic dynamics, we characterize the topological entropy associated to the maps, which allows us to quantify and to distinguish different chaotic regimes. In particular, we exhibit numerical results about the effect of the coupling strength on the variation of the topological entropy. Finally, we show that complicated behavior arising from the chaotic coupled maps can be controlled, without changing of its original properties, and turned into a desired attracting time periodic motion (a regular cycle). The control is illustrated by an application of a feedback control technique developed by Romeiras et al. [Romeiras

  19. Biophysical Puzzles Concerning Magnetite-Based Magnetoreception in the Common Nematode, Caenorhabditis elegans.

    Science.gov (United States)

    Kirschvink, J. L.; Kobayashi, A. K.

    2015-12-01

    A recent report demonstrating magnetotactic behavior in the nematode worm, C. elegans, presents two intriguing biophysical puzzles. Vidal-Gadea et al. (2015, DOI: 10.7554/eLife.07493) show that wild-type, well-fed populations from both Hemispheres migrate upwards when their soil environment is moist and wet, and downward when starved. Their data show that inverting the vertical component of the magnetic field reverses the migration direction, indicating that it is a magnetically polar (not axial) response. Also, the angle of magnetic migration varies with the inclination angle of the local geomagnetic field at the native site, minimizing travel time. This ancestral magnetic migration direction persists even when strains are taken to different areas. We note that only a single-domain ferromagnetic magnetoreceptor (e.g, magnetite) is capable of producing a polar magnetotactic response, and in support there is one report of magnetosomes in C. elegans (Cranfield et al., 2004;DOI 10.1098/rsbl.2004.0209). However, the polarity of a magnetosome is determined at the time it grows across the SPM/SD threshold, and the magnetic orientation will lock-in randomly unless biased by the strong field of adjacent magnetosomes. Hence, the persistence of a North or South seeking direction preference within these populations demands that stable magnetosome chains of fixed polarity must be transmitted from parents, to the eggs, to the larvae, and then to the new adults. This is similar to the non-genetic inheritance process by which populations of magnetotactic bacteria can maintain North- or South-seeking swimming preference. Furthermore, for a magnetotactic organism to maintain a consistent angle from the magnetic axis is not enough to make it go vertical; it would go in a cone. For them to go vertical as reported (or to deviate at their natal magnetic inclination) demands that they must have a separate gravity sensor with which to measure the inclination angle relative to the

  20. Biophysical controls on accretion and elevation change in Caribbean mangrove ecosystems

    Science.gov (United States)

    McKee, K.L.

    2011-01-01

    Habitat stability of coastal ecosystems, such as marshes and mangroves, depends on maintenance of soil elevations relative to sea level. Many such systems are characterized by limited mineral sedimentation and/or rapid subsidence and are consequently dependent upon accumulation of organic matter to maintain elevations. However, little field information exists regarding the contribution of specific biological processes to vertical accretion and elevation change. This study used biogenic mangrove systems in carbonate settings in Belize (BZ) and southwest Florida (FL) to examine biophysical controls on elevation change. Rates of elevation change, vertical accretion, benthic mat formation, and belowground root accumulation were measured in fringe, basin, scrub, and dwarf forest types plus a restored forest. Elevation change rates (mm yr-1) measured with Surface Elevation Tables varied widely: BZ-Dwarf (-3.7), BZ-Scrub (-1.1), FL-Fringe (0.6), FL-Basin (2.1), BZ-Fringe (4.1), and FL-Restored (9.9). Root mass accumulation varied across sites (82-739 g m-2 yr-1) and was positively correlated with elevation change. Root volumetric contribution to vertical change (mm yr-1) was lowest in BZ-Dwarf (1.2) and FL-Fringe (2.4), intermediate in FL-Basin (4.1) and BZ-Scrub (4.3), and highest in BZ-Fringe (8.8) and FL-Restored (11.8) sites. Surface growth of turf-forming algae, microbial mats, or accumulation of leaf litter and detritus also made significant contributions to vertical accretion. Turf algal mats in fringe and scrub forests accreted faster (2.7 mm yr-1) than leaf litter mats in basin forests (1.9 mm yr-1), but similarly to microbial mats in dwarf forests (2.1 mm yr-1). Surface accretion of mineral material accounted for only 0.2-3.3% of total vertical change. Those sites with high root contributions and/or rapid growth of living mats exhibited an elevation surplus (+2 to +8 mm yr-1), whereas those with low root inputs and low (or non-living) mat accumulation showed an