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Sample records for dynamics determines cell

  1. Progenitor/Stem Cell Fate Determination: Interactive Dynamics of Cell Cycle and Microvesicles

    Science.gov (United States)

    Lee, David; Puente, Napoleon; Faradyan, Sam; Sears, Edmund H.; Amaral, Ashley; Goldberg, Laura; Dooner, Mark S.; Pereira, Mandy; Quesenberry, Peter J.

    2012-01-01

    We have shown that hematopoietic stem/progenitor cell phenotype and differentiative potential change throughout cell cycle. Lung-derived microvesicles (LDMVs) also change marrow cell phenotype by inducing them to express pulmonary epithelial cell-specific mRNA and protein. These changes are accentuated when microvesicles isolated from injured lung. We wish to determine if microvesicle-treated stem/progenitor cell phenotype is linked to cell cycle and to the injury status of the lung providing microvesicles. Lineage depleted, Sca-1+ (Lin-/Sca-1+) marrow isolated from mice were cultured with interleukin 3 (IL-3), IL-6, IL-11, and stem cell factor (cytokine-cultured cells), removed at hours zero (cell cycle phase G0/G1), 24 (late G1/early S), and 48 (late S/early G2/M), and cocultured with lung tissue, lung conditioned media (LCM), or LDMV from irradiated or nonirradiated mice. Alternatively, Lin-/Sca-1+ cells not exposed to exogenous cytokines were separated into G0/G1 and S/G2/M cell cycle phase populations by fluorescence-activated cell sorting (FACS) and used in coculture. Separately, LDMV from irradiated and nonirradiated mice were analyzed for the presence of adhesion proteins. Peak pulmonary epithelial cell-specific mRNA expression was seen in G0/G1 cytokine-cultured cells cocultured with irradiated lung and in late G1/early S cells cocultured with nonirradiated lung. The same pattern was seen in cytokine-cultured Lin-/Sca-1 cells cocultured with LCM and LDMV and when FACS-separated Lin-/Sca-1 cells unexposed to exogenous cytokines were used in coculture. Cells and LDMV expressed adhesion proteins whose levels differed based on cycle status (cells) or radiation injury (LDMV), suggesting a mechanism for microvesicle entry. These data demonstrate that microvesicle modification of progenitor/stem cells is influenced by cell cycle and the treatment of the originator lung tissue. PMID:22214238

  2. Coupling of cytoplasm and adhesion dynamics determines cell polarization and locomotion

    CERN Document Server

    Bock, Martin; Möhl, Christoph

    2009-01-01

    Observations of single epidermal cells on flat adhesive substrates have revealed two distinct morphological and functional states, namely a non-migrating symmetric unpolarized state and a migrating asymmetric polarized state. These states are characterized by different spatial distributions and dynamics of important biochemical cell components: F-actin and myosin-II form the contractile part of the cytoskeleton, and integrin receptors in the plasma membrane connect F-actin filaments to the substratum. In this way, focal adhesion complexes are assembled, which determine cytoskeletal force transduction and subsequent cell locomotion. So far, physical models have reduced this phenomenon either to gradients in regulatory control molecules or to different mechanics of the actin filament system in different regions of the cell. Here we offer an alternative and self-organizational model incorporating polymerization, pushing and sliding of filaments, as well as formation of adhesion sites and their force dependent ki...

  3. Determination of total selenium and Se-77 in isotopically enriched human samples by ICP-dynamic reaction cell-MS

    DEFF Research Database (Denmark)

    Sloth, Jens Jørgen; Larsen, Erik Huusfeldt; Bügel, Susanne H.;

    2003-01-01

    This paper describes an analytical method for the simultaneous quantitative determination of total selenium (Se) and Se-77 in isotopically enriched human plasma, urine and faeces by inductively coupled plasma- dynamic reaction cell- mass spectrometry ( ICP- DRC- MS). The samples originated from...... and the digested faecal samples were diluted using an aqueous diluent containing 0.5% Triton X-100, 2% nitric acid and 3% methanol. Selenium was detected as Se-76, Se-77 and Se-80 by ICP- DRC- MS. Selenium originating from the natural isotope abundance yeast and other selenium sources from the diet was determined...

  4. Mean-cluster approach indicates cell sorting time scales are determined by collective dynamics

    Science.gov (United States)

    Beatrici, Carine P.; de Almeida, Rita M. C.; Brunnet, Leonardo G.

    2017-03-01

    Cell migration is essential to cell segregation, playing a central role in tissue formation, wound healing, and tumor evolution. Considering random mixtures of two cell types, it is still not clear which cell characteristics define clustering time scales. The mass of diffusing clusters merging with one another is expected to grow as td /d +2 when the diffusion constant scales with the inverse of the cluster mass. Cell segregation experiments deviate from that behavior. Explanations for that could arise from specific microscopic mechanisms or from collective effects, typical of active matter. Here we consider a power law connecting diffusion constant and cluster mass to propose an analytic approach to model cell segregation where we explicitly take into account finite-size corrections. The results are compared with active matter model simulations and experiments available in the literature. To investigate the role played by different mechanisms we considered different hypotheses describing cell-cell interaction: differential adhesion hypothesis and different velocities hypothesis. We find that the simulations yield normal diffusion for long time intervals. Analytic and simulation results show that (i) cluster evolution clearly tends to a scaling regime, disrupted only at finite-size limits; (ii) cluster diffusion is greatly enhanced by cell collective behavior, such that for high enough tendency to follow the neighbors, cluster diffusion may become independent of cluster size; (iii) the scaling exponent for cluster growth depends only on the mass-diffusion relation, not on the detailed local segregation mechanism. These results apply for active matter systems in general and, in particular, the mechanisms found underlying the increase in cell sorting speed certainly have deep implications in biological evolution as a selection mechanism.

  5. Optimization and application of ICPMS with dynamic reaction cell for precise determination of 44Ca/40Ca isotope ratios.

    Science.gov (United States)

    Boulyga, Sergei F; Klötzli, Urs; Stingeder, Gerhard; Prohaska, Thomas

    2007-10-15

    An inductively coupled plasma mass spectrometer with dynamic reaction cell (ICP-DRC-MS) was optimized for determining (44)Ca/(40)Ca isotope ratios in aqueous solutions with respect to (i) repeatability, (ii) robustness, and (iii) stability. Ammonia as reaction gas allowed both the removal of (40)Ar+ interference on (40)Ca+ and collisional damping of ion density fluctuations of an ion beam extracted from an ICP. The effect of laboratory conditions as well as ICP-DRC-MS parameters such a nebulizer gas flow rate, rf power, lens potential, dwell time, or DRC parameters on precision and mass bias was studied. Precision (calculated using the "unbiased" or "n - 1" method) of a single isotope ratio measurement of a 60 ng g(-1) calcium solution (analysis time of 6 min) is routinely achievable in the range of 0.03-0.05%, which corresponded to the standard error of the mean value (n = 6) of 0.012-0.020%. These experimentally observed RSDs were close to theoretical precision values given by counting statistics. Accuracy of measured isotope ratios was assessed by comparative measurements of the same samples by ICP-DRC-MS and thermal ionization mass spectrometry (TIMS) by using isotope dilution with a (43)Ca-(48)Ca double spike. The analysis time in both cases was 1 h per analysis (10 blocks, each 6 min). The delta(44)Ca values measured by TIMS and ICP-DRC-MS with double-spike calibration in two samples (Ca ICP standard solution and digested NIST 1486 bone meal) coincided within the obtained precision. Although the applied isotope dilution with (43)Ca-(48)Ca double-spike compensates for time-dependent deviations of mass bias and allows achieving accurate results, this approach makes it necessary to measure an additional isotope pair, reducing the overall analysis time per isotope or increasing the total analysis time. Further development of external calibration by using a bracketing method would allow a wider use of ICP-DRC-MS for routine calcium isotopic measurements, but it

  6. Dynamics of cell orientation

    Science.gov (United States)

    de, Rumi; Zemel, Assaf; Safran, Samuel A.

    2007-09-01

    Many physiological processes depend on the response of biological cells to mechanical forces generated by the contractile activity of the cell or by external stresses. Using a simple theoretical model that includes the forces due to both the mechanosensitivity of cells and the elasticity of the matrix, we predict the dynamics and orientation of cells in both the absence and presence of applied stresses. The model predicts many features observed in measurements of cellular forces and orientation including the increase with time of the cellular forces in the absence of applied stress and the consequent decrease of the force in the presence of quasi-static stresses. We also explain the puzzling observation of parallel alignment of cells for static and quasi-static stresses and of nearly perpendicular alignment for dynamically varying stresses. In addition, we predict the response of the cellular orientation to a sinusoidally varying applied stress as a function of frequency.

  7. Single cell dynamic phenotyping

    OpenAIRE

    Katherin Patsch; Chi-Li Chiu; Mark Engeln; Agus, David B.; Parag Mallick; Shannon M. Mumenthaler; Daniel Ruderman

    2016-01-01

    Live cell imaging has improved our ability to measure phenotypic heterogeneity. However, bottlenecks in imaging and image processing often make it difficult to differentiate interesting biological behavior from technical artifact. Thus there is a need for new methods that improve data quality without sacrificing throughput. Here we present a 3-step workflow to improve dynamic phenotype measurements of heterogeneous cell populations. We provide guidelines for image acquisition, phenotype track...

  8. Application of a dynamic reaction cell (DRC) ICP-MS in chromium and iron determinations in rock, soil and terrestrial water samples.

    Science.gov (United States)

    Ogawa, Yasumasa; Yamasaki, Shin-ichi; Tsuchiya, Noriyoshi

    2010-01-01

    Despite environmental and geochemical interests, Cr and Fe have been left beyond the reach of determinations by ICP-MS due to severe interferences originating from Ar. The applicability of a dynamic reaction cell (DRC)-ICP-MS has been examined for determinations in environmental and geochemical samples. The reaction with NH(3) in the DRC system provides an eligible technique to determine Cr, because of a greater improvement in the signal/noise (S/N) ratio due to an effective elimination of interferences arising from Ar (ArC, ArN and ArO), and makes it possible to analyze Cr even at sub-microg L(-1) levels. As compared to non-DRC mode analyses, the DRC technique using m/z 56 appeared to be preferable for Fe determination in most terrestrial waters because of effective suppression of (40)Ar(16)O(+). In addition, the effects of cluster ions, such as (39)K(14)N(1)H(3)(+) and (40)Ca(14)N(1)H(2)(+), on Fe determination were also negligibly small. Measurements using (54)Fe by the DRC mode are also advantageous for Ca-rich samples, such as limestone and dolomite.

  9. Determination of depleted uranium in fish: validation of a confirmatory method by dynamic reaction cell inductively coupled plasma mass spectrometry (DRC-ICP-MS).

    Science.gov (United States)

    D'Ilio, S; Violante, N; Senofonte, O; Petrucci, F

    2007-08-06

    Depleted uranium (DU) is a by-product of the uranium enrichment process for nuclear fuel. According to the Commission Decision 2002/657/EC, a confirmatory method for the quantification of DU in freeze-dried fish was developed by isotope ratio dynamic reaction cell inductively coupled plasma-mass spectrometry (IR-DRC-ICP-MS). A preliminary study was performed to determine the following parameters: instrumental detection limit (IDL), isotopic ratio measurement limit (IRML), percentage of DU (P(DU)) in presence of natural uranium (NU) and limit of quantification (LoQ(DU)). The analyses were carried out by means of IR-DRC-ICP-MS. Ammonia was the reaction gas used for the dynamic reaction cell. In addition, a sector field inductively coupled plasma mass spectrometer (SF-ICP-MS) was employed to calculate the within-laboratory reproducibility. For the confirmatory method the following parameters were determined: (a) trueness; (b) precision; (c) critical concentrations alpha and beta (CC(alpha), CC(beta)); (d) specificity; (e) stability. Trueness was assessed by using the recovery tests. The recovery and within-laboratory reproducibility were determined by fortifying the blank digested solution of dogfish tissue: six aliquots were fortified at 1, 1.5 and 2 times the LOQ(DU) with 25.0, 37.5 and 50.0 ng L(-1) or 4.16, 6.24, 8.32 microg kg(-1) with a recovery of -8.2, +9.5 and +9.6%, respectively and a within-laboratory reproducibility (three analytical run) of 15.5, 8.0 and 11.0%, respectively. The results for the decision limit and the detection capability were: CC(alpha) = 11.69 ng L(-1) and CC(beta) = 19.8 ng L(-1). The digested solutions resulted to be stable during testing time (60 days) and the method can be considered highly specific as well.

  10. Semiautomatic determination of arterial input functions for quantitative dynamic contrast-enhanced magnetic resonance imaging in non-small cell lung cancer patients.

    Science.gov (United States)

    Chung, Julius; Kim, Jae-Hun; Lee, Eun Ju; Kim, Yoo Na; Yi, Chin A

    2015-03-01

    The aim of this study was to validate a semiautomatic detection method for the arterial input functions (AIFs) using Kendall coefficient of concordance (KCC) for quantitative analysis of dynamic contrast-enhanced magnetic resonance imaging in non-small cell lung cancer patients. We prospectively enrolled 28 patients (17 men, 11 women; mean age, 62 years) who had biopsy-proven non-small cell lung cancer. All enrolled patients underwent dynamic contrast-enhanced magnetic resonance imaging of the entire thorax. For the quantitative measurement of pharmacokinetic parameters, K and ve, of the lung cancers, AIFs were determined in 2 different ways: a manual method that involved 3 independent thoracic radiologists selecting a region of interest (ROI) within the aortic arch in the 2D coronal plane and a semiautomatic method that used in-house software to establish a KCC score, which provided a measure of similarity to typical AIF pattern. Three independent readers selected voxel clusters with high KCC scores calculated 3-dimensionally across planes in the data set. K and ve were correlated using intraclass correlation coefficients (ICCs), and Bland-Altman plots were used to examine agreement across methods and reproducibility within a method. Arterial input functions were determined using the data from ROI volumes that were significantly larger in the semiautomatic method (mean ± SD, 3360 ± 768 mm) than in the manual method (677 ± 380 mm) (P methods. The reproducibility for K (ICCmanual, 0.813 and ICCsemiautomatic, 0.998; P method than the manual method. We found semiautomated detection using KCC to be a robust method for determining the AIF. This method allows for larger ROIs specified in 3D across planes as opposed to manually selected ROIs restricted to the 2D coronal images seen by the reader and provides increased reproducibility that is comparable with manual specification.

  11. Microbial Cell Dynamics Lab (MCDL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Microbial Cell Dynamics Laboratory at PNNL enables scientists to study the molecular details of microbes under relevant environmental conditions. The MCDL seeks...

  12. Manual for Dynamic Triaxial Cell

    DEFF Research Database (Denmark)

    Pedersen, Thomas Schmidt; Ibsen, Lars Bo

    This report is a test report that describes the test setup for a dynamic triaxial cell at the Laboratory for Geotechnique at Aalborg University.......This report is a test report that describes the test setup for a dynamic triaxial cell at the Laboratory for Geotechnique at Aalborg University....

  13. Simultaneous determination of protein structure and dynamics

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Best, Robert B.; DePristo, M. A.

    2005-01-01

    We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy-for obtaining experimental information at ...

  14. Dynamized Preparations in Cell Culture

    Directory of Open Access Journals (Sweden)

    Ellanzhiyil Surendran Sunila

    2009-01-01

    Full Text Available Although reports on the efficacy of homeopathic medicines in animal models are limited, there are even fewer reports on the in vitro action of these dynamized preparations. We have evaluated the cytotoxic activity of 30C and 200C potencies of ten dynamized medicines against Dalton's Lymphoma Ascites, Ehrlich's Ascites Carcinoma, lung fibroblast (L929 and Chinese Hamster Ovary (CHO cell lines and compared activity with their mother tinctures during short-term and long-term cell culture. The effect of dynamized medicines to induce apoptosis was also evaluated and we studied how dynamized medicines affected genes expressed during apoptosis. Mother tinctures as well as some dynamized medicines showed significant cytotoxicity to cells during short and long-term incubation. Potentiated alcohol control did not produce any cytotoxicity at concentrations studied. The dynamized medicines were found to inhibit CHO cell colony formation and thymidine uptake in L929 cells and those of Thuja, Hydrastis and Carcinosinum were found to induce apoptosis in DLA cells. Moreover, dynamized Carcinosinum was found to induce the expression of p53 while dynamized Thuja produced characteristic laddering pattern in agarose gel electrophoresis of DNA. These results indicate that dynamized medicines possess cytotoxic as well as apoptosis-inducing properties.

  15. Exploiting dynamic reaction cell inductively coupled plasma mass spectrometry (DRC-ICP-MS) for sequential determination of trace elements in blood using a dilute-and-shoot procedure.

    Science.gov (United States)

    Batista, Bruno Lemos; Rodrigues, Jairo Lisboa; Nunes, Juliana Andrade; Souza, Vanessa Cristina de Oliveira; Barbosa, Fernando

    2009-04-20

    Inductively coupled plasma mass spectrometry with quadrupole (q-ICP-MS) and dynamic reaction cell (DRC-ICP-MS) were evaluated for sequential determination of As, Cd, Co, Cr, Cu, Mn, Pb, Se, Tl, V and Zn in blood. The method requires as little as 100 microL of blood. Prior to analysis, samples (100 microL) were diluted 1:50 in a solution containing 0.01% (v/v) Triton X-100 and 0.5% (v/v) nitric acid. The use of the DRC was only mandatory for Cr, Cu, V and Zn. For the other elements the equipment may be operated in a standard mode (q-ICP-MS). Ammonia was used as reaction gas. Selection of best flow rate of ammonium gas and optimization of the quadrupole dynamic band-pass tuning parameter (RPq) were carried out, using a ovine base blood for Cr and V and a synthetic matrix solution (SMS) for Zn and Cu diluted 1:50 and spiked to contain 1 microg L(-1) of each element. Method detection limits (3 s) for (75)As, (114)Cd, (59)Co, (51)Cr, (63)Cu (55)Mn, (208)Pb, (82)Se, (205)Tl, (51)V, and (64)Zn were 14.0, 3.0, 11.0, 7.0, 280, 9.0, 3.0, 264, 0.7, 6.0 and 800 ng L(-1), respectively. Method validation was accomplished by the analysis of blood Reference Materials produced by the L'Institut National de Santé Publique du Quebec (Canada).

  16. Determining physical properties of the cell cortex

    CERN Document Server

    Saha, A; Behrndt, M; Heisenberg, C -P; Jülicher, F; Grill, S W

    2015-01-01

    Actin and myosin assemble into a thin layer of a highly dynamic network underneath the membrane of eukaryotic cells. This network generates the forces that drive cell and tissue-scale morphogenetic processes. The effective material properties of this active network determine large-scale deformations and other morphogenetic events. For example,the characteristic time of stress relaxation (the Maxwell time)in the actomyosin sets the time scale of large-scale deformation of the cortex. Similarly, the characteristic length of stress propagation (the hydrodynamic length) sets the length scale of slow deformations, and a large hydrodynamic length is a prerequisite for long-ranged cortical flows. Here we introduce a method to determine physical parameters of the actomyosin cortical layer (in vivo). For this we investigate the relaxation dynamics of the cortex in response to laser ablation in the one-cell-stage {\\it C. elegans} embryo and in the gastrulating zebrafish embryo. These responses can be interpreted using ...

  17. Variability in primary productivity determines metapopulation dynamics.

    Science.gov (United States)

    Fernández, Néstor; Román, Jacinto; Delibes, Miguel

    2016-04-13

    Temporal variability in primary productivity can change habitat quality for consumer species by affecting the energy levels available as food resources. However, it remains unclear how habitat-quality fluctuations may determine the dynamics of spatially structured populations, where the effects of habitat size, quality and isolation have been customarily assessed assuming static habitats. We present the first empirical evaluation on the effects of stochastic fluctuations in primary productivity--a major outcome of ecosystem functions--on the metapopulation dynamics of a primary consumer. A unique 13-year dataset from an herbivore rodent was used to test the hypothesis that inter-annual variations in primary productivity determine spatiotemporal habitat occupancy patterns and colonization and extinction processes. Inter-annual variability in productivity and in the growing season phenology significantly influenced habitat colonization patterns and occupancy dynamics. These effects lead to changes in connectivity to other potentially occupied habitat patches, which then feed back into occupancy dynamics. According to the results, the dynamics of primary productivity accounted for more than 50% of the variation in occupancy probability, depending on patch size and landscape configuration. Evidence connecting primary productivity dynamics and spatiotemporal population processes has broad implications for metapopulation persistence in fluctuating and changing environments.

  18. Fermion Determinant with Dynamical Chiral Symmetry Breaking

    Institute of Scientific and Technical Information of China (English)

    LU Qin; YANG Hua; WANG Qing

    2002-01-01

    One-loop fermion determinant is discussed for the case in which the dynamical chiral symmetry breakingcaused by momentum-dependent fermion self-energy ∑(p2) takes place. The obtained series generalizes the heat kernelexpansion for hard fermion mass.

  19. Sorting cells by their dynamical properties

    Science.gov (United States)

    Henry, Ewan; Holm, Stefan H.; Zhang, Zunmin; Beech, Jason P.; Tegenfeldt, Jonas O.; Fedosov, Dmitry A.; Gompper, Gerhard

    2016-10-01

    Recent advances in cell sorting aim at the development of novel methods that are sensitive to various mechanical properties of cells. Microfluidic technologies have a great potential for cell sorting; however, the design of many micro-devices is based on theories developed for rigid spherical particles with size as a separation parameter. Clearly, most bioparticles are non-spherical and deformable and therefore exhibit a much more intricate behavior in fluid flow than rigid spheres. Here, we demonstrate the use of cells’ mechanical and dynamical properties as biomarkers for separation by employing a combination of mesoscale hydrodynamic simulations and microfluidic experiments. The dynamic behavior of red blood cells (RBCs) within deterministic lateral displacement (DLD) devices is investigated for different device geometries and viscosity contrasts between the intra-cellular fluid and suspending medium. We find that the viscosity contrast and associated cell dynamics clearly determine the RBC trajectory through a DLD device. Simulation results compare well to experiments and provide new insights into the physical mechanisms which govern the sorting of non-spherical and deformable cells in DLD devices. Finally, we discuss the implications of cell dynamics for sorting schemes based on properties other than cell size, such as mechanics and morphology.

  20. Determination of (90)Sr in soil samples using inductively coupled plasma mass spectrometry equipped with dynamic reaction cell (ICP-DRC-MS).

    Science.gov (United States)

    Feuerstein, J; Boulyga, S F; Galler, P; Stingeder, G; Prohaska, T

    2008-11-01

    A rapid method is reported for the determination of (90)Sr in contaminated soil samples in the vicinity of the Chernobyl Nuclear Power Plant by ICP-DRC-MS. Sample preparation and measurement procedures focus on overcoming the isobaric interference of (90)Zr, which is present in soils at concentrations higher by more than six orders of magnitude than (90)Sr. Zirconium was separated from strontium in two steps to reduce the interference by (90)Zr(+) ions by a factor of more than 10(7): (i) by ion exchange using a Sr-specific resin and (ii) by reaction with oxygen as reaction gas in a dynamic reaction cell (DRC) of a quadrupole ICP-MS. The relative abundance sensitivity of the ICP-MS was studied systematically and the peak tailing originating from (88)Sr on mass 90 u was found to be about 3 x 10(-9). Detection limits of 4 fg g(-1) (0.02 Bq g(-1)) were achieved when measuring Sr solutions containing no Zr. In digested uncontaminated soil samples after matrix separation as well as in a solution of 5 microg g(-1) Sr and 50 ng g(-1) Zr a detection limit of 0.2 pg g(-1) soil (1 Bq g(-1) soil) was determined. (90)Sr concentrations in three soil samples collected in the vicinity of the Chernobyl Nuclear Power Plant were 4.66+/-0.27, 13.48+/-0.68 and 12.9+/-1.5 pg g(-1) corresponding to specific activities of 23.7+/-1.3, 68.6+/-3.5 and 65.6+/-7.8 Bq g(-1), respectively. The ICP-DRC-MS results were compared to the activities measured earlier by radiometry. Although the ICP-DRC-MS is inferior to commonly used radiometric methods with respect to the achievable minimum detectable activity it represents a time- and cost-effective alternative technique for fast monitoring of high-level (90)Sr contamination in environmental or nuclear industrial samples down to activities of about 1 Bq g(-1).

  1. Determination of {sup 90}Sr in soil samples using inductively coupled plasma mass spectrometry equipped with dynamic reaction cell (ICP-DRC-MS)

    Energy Technology Data Exchange (ETDEWEB)

    Feuerstein, J.; Boulyga, S.F.; Galler, P.; Stingeder, G. [Department of Chemistry, Division of Analytical Chemistry-VIRIS Laboratory, University of Natural Resources and Applied Life Sciences, Muthgasse 18, A-1190 Vienna (Austria); Prohaska, T. [Department of Chemistry, Division of Analytical Chemistry-VIRIS Laboratory, University of Natural Resources and Applied Life Sciences, Muthgasse 18, A-1190 Vienna (Austria)], E-mail: thomas.prohaska@boku.ac.at

    2008-11-15

    A rapid method is reported for the determination of {sup 90}Sr in contaminated soil samples in the vicinity of the Chernobyl Nuclear Power Plant by ICP-DRC-MS. Sample preparation and measurement procedures focus on overcoming the isobaric interference of {sup 90}Zr, which is present in soils at concentrations higher by more than six orders of magnitude than {sup 90}Sr. Zirconium was separated from strontium in two steps to reduce the interference by {sup 90}Zr{sup +} ions by a factor of more than 10{sup 7}: (i) by ion exchange using a Sr-specific resin and (ii) by reaction with oxygen as reaction gas in a dynamic reaction cell (DRC) of a quadrupole ICP-MS. The relative abundance sensitivity of the ICP-MS was studied systematically and the peak tailing originating from {sup 88}Sr on mass 90 u was found to be about 3 x 10{sup -9}. Detection limits of 4 fg g{sup -1} (0.02 Bq g{sup -1}) were achieved when measuring Sr solutions containing no Zr. In digested uncontaminated soil samples after matrix separation as well as in a solution of 5 {mu}g g{sup -1} Sr and 50 ng g{sup -1} Zr a detection limit of 0.2 pg g{sup -1} soil (1 Bq g{sup -1} soil) was determined. {sup 90}Sr concentrations in three soil samples collected in the vicinity of the Chernobyl Nuclear Power Plant were 4.66 {+-} 0.27, 13.48 {+-} 0.68 and 12.9 {+-} 1.5 pg g{sup -1} corresponding to specific activities of 23.7 {+-} 1.3, 68.6 {+-} 3.5 and 65.6 {+-} 7.8 Bq g{sup -1}, respectively. The ICP-DRC-MS results were compared to the activities measured earlier by radiometry. Although the ICP-DRC-MS is inferior to commonly used radiometric methods with respect to the achievable minimum detectable activity it represents a time- and cost-effective alternative technique for fast monitoring of high-level {sup 90}Sr contamination in environmental or nuclear industrial samples down to activities of about 1 Bq g{sup -1}.

  2. Transcription Dynamics in Living Cells.

    Science.gov (United States)

    Lenstra, Tineke L; Rodriguez, Joseph; Chen, Huimin; Larson, Daniel R

    2016-07-01

    The transcription cycle can be roughly divided into three stages: initiation, elongation, and termination. Understanding the molecular events that regulate all these stages requires a dynamic view of the underlying processes. The development of techniques to visualize and quantify transcription in single living cells has been essential in revealing the transcription kinetics. They have revealed that (a) transcription is heterogeneous between cells and (b) transcription can be discontinuous within a cell. In this review, we discuss the progress in our quantitative understanding of transcription dynamics in living cells, focusing on all parts of the transcription cycle. We present the techniques allowing for single-cell transcription measurements, review evidence from different organisms, and discuss how these experiments have broadened our mechanistic understanding of transcription regulation.

  3. Simultaneous determination of protein structure and dynamics

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Best, Robert B.; DePristo, M. A.

    2005-01-01

    We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy-for obtaining experimental information...... at the atomic level about the structural and dynamical features of proteins-with the ability of molecular dynamics simulations to explore a wide range of protein conformations. We illustrate the method for human ubiquitin in solution and find that there is considerable conformational heterogeneity throughout...... the protein structure. The interior atoms of the protein are tightly packed in each individual conformation that contributes to the ensemble but their overall behaviour can be described as having a significant degree of liquid-like character. The protocol is completely general and should lead to significant...

  4. Magnetic Particle Spectroscopy Reveals Dynamic Changes in the Magnetic Behavior of Very Small Superparamagnetic Iron Oxide Nanoparticles During Cellular Uptake and Enables Determination of Cell-Labeling Efficacy.

    Science.gov (United States)

    Poller, Wolfram C; Löwa, Norbert; Wiekhorst, Frank; Taupitz, Matthias; Wagner, Susanne; Möller, Konstantin; Baumann, Gert; Stangl, Verena; Trahms, Lutz; Ludwig, Antje

    2016-02-01

    In vivo tracking of nanoparticle-labeled cells by magnetic resonance imaging (MRI) crucially depends on accurate determination of cell-labeling efficacy prior to transplantation. Here, we analyzed the feasibility and accuracy of magnetic particle spectroscopy (MPS) for estimation of cell-labeling efficacy in living THP-1 cells incubated with very small superparamagnetic iron oxide nanoparticles (VSOP). Cell viability and proliferation capacity were not affected by the MPS measurement procedure. In VSOP samples without cell contact, MPS enabled highly accurate quantification. In contrast, MPS constantly overestimated the amount of cell associated and internalized VSOP. Analyses of the MPS spectrum shape expressed as harmonic ratio A₅/A₃ revealed distinct changes in the magnetic behavior of VSOP in response to cellular uptake. These changes were proportional to the deviation between MPS and actual iron amount, therefore allowing for adjusted iron quantification. Transmission electron microscopy provided visual evidence that changes in the magnetic properties correlated with cell surface interaction of VSOP as well as with alterations of particle structure and arrangement during the phagocytic process. Altogether, A₅/A₃-adjusted MPS enables highly accurate, cell-preserving VSOP quantification and furthermore provides information on the magnetic characteristics of internalized VSOP.

  5. Noise and determinism in synchronized sheep dynamics

    Science.gov (United States)

    Grenfell, B. T.; Wilson, K.; Finkenstädt, B. F.; Coulson, T. N.; Murray, S.; Albon, S. D.; Pemberton, J. M.; Clutton-Brock, T. H.; Crawley, M. J.

    1998-08-01

    A major debate in ecology concerns the relative importance of intrinsic factors and extrinsic environmental variations in determining population size fluctuations. Spatial correlation of fluctuations in different populations caused by synchronous environmental shocks,, is a powerful tool for quantifying the impact of environmental variations on population dynamics,. However, interpretation of synchrony is often complicated by migration between populations,. Here we address this issue by using time series from sheep populations on two islands in the St Kilda archipelago. Fluctuations in the sizes of the two populations are remarkably synchronized over a 40-year period. A nonlinear time-series model shows that a high and frequent degree of environmental correlation is required to achieve this level of synchrony. The model indicates that if there were less environmental correlation, population dynamics would be much less synchronous than is observed. This is because of a threshold effect that is dependent on population size; the threshold magnifies random differences between populations. A refined model showsthat part of the required environmental synchronicity can be accounted for by large-scale weather variations. These results underline the importance of understanding the interaction between intrinsic and extrinsic influences on population dynamics.

  6. Recombination dynamics as a key determinant of open circuit voltage in organic bulk heterojunction solar cells: a comparison of four different donor polymers

    Energy Technology Data Exchange (ETDEWEB)

    Maurano, Andrea; Hamilton, Rick; Shuttle, Chris G.; O' Regan, Brian; Zhang, Weimin; McCulloch, Iain; Durrant, James R. [Departments of Chemistry, Imperial College London, South Kensington SW7 2AZ (United Kingdom); Ballantyne, Amy M.; Nelson, Jenny [Departments of Physics, Imperial College London, South Kensington SW7 2AZ (United Kingdom); Azimi, Hamed [Konarka Austria, Altenbergerstrasse 69, A-4040 Linz (Austria); Christian Doppler Laboratory for Surface Optics, Johannes Kepler University, Linz (Austria); Morana, Mauro; Brabec, Christoph J. [Konarka Austria, Altenbergerstrasse 69, A-4040 Linz (Austria)

    2010-11-24

    Transient photovoltage and charge extraction analyses are employed to analyzes charge carrier densities and bimolecular recombination dynamics in organic polymer: fullerene solar cells under open circuit operating conditions, employing four different donor polymers. An equation is derived which allows us to calculate the device V{sub OC} from these kinetic measurements. This equation allows us to calculate voltage output of devices within {+-} 25 meV of directly measured values. This analysis thus allows us to relate device open circuit voltage directly to the kinetics of bimolecular recombination, and thereby the influence of nanomorphology upon device voltage output. (Copyright copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  7. Development of a method based on inductively coupled plasma-dynamic reaction cell-mass spectrometry for the simultaneous determination of phosphorus, calcium and strontium in bone and dental tissue

    Energy Technology Data Exchange (ETDEWEB)

    De Muynck, David [Ghent University, Department of Analytical Chemistry, Krijgslaan 281-S12, BE-9000 Ghent (Belgium)], E-mail: David.DeMuynck@UGent.be; Vanhaecke, Frank [Ghent University, Department of Analytical Chemistry, Krijgslaan 281-S12, BE-9000 Ghent (Belgium)], E-mail: Frank.Vanhaecke@UGent.be

    2009-05-15

    A method, based on the use of a quadrupole-based inductively coupled plasma-mass spectrometry instrument equipped with a quadrupole-based collision/reaction cell (dynamic reaction cell, DRC), was developed for the simultaneous determination of phosphorus, calcium and strontium in bone and dental (enamel and dentine) tissue. The use of NH{sub 3}, introduced at a gas flow rate of 0.8 mL min{sup -1} in the dynamic reaction cell, combined with a rejection parameter q (RPq) setting of 0.65, allows interference-free determination of calcium via its low-abundant isotopes {sup 42}Ca, {sup 43}Ca and {sup 44}Ca, and of strontium via its isotopes {sup 86}Sr and {sup 88}Sr that are freed from overlap due to the occurrence of ArCa{sup +} and/or Ca{sub 2}{sup +} ions. Also the determination of phosphorus ({sup 31}P, mono-isotopic) was shown to be achievable using the same dynamic reaction cell operating conditions. The bone certified reference materials NIST SRM 1400 Bone Ash and NIST SRM 1486 Bone Meal were used for validation of the measurement protocol that was shown capable of providing accurate and reproducible results. Detection limits of P, Ca and Sr in dental tissue digests were established as 3 {mu}g L{sup -1} for P, 2 {mu}g L{sup -1} for Ca and 0.2 {mu}g L{sup -1} for Sr. This method can be used to simultaneously (i) evaluate the impact of diagenesis on the elemental and isotopic composition of buried skeletal tissue via its Ca/P ratio and (ii) determine its Sr concentration. The measurement protocol was demonstrated as fit-for-purpose by the analysis of a set of teeth of archaeological interest for their Ca/P ratio and Sr concentration.

  8. Cell elasticity determines macrophage function.

    Directory of Open Access Journals (Sweden)

    Naimish R Patel

    Full Text Available Macrophages serve to maintain organ homeostasis in response to challenges from injury, inflammation, malignancy, particulate exposure, or infection. Until now, receptor ligation has been understood as being the central mechanism that regulates macrophage function. Using macrophages of different origins and species, we report that macrophage elasticity is a major determinant of innate macrophage function. Macrophage elasticity is modulated not only by classical biologic activators such as LPS and IFN-γ, but to an equal extent by substrate rigidity and substrate stretch. Macrophage elasticity is dependent upon actin polymerization and small rhoGTPase activation, but functional effects of elasticity are not predicted by examination of gene expression profiles alone. Taken together, these data demonstrate an unanticipated role for cell elasticity as a common pathway by which mechanical and biologic factors determine macrophage function.

  9. Determining Physical Properties of the Cell Cortex

    Science.gov (United States)

    Saha, Arnab; Nishikawa, Masatoshi; Behrndt, Martin; Heisenberg, Carl-Philipp; Jülicher, Frank; Grill, Stephan W.

    2016-03-01

    Actin and myosin assemble into a thin layer of a highly dynamic network underneath the membrane of eukaryotic cells. This network generates the forces that drive cell and tissue-scale morphogenetic processes. The effective material properties of this active network determine large-scale deformations and other morphogenetic events. For example,the characteristic time of stress relaxation (the Maxwell time)in the actomyosin sets the time scale of large-scale deformation of the cortex. Similarly, the characteristic length of stress propagation (the hydrodynamic length) sets the length scale of slow deformations, and a large hydrodynamic length is a prerequisite for long-ranged cortical flows. Here we introduce a method to determine physical parameters of the actomyosin cortical layer (in vivo). For this we investigate the relaxation dynamics of the cortex in response to laser ablation in the one-cell-stage {\\it C. elegans} embryo and in the gastrulating zebrafish embryo. These responses can be interpreted using a coarse grained physical description of the cortex in terms of a two dimensional thin film of an active viscoelastic gel. To determine the Maxwell time, the hydrodynamic length and the ratio of active stress and per-area friction, we evaluated the response to laser ablation in two different ways: by quantifying flow and density fields as a function of space and time, and by determining the time evolution of the shape of the ablated region. Importantly, both methods provide best fit physical parameters that are in close agreement with each other and that are similar to previous estimates in the two systems. We provide an accurate and robust means for measuring physical parameters of the actomyosin cortical layer.It can be useful for investigations of actomyosin mechanics at the cellular-scale, but also for providing insights in the active mechanics processes that govern tissue-scale morphogenesis.

  10. Determining gastric cancer resectability by dynamic MDCT

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Zilai; Zhang, Huan; Du, Lianjun; Ding, Bei; Song, Qi; Ling, Huawei; Huang, Baisong; Chen, Kemin [Jiaotong University, Department of Radiology, Shanghai (China); Yan, Chao [Jiaotong University, Department of Surgery, Shanghai (China)

    2010-03-15

    Multi-detector row CT (MDCT) has been widely used to detect primary lesions and to evaluate TNM staging. In this study we evaluated the accuracy of dynamic MDCT in the preoperative determination of the resectability of gastric cancer. MDCT was used to image 350 cases of gastric cancer diagnosed by biopsy before surgery. MDCT findings regarding TNM staging and resectability were correlated with surgical and pathological findings. The accuracy of MDCT for staging gastric cancer was high, especially for tumour stage T1 (94.3%), lymph node stage N2 (87.3%), and for predicting distant metastases (>96.6%). When resectability was considered to be the outcome, the total accuracy of MDCT was 87.4%, sensitivity was 89.7% and specificity was 76.7%. Results showed high sensitivity for identifying peritoneal seeding (90.0%) and for predicting liver metastasis (80.0%). Dynamic enhanced MDCT is useful for TNM staging of gastric cancers and for predicting tumour respectability preoperatively. (orig.)

  11. Shape dynamics of growing cell walls

    CERN Document Server

    Banerjee, Shiladitya; Dinner, Aaron R

    2015-01-01

    We introduce a general theoretical framework to study the shape dynamics of actively growing and remodeling surfaces. Using this framework we develop a physical model for growing bacterial cell walls and study the interplay of cell shape with the dynamics of growth and constriction. The model allows us to derive constraints on cell wall mechanical energy based on the observed dynamics of cell shape. We predict that exponential growth in cell size requires a constant amount of cell wall energy to be dissipated per unit volume. We use the model to understand and contrast growth in bacteria with different shapes such as spherical, ellipsoidal, cylindrical and toroidal morphologies. Coupling growth to cell wall constriction, we predict a discontinuous shape transformation, from partial constriction to cell division, as a function of the chemical potential driving cell-wall synthesis. Our model for cell wall energy and shape dynamics relates growth kinetics with cell geometry, and provides a unified framework to d...

  12. Nonlinear dynamics of cell orientation

    Science.gov (United States)

    Safran, S. A.; de, Rumi

    2009-12-01

    The nonlinear dependence of cellular orientation on an external, time-varying stress field determines the distribution of orientations in the presence of noise and the characteristic time, τc , for the cell to reach its steady-state orientation. The short, local cytoskeletal relaxation time distinguishes between high-frequency (nearly perpendicular) and low-frequency (random or parallel) orientations. However, τc is determined by the much longer, orientational relaxation time. This behavior is related to experiments for which we predict the angle and characteristic time as a function of frequency.

  13. Determination of copper in coal fly ash in the presence of excess titanium by dynamic reaction cell inductively coupled plasma mass spectrometry.

    Science.gov (United States)

    Liu, Hui-Tao; Jiang, Shiuh-Jen

    2003-01-01

    Inductively coupled plasma quadrupole mass spectrometry (ICP-QMS) was used for the accurate determination of copper in coal fly ash samples in the presence of excess titanium, using the reaction of Cu(+) ions with NH(3) in the cell. The method eliminated the effect of polyatomic isobaric interferences at m/z 63 and 65 caused by the formation of (47)Ti(16)O(+), (49)Ti(16)O(+) and (47)Ti(18)O(+) on (63)Cu(+) and (65)Cu(+) by detecting Cu(+) as the product cluster ion Cu(NH(3))(2)(+). As the signal of (63)Cu(NH(3))(2)(+) overlapped with that of (97)Mo(+) which existed in the samples, (65)Cu(NH(3))(2)(+) was detected at m/z 99. The effect of the operating conditions of DRC system was studied in order to obtain the best signal to noise ratio for Cu(NH(3))(2)(+) at m/z 99. The formation of Cu(NH(3))(2)(+) was through the clustering reaction Cu(+)+2NH(3)-->Cu(NH(3))(2)(+) which resulted in the separation of analyte from the interfering oxide. The detection limit for Cu(NH(3))(2)(+) was 0.015 ng mL(-1) as Cu. The method was applied to the determination of copper in NIST SRM 1633a and 1633b coal fly ash reference materials. The precision between sample replicates was better than 2.0% and the analysis results were in good agreement with the certified values.

  14. Determination of copper in coal fly ash in the presence of excess titanium by dynamic reaction cell inductively coupled plasma mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Hui-Tao [Department of Chemistry, Lanzhou University, Lanzhou 730000 (China); Jiang, Shiuh-Jen [Department of Chemistry, National Sun Yat-sen University, Kaohsiung 80424 (Taiwan)

    2003-01-01

    Inductively coupled plasma quadrupole mass spectrometry (ICP-QMS) was used for the accurate determination of copper in coal fly ash samples in the presence of excess titanium, using the reaction of Cu{sup +} ions with NH{sub 3} in the cell. The method eliminated the effect of polyatomic isobaric interferences at m/z 63 and 65 caused by the formation of {sup 47}Ti{sup 16}O{sup +}, {sup 49}Ti{sup 16}O{sup +} and {sup 47}Ti{sup 18}O{sup +} on {sup 63}Cu{sup +} and {sup 65}Cu{sup +} by detecting Cu{sup +} as the product cluster ion Cu(NH{sub 3}){sub 2}{sup +}. As the signal of {sup 63}Cu(NH{sub 3}){sub 2}{sup +} overlapped with that of {sup 97}Mo{sup +} which existed in the samples, {sup 65}Cu(NH{sub 3}){sub 2}{sup +} was detected at m/z 99. The effect of the operating conditions of DRC system was studied in order to obtain the best signal to noise ratio for Cu(NH{sub 3}){sub 2}{sup +} at m/z 99. The formation of Cu(NH{sub 3}){sub 2}{sup +} was through the clustering reaction Cu{sup +}+2NH{sub 3}{yields}Cu(NH{sub 3}){sub 2}{sup +} which resulted in the separation of analyte from the interfering oxide. The detection limit for Cu(NH{sub 3}){sub 2}{sup +} was 0.015 ng mL{sup -1} as Cu. The method was applied to the determination of copper in NIST SRM 1633a and 1633b coal fly ash reference materials. The precision between sample replicates was better than 2.0% and the analysis results were in good agreement with the certified values. (orig.)

  15. Dynamic imaging of cell-free and cell-associated viral capture in mature dendritic cells.

    Science.gov (United States)

    Izquierdo-Useros, Nuria; Esteban, Olga; Rodriguez-Plata, Maria T; Erkizia, Itziar; Prado, Julia G; Blanco, Julià; García-Parajo, Maria F; Martinez-Picado, Javier

    2011-12-01

    Dendritic cells (DCs) capture human immunodeficiency virus (HIV) through a non-fusogenic mechanism that enables viral transmission to CD4(+) T cells, contributing to in vivo viral dissemination. Although previous studies have provided important clues to cell-free viral capture by mature DCs (mDCs), dynamic and kinetic insight on this process is still missing. Here, we used three-dimensional video microscopy and single-particle tracking approaches to dynamically dissect both cell-free and cell-associated viral capture by living mDCs. We show that cell-free virus capture by mDCs operates through three sequential phases: virus binding through specific determinants expressed in the viral particle, polarized or directional movements toward concrete regions of the cell membrane and virus accumulation in a sac-like structure where trapped viral particles display a hindered diffusive behavior. Moreover, real-time imaging of cell-associated viral transfer to mDCs showed a similar dynamics to that exhibited by cell-free virus endocytosis leading to viral accumulation in compartments. However, cell-associated HIV type 1 transfer to mDCs was the most effective pathway, boosted throughout enhanced cellular contacts with infected CD4(+) T cells. Our results suggest that in lymphoid tissues, mDC viral uptake could occur either by encountering cell-free or cell-associated virus produced by infected cells generating the perfect scenario to promote HIV pathogenesis and impact disease progression.

  16. Fluid dynamics and noise in bacterial cell-cell and cell-surface scattering

    CERN Document Server

    Drescher, Knut; Cisneros, Luis H; Ganguly, Sujoy; Goldstein, Raymond E; 10.1073/pnas.1019079108

    2011-01-01

    Bacterial processes ranging from gene expression to motility and biofilm formation are constantly challenged by internal and external noise. While the importance of stochastic fluctuations has been appreciated for chemotaxis, it is currently believed that deterministic long-range fluid dynamical effects govern cell-cell and cell-surface scattering - the elementary events that lead to swarming and collective swimming in active suspensions and to the formation of biofilms. Here, we report the first direct measurements of the bacterial flow field generated by individual swimming Escherichia coli both far from and near to a solid surface. These experiments allowed us to examine the relative importance of fluid dynamics and rotational diffusion for bacteria. For cell-cell interactions it is shown that thermal and intrinsic stochasticity drown the effects of long-range fluid dynamics, implying that physical interactions between bacteria are determined by steric collisions and near-field lubrication forces. This dom...

  17. About supramolecular systems for dynamically probing cells

    NARCIS (Netherlands)

    Brinkmann, J.; Cavatorta, E.; Sankaran, S.; Schmidt, B.; van Weerd, Jasper; Jonkheijm, Pascal

    2014-01-01

    This article reviews the state of the art in the development of strategies for generating supramolecular systems for dynamic cell studies. Dynamic systems are crucial to further our understanding of cell biology and are consequently at the heart of many medical applications. Increasing interest has

  18. Determinants of Price Dynamics in Ethiopia

    African Journals Online (AJOL)

    the National bank of Ethiopia exercised tight monetary and fiscal policy, which in .... to apply standard estimation or testing procedures in a dynamic time series model, it is ... and SC indicate that lag order of two is appropriate for the model.

  19. Simultaneous determination of Se, trace elements and major elements in Se-rich rice by dynamic reaction cell inductively coupled plasma mass spectrometry (DRC-ICP-MS) after microwave digestion.

    Science.gov (United States)

    Wei, Yi Hua; Zhang, Jin Yan; Zhang, Da Wen; Luo, Lin Guang; Tu, Tian Hua

    2014-09-15

    A quick and accurate method was devised to determine Se, As, Ba, Ca, Cd, Cr, Cu, Fe, Mg, Mn, Ni, Pb, Sr and Zn in Se-rich rice samples by microwave digestion and inductively coupled plasma-mass spectrometry (ICP-MS). Spectral interferences on Se were eliminated using methane as a reaction gas in the dynamic reaction cell (DRC). Rhodium was used as an internal standard to compensate for sample matrix effects. A rice-certified reference material (CRM) (GBW 10010) was used to verify the accuracy of the method. The method detection limits were 0.001-0.03 mg/kg, analyte recoveries were 85-108% and precisions (RSDs) ranged from 2.1% to 5.8%. Correlation analysis showed that the Se concentrations in the Se-rich rice samples correlated well with the Cu concentrations (r=0.53, p<0.05).

  20. Multispectral fingerprinting for improved in vivo cell dynamics analysis

    Directory of Open Access Journals (Sweden)

    Cooper Cameron HJ

    2010-09-01

    Full Text Available Abstract Background Tracing cell dynamics in the embryo becomes tremendously difficult when cell trajectories cross in space and time and tissue density obscure individual cell borders. Here, we used the chick neural crest (NC as a model to test multicolor cell labeling and multispectral confocal imaging strategies to overcome these roadblocks. Results We found that multicolor nuclear cell labeling and multispectral imaging led to improved resolution of in vivo NC cell identification by providing a unique spectral identity for each cell. NC cell spectral identity allowed for more accurate cell tracking and was consistent during short term time-lapse imaging sessions. Computer model simulations predicted significantly better object counting for increasing cell densities in 3-color compared to 1-color nuclear cell labeling. To better resolve cell contacts, we show that a combination of 2-color membrane and 1-color nuclear cell labeling dramatically improved the semi-automated analysis of NC cell interactions, yet preserved the ability to track cell movements. We also found channel versus lambda scanning of multicolor labeled embryos significantly reduced the time and effort of image acquisition and analysis of large 3D volume data sets. Conclusions Our results reveal that multicolor cell labeling and multispectral imaging provide a cellular fingerprint that may uniquely determine a cell's position within the embryo. Together, these methods offer a spectral toolbox to resolve in vivo cell dynamics in unprecedented detail.

  1. Determination of Reference Chemical Potential Using Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Krishnadeo Jatkar

    2010-01-01

    Full Text Available A new method implementing molecular dynamics (MD simulations for calculating the reference properties of simple gas hydrates has been proposed. The guest molecules affect interaction between adjacent water molecules distorting the hydrate lattice, which requires diverse values of reference properties for different gas hydrates. We performed simulations to validate the experimental data for determining Δ0, the chemical potential difference between water and theoretical empty cavity at the reference state, for structure II type gas hydrates. Simulations have also been used to observe the variation of the hydrate unit cell volume with temperature. All simulations were performed using TIP4P water molecules at the reference temperature and pressure conditions. The values were close to the experimental values obtained by the Lee-Holder model, considering lattice distortion.

  2. Cell polarity determinants establish asymmetry in MEN signaling.

    Science.gov (United States)

    Monje-Casas, Fernando; Amon, Angelika

    2009-01-01

    Components of the mitotic exit network (MEN), a signaling pathway that triggers exit from mitosis, localize to the spindle pole body (SPB) that migrates into the daughter cell during anaphase but are largely absent from the SPB that remains in the mother cell. Through the analysis of one of the determinants of this asymmetry, Bfa1, we find that the machinery responsible for establishing cell polarity and cytoplasmic microtubules collaborate to establish MEN asymmetry. In cells defective in the Cdc42 signaling pathway or the formin Bni1, Bfa1 localizes to both SPBs. The quantitative analysis of Bfa1 localization further shows that Bfa1 can associate with both SPBs in a transient and highly dynamic fashion, but the protein is stabilized on the SPB that migrates into the daughter cell during anaphase through microtubule-bud cortex interactions. Our results indicate that mother-daughter cell asymmetry determinants establish MEN signaling asymmetry through microtubule-bud cortex interactions.

  3. Cell Division, Differentiation and Dynamic Clustering

    CERN Document Server

    Kaneko, K; Kaneko, Kunihiko; Yomo, Tetsuya

    1993-01-01

    A novel mechanism for cell differentiation is proposed, based on the dynamic clustering in a globally coupled chaotic system. A simple model with metabolic reaction, active transport of chemicals from media, and cell division is found to show three successive stages with the growth of the number of cells; coherent growth, dynamic clustering, and fixed cell differentiation. At the last stage, disparity in activities, germ line segregation, somatic cell differentiation, and homeochaotic stability against external perturbation are found. Our results, in consistency with the experiments of the preceding paper, imply that cell differentiation can occur without a spatial pattern. From dynamical systems viewpoint, the new concept of ``open chaos" is proposed, as a novel and general scenario for systems with growing numbers of elements, also seen in economics and sociology.A

  4. Universal signal generator for dynamic cell stimulation.

    Science.gov (United States)

    Piehler, Andreas; Ghorashian, Navid; Zhang, Ce; Tay, Savaş

    2017-06-27

    Dynamic cell stimulation is a powerful technique for probing gene networks and for applications in stem cell differentiation, immunomodulation and signaling. We developed a robust and flexible method and associated microfluidic devices to generate a wide-range of precisely formulated dynamic chemical signals to stimulate live cells and measure their dynamic response. This signal generator is capable of digital to analog conversion (DAC) through combinatoric selection of discrete input concentrations, and outperforms existing methods by both achievable resolution, dynamic range and simplicity in design. It requires no calibration, has minimal space requirements and can be easily integrated into microfluidic cell culture devices. The signal generator hardware and software we developed allows to choose the waveform, period and amplitude of chemical input signals and features addition of well-defined chemical noise to study the role of stochasticity in cellular information processing.

  5. Determining Outdoor CPV Cell Temperature (Presentation)

    Energy Technology Data Exchange (ETDEWEB)

    Muller, M.

    2011-04-01

    An accurate method is needed for determining cell temperature when measuring CPV modules outdoors. It has been suggested that cell temperature can be calculated though a procedure that shutters sunlight to the cells while measuring the transients in open-circuit voltage (Voc) and heat sink temperature. This presentation documents application of this shutter procedure to multiple CPV modules at NREL. The challenges and limitations are presented along with an alternate approach to measuring CPV cell operating temperature.

  6. Determinants of Welfare Dynamics in Rural Nicaragua

    DEFF Research Database (Denmark)

    Jakobsen, Kristian Thor

    2011-01-01

    This article explores the determinants of poverty movements in rural Nicaragua by introducing a bivariate probate model, making it possible to treat the initial state of poverty as endogenous and thus avoiding introducing selection bias. The results indicate that this is relevant when exploring...... in explaining poverty movements. Moreover, climate-related shocks such as droughts and pest attacks not only have persistent and adverse impacts on household consumption, but also affect households’ productive asset holdings, which could affect their income-generating potential in the longer term....

  7. Determining habitat quality for species that demonstrate dynamic habitat selection

    Science.gov (United States)

    Beerens, James; Frederick, Peter C; Noonburg, Erik G; Gawlik, Dale E.

    2015-01-01

    Determining habitat quality for wildlife populations requires relating a species' habitat to its survival and reproduction. Within a season, species occurrence and density can be disconnected from measures of habitat quality when resources are highly seasonal, unpredictable over time, and patchy. Here we establish an explicit link among dynamic selection of changing resources, spatio-temporal species distributions, and fitness for predictive abundance and occurrence models that are used for short-term water management and long-term restoration planning. We used the wading bird distribution and evaluation models (WADEM) that estimate (1) daily changes in selection across resource gradients, (2) landscape abundance of flocks and individuals, (3) conspecific foraging aggregation, and (4) resource unit occurrence (at fixed 400 m cells) to quantify habitat quality and its consequences on reproduction for wetland indicator species. We linked maximum annual numbers of nests detected across the study area and nesting success of Great Egrets (Ardea alba), White Ibises (Eudocimus albus), and Wood Storks (Mycteria americana) over a 20-year period to estimated daily dynamics of food resources produced by WADEM over a 7490 km2 area. For all species, increases in predicted species abundance in March and high abundance in April were strongly linked to breeding responses. Great Egret nesting effort and success were higher when birds also showed greater conspecific foraging aggregation. Synthesis and applications: This study provides the first empirical evidence that dynamic habitat selection processes and distributions of wading birds over environmental gradients are linked with reproductive measures over periods of decades. Further, predictor variables at a variety of temporal (daily-multiannual) resolutions and spatial (400 m to regional) scales effectively explained variation in ecological processes that change habitat quality. The process used here allows managers to develop

  8. A novel methodology for rapid digestion of rare earth element ores and determination by microwave plasma-atomic emission spectrometry and dynamic reaction cell-inductively coupled plasma-mass spectrometry.

    Science.gov (United States)

    Helmeczi, Erick; Wang, Yong; Brindle, Ian D

    2016-11-01

    Short-wavelength infrared radiation has been successfully applied to accelerate the acid digestion of refractory rare-earth ore samples. Determinations were achieved with microwave plasma-atomic emission spectrometry (MP-AES) and dynamic reaction cell - inductively coupled plasma-mass spectrometry (DRC-ICP-MS). The digestion method developed was able to tackle high iron-oxide and silicate matrices using only phosphoric acid in a time frame of only 8min, and did not require perchloric or hydrofluoric acid. Additionally, excellent recoveries and reproducibilities of the rare earth elements, as well as uranium and thorium, were achieved. Digestions of the certified reference materials OREAS-465 and REE-1, with radically different mineralogies, delivered results that mirror those obtained by fusion processes. For the rare-earth CRM OKA-2, whose REE data are provisional, experimental data for the rare-earth elements were generally higher than the provisional values, often exceeding z-values of +2. Determined values for Th and U in this reference material, for which certified values are available, were in excellent agreement. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Dynamic culture improves cell reprogramming efficiency.

    Science.gov (United States)

    Sia, Junren; Sun, Raymond; Chu, Julia; Li, Song

    2016-06-01

    Cell reprogramming to pluripotency is an inefficient process and various approaches have been devised to improve the yield of induced pluripotent stem cells. However, the effect of biophysical factors on cell reprogramming is not well understood. Here we showed that, for the first time, dynamic culture with orbital shaking significantly improved the reprogramming efficiency in adherent cells. Manipulating the viscosity of the culture medium suggested that the improved efficiency is mainly attributed to convective mixing rather than hydrodynamic shear stress. Temporal studies demonstrated that the enhancement of reprogramming efficiency required the dynamic culture in the middle but not early phase. In the early phase, fibroblasts had a high proliferation rate, but as the culture became over-confluent in the middle phase, expression of p57 was upregulated to inhibit cell proliferation and consequently, cell reprogramming. Subjecting the over confluent culture to orbital shaking prevented the upregulation of p57, thus improving reprogramming efficiency. Seeding cells at low densities to avoid over-confluency resulted in a lower efficiency, and optimal reprogramming efficiency was attained at a high seeding density with dynamic culture. Our findings provide insight into the underlying mechanisms of how dynamic culture condition regulate cell reprogramming, and will have broad impact on cell engineering for regenerative medicine and disease modeling.

  10. Epigenetic dynamics across the cell cycle

    DEFF Research Database (Denmark)

    Kheir, Tony Bou; Lund, Anders H.

    2010-01-01

    Progression of the mammalian cell cycle depends on correct timing and co-ordination of a series of events, which are managed by the cellular transcriptional machinery and epigenetic mechanisms governing genome accessibility. Epigenetic chromatin modifications are dynamic across the cell cycle......, and are shown to influence and be influenced by cell-cycle progression. Chromatin modifiers regulate cell-cycle progression locally by controlling the expression of individual genes and globally by controlling chromatin condensation and chromosome segregation. The cell cycle, on the other hand, ensures...... a correct inheritance of epigenetic chromatin modifications to daughter cells. In this chapter, we summarize the current knowledge on the dynamics of epigenetic chromatin modifications during progression of the cell cycle....

  11. Dynamical Adaptation in Terrorist Cells/Networks

    DEFF Research Database (Denmark)

    Hussain, Dil Muhammad Akbar; Ahmed, Zaki

    2010-01-01

    Typical terrorist cells/networks have dynamical structure as they evolve or adapt to changes which may occur due to capturing or killing of a member of the cell/network. Analytical measures in graph theory like degree centrality, betweenness and closeness centralities are very common and have long...

  12. Intergenerational continuity of cell shape dynamics in Caulobacter crescentus

    Science.gov (United States)

    Wright, Charles S.; Banerjee, Shiladitya; Iyer-Biswas, Srividya; Crosson, Sean; Dinner, Aaron R.; Scherer, Norbert F.

    2015-03-01

    We investigate the intergenerational shape dynamics of single Caulobacter crescentus cells using a novel combination of imaging techniques and theoretical modeling. We determine the dynamics of cell pole-to-pole lengths, cross-sectional widths, and medial curvatures from high accuracy measurements of cell contours. Moreover, these shape parameters are determined for over 250 cells across approximately 10000 total generations, which affords high statistical precision. Our data and model show that constriction is initiated early in the cell cycle and that its dynamics are controlled by the time scale of exponential longitudinal growth. Based on our extensive and detailed growth and contour data, we develop a minimal mechanical model that quantitatively accounts for the cell shape dynamics and suggests that the asymmetric location of the division plane reflects the distinct mechanical properties of the stalked and swarmer poles. Furthermore, we find that the asymmetry in the division plane location is inherited from the previous generation. We interpret these results in terms of the current molecular understanding of shape, growth, and division of C. crescentus.

  13. Sensitivity Analysis of Centralized Dynamic Cell Selection

    DEFF Research Database (Denmark)

    Lopez, Victor Fernandez; Alvarez, Beatriz Soret; Pedersen, Klaus I.;

    2016-01-01

    mechanism and solutions involving cell switching in general. Simulation results show that such solutions can greatly benefit from the use of receivers with interference suppression capabilities and a larger number of antennas, with a maximum data rate gain of 120%. High performance gains are observed...... with two different traffic models, and it is not necessary to be able to connect to a large number of cells in order to reap most of the benefits of the centralized dynamic cell selection....

  14. Intermediate filaments: a dynamic network that controls cell mechanics.

    Science.gov (United States)

    Gruenbaum, Yosef; Aebi, Ueli

    2014-01-01

    In humans the superfamily of intermediate filament (IF) proteins is encoded by more than 70 different genes, which are expressed in a cell- and tissue-specific manner. IFs assemble into approximately 10 nm-wide filaments that account for the principal structural elements at the nuclear periphery, nucleoplasm, and cytoplasm. They are also required for organizing the microtubule and microfilament networks. In this review, we focus on the dynamics of IFs and how modifications regulate it. We also discuss the role of nuclear IF organization in determining nuclear mechanics as well as that of cytoplasmic IFs organization in maintaining cell stiffness, formation of lamellipodia, regulation of cell migration, and permitting cell adhesion.

  15. Determination of glyphosate and AMPA in surface and waste water using high-performance ion chromatography coupled to inductively coupled plasma dynamic reaction cell mass spectrometry (HPIC-ICP-DRC-MS).

    Science.gov (United States)

    Popp, Maximilian; Hann, Stephan; Mentler, Axel; Fuerhacker, Maria; Stingeder, Gerhard; Koellensperger, Gunda

    2008-05-01

    A novel method employing high-performance cation chromatography in combination with inductively coupled plasma dynamic reaction cell mass spectrometry (ICP-DRC-MS) for the simultaneous determination of the herbicide glyphosate (N-phosphonomethylglycine) and its main metabolite aminomethyl phosphonic acid (AMPA) is presented. P was measured as (31)P(16)O(+) using oxygen as reaction gas. For monitoring the stringent target value of 0.1 μg L(-1) for glyphosate, applicable for drinking and surface water within the EU, a two-step enrichment procedure employing Chelex 100 and AG1-X8 resins was applied prior to HPIC-ICP-MS analysis. The presented approach was validated for surface water, revealing concentrations of 0.67 μg L(-1) glyphosate and 2.8 μg L(-1) AMPA in selected Austrian river water samples. Moreover, investigations at three waste water-treatment plants showed that elimination of the compounds at the present concentration levels was not straightforward. On the contrary, all investigated plant effluents showed significant amounts of both compounds. Concentration levels ranged from 0.5-2 μg L(-1) and 4-14 μg L(-1) for glyphosate and AMPA, respectively.

  16. Determinative developmental cell lineages are robust to cell deaths.

    Directory of Open Access Journals (Sweden)

    Jian-Rong Yang

    2014-07-01

    Full Text Available All forms of life are confronted with environmental and genetic perturbations, making phenotypic robustness an important characteristic of life. Although development has long been viewed as a key component of phenotypic robustness, the underlying mechanism is unclear. Here we report that the determinative developmental cell lineages of two protostomes and one deuterostome are structured such that the resulting cellular compositions of the organisms are only modestly affected by cell deaths. Several features of the cell lineages, including their shallowness, topology, early ontogenic appearances of rare cells, and non-clonality of most cell types, underlie the robustness. Simple simulations of cell lineage evolution demonstrate the possibility that the observed robustness arose as an adaptation in the face of random cell deaths in development. These results reveal general organizing principles of determinative developmental cell lineages and a conceptually new mechanism of phenotypic robustness, both of which have important implications for development and evolution.

  17. Collective Calcium Dynamics in Networks of Communicating Cells

    Science.gov (United States)

    Byrd, Tommy; Potter, Garrett; Sun, Bo; Mugler, Andrew

    Cells can sense and encode information about their environment with remarkable precision. These properties have been studied extensively for single cells, but intercellular communication is known to be important for both single- and multicellular organisms. Here, we examine calcium dynamics of fibroblast cells exposed to external ATP stimuli, and the effects of communication and stimulus strength on cells' response. Experimental results show that increasing communication strength induces a greater fraction of cells to exhibit oscillatory calcium dynamics, but the frequencies of oscillation do not systematically shift with ATP strength. We developed a model of calcium signaling by adding noise, communication, and cell-to-cell variability to the model of Tang and Othmer. This model reproduces cells' increased tendency to oscillate as a function of communication strength, and frequency encoding is nearly removed at the global level. Our model therefore suggests that the propensity of cells to oscillate, rather than frequency encoding, determines the response to external ATP. These results suggest that the system lies near a critical boundary separating non-oscillatory and oscillatory calcium dynamics.

  18. A stochastic phase-field model determined from molecular dynamics

    KAUST Repository

    von Schwerin, Erik

    2010-03-17

    The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.

  19. Determining of the CME dynamics by digital image

    Science.gov (United States)

    Rigozo, Nivaor R.; Dal Lago, Alisson; Schuch, Nelson Jorge

    We have developed a new technique to detection of Coronal Mass Eject (CME) by used image processing. This is technique permit determined the CME dynamic (distance, velocity and acceleration radial, and distance, velocity and acceleration expansion). The CME dynamic is determined by selection a direction radial in a given LASCO image, which starts just before the occulter (close to the center) and extends to the extremity of the image. By tacking a series of image and extracting the same direction radial, for each of them and placing them side by side. It is possible to have a time history of any moving feature inside this direction. This technique allows you to choose the number of directions that will be used in CME detecting, i.e., in determining its dynamics.

  20. Mechanobiology of cell migration in the context of dynamic two-way cell-matrix interactions.

    Science.gov (United States)

    Kurniawan, Nicholas A; Chaudhuri, Parthiv Kant; Lim, Chwee Teck

    2016-05-24

    Migration of cells is integral in various physiological processes in all facets of life. These range from embryonic development, morphogenesis, and wound healing, to disease pathology such as cancer metastasis. While cell migratory behavior has been traditionally studied using simple assays on culture dishes, in recent years it has been increasingly realized that the physical, mechanical, and chemical aspects of the matrix are key determinants of the migration mechanism. In this paper, we will describe the mechanobiological changes that accompany the dynamic cell-matrix interactions during cell migration. Furthermore, we will review what is to date known about how these changes feed back to the dynamics and biomechanical properties of the cell and the matrix. Elucidating the role of these intimate cell-matrix interactions will provide not only a better multi-scale understanding of cell motility in its physiological context, but also a more holistic perspective for designing approaches to regulate cell behavior.

  1. Human T Cell Memory: A Dynamic View

    Directory of Open Access Journals (Sweden)

    Derek C. Macallan

    2017-02-01

    Full Text Available Long-term T cell-mediated protection depends upon the formation of a pool of memory cells to protect against future pathogen challenge. In this review we argue that looking at T cell memory from a dynamic viewpoint can help in understanding how memory populations are maintained following pathogen exposure or vaccination. For example, a dynamic view resolves the apparent paradox between the relatively short lifespans of individual memory cells and very long-lived immunological memory by focussing on the persistence of clonal populations, rather than individual cells. Clonal survival is achieved by balancing proliferation, death and differentiation rates within and between identifiable phenotypic pools; such pools correspond broadly to sequential stages in the linear differentiation pathway. Each pool has its own characteristic kinetics, but only when considered as a population; single cells exhibit considerable heterogeneity. In humans, we tend to concentrate on circulating cells, but memory T cells in non-lymphoid tissues and bone marrow are increasingly recognised as critical for immune defence; their kinetics, however, remain largely unexplored. Considering vaccination from this viewpoint shifts the focus from the size of the primary response to the survival of the clone and enables identification of critical system pinch-points and opportunities to improve vaccine efficacy.

  2. Collective dynamics of cell migration and cell rearrangements

    Science.gov (United States)

    Kabla, Alexandre

    Understanding multicellular processes such as embryo development or cancer metastasis requires to decipher the contributions of local cell autonomous behaviours and long range interactions with the tissue environment. A key question in this context concerns the emergence of large scale coordination in cell behaviours, a requirement for collective cell migration or convergent extension. I will present a few examples where physical and mechanical aspects play a significant role in driving tissue scale dynamics. Geometrical confinement is one of the key external factors influencing large scale coordination during collective migration. Using a combination of in vitro experiments and numerical simulations, we show that the velocity correlation length, measured in unconfined conditions, provides a convenient length scale to predict the dynamic response under confinement. The same length scale can also be used to quantify the influence range of directional cues within the cell population. Heterogeneity within motile cell populations is frequently associated with an increase in their invasive capability and appears to play an important role during cancer metastasis. Using in silico experiments, we studied the way cell invasion is influenced by both the degree of cell coordination and the amount of variability in the motile force of the invading cells. Results suggest that mechanical heterogeneity dramatically enhances the invasion rate through an emerging cooperative process between the stronger and weaker cells, accounting for a number of observed invasion phenotypes. Effective convergent extension requires on a consistent orientation of cell intercalation at the tissue scale, most often in relation with planar cell polarity mechanisms to define the primary axes of deformation. Using a novel modelling approach for cells mechanical interactions, we studied the dynamics of substrate free motile cell populations. Ongoing work shows in particular that nematic order emerges

  3. Factors Determining Particle Dynamics over the Air-Sea Interface

    NARCIS (Netherlands)

    Leeuw, G. de; Larsen, S.E.; Mestayer, P.G.

    2000-01-01

    Work done in the framework of the ASE subproject, topic 5, on factors determining particle dynamics over the air-sea interface, is briefly reviewed. Emphasis is on the cooperative efforts between the authors, covering a period of roughly 8 years, from 1988 until 1996 [1–16], which in part were

  4. Dynamics of B cells in germinal centres.

    Science.gov (United States)

    De Silva, Nilushi S; Klein, Ulf

    2015-03-01

    Humoral immunity depends on the germinal centre (GC) reaction during which somatically mutated high-affinity memory B cells and plasma cells are generated. Recent studies have uncovered crucial cues that are required for the formation and the maintenance of GCs and for the selection of high-affinity antibody mutants. In addition, it is now clear that these events are promoted by the dynamic movements of cells within and between GCs. These findings have resolved the complexities of the GC reaction in greater detail than ever before. This Review focuses on these recent advances and discusses their implications for the establishment of humoral immunity.

  5. Dynamic synchrony of local cell assembly.

    Science.gov (United States)

    Sakurai, Yoshio; Takahashi, Susumu

    2008-01-01

    In the present paper, we focus on the problem of the dynamic size of a cell assembly and discuss how we can detect synchronized firing of a local cell assembly consisting of closely neighboring neurons in the working brain. A local cell assembly is difficult to detect because of the problem of spike overlapping of neighboring neurons, which cannot be overcome by ordinary spike-sorting techniques. We introduce a unique technique of spike-sorting that combines independent component analysis (ICA) and an ordinary sorting method to separate individual neighboring neurons and analyze their firing synchrony in behaving animals. One of our experiments employing this method showed that some closely neighboring neurons in the monkey prefrontal cortex have dynamic and sharp synchrony of firing reflecting local cell assemblies during working-memory processes. Another experiment showed that our other method (ICSort) of novel spike-sorting by ICA using special electrodes (dodecatrodes) can distinguish firing signals from the soma and those from the dendrites of individual neurons in behaving rats and suggests that the somatic and dendritic signals have different roles in information processing. This indicates that functional connectivity among neurons may be more dynamic and complex and spikes from the soma and dendrites of individual neurons should be considered in the investigation of the activity of local cell assemblies. We finally propose that detailed and real features of a local cell assembly consisting of closely neighboring neurons should be examined further and detection of local cell assemblies could be applied to the development of neuronal prosthetic devices, that is, brain-machine interfaces (BMIs).

  6. Pea border cell maturation and release involve complex cell wall structural dynamics

    DEFF Research Database (Denmark)

    Mravec, Jozef; Guo, Xiaoyuan; Hansen, Aleksander Riise

    2017-01-01

    The adhesion of plant cells is vital for support and protection of the plant body and is maintained by a variety of molecular associations between cell wall components. In some specialized cases though, plant cells are programmed to detach and root cap-derived border cells are examples of this....... Border cells (in some species known as border-like cells) provide an expendable barrier between roots and the environment. Their maturation and release is an important but poorly characterized cell separation event. To gain a deeper insight into the complex cellular dynamics underlying this process, we...... undertook a systematic, detailed analysis of pea (Pisum sativum) root tip cell walls. Our study included immuno-carbohydrate microarray profiling, monosaccharide composition determination, Fourier-transformed infrared microspectroscopy (FT-IR), quantitative RT-PCR of cell wall biosynthetic genes, analysis...

  7. Modeling cell dynamics under mobile phone radiation.

    Science.gov (United States)

    Minelli, Tullio Antonio; Balduzzo, Maurizio; Milone, Francesco Ferro; Nofrate, Valentina

    2007-04-01

    Perturbations by pulse-modulated microwave radiation from GSM mobile phones on neuron cell membrane gating and calcium oscillations have been suggested as a possible mechanism underlying activation of brain states and electroencephalographic epiphenomena. As the employ of UMTS phones seems to reveal other symptoms, a unified phenomenological framework is needed. In order to explain possible effects of mobile phone radiation on cell oscillations, GSM and UMTS low-frequency envelopes have been detected, recorded and used as input in cell models. Dynamical systems endowed with contiguous regular and chaotic regimes suitable to produce stochastic resonance can both account for the perturbation of the neuro-electrical activity and even for the low intensity of the signal perceived by high sensitive subjects. Neuron models of this kind can be employed as a reductionist hint for the mentioned phenomenology. The Hindmarsh-Rose model exhibits frequency enhancement and regularization phenomena induced by weak GSM and UMTS. More realistic simulations of cell membrane gating and calcium oscillations have been performed with the help of an adaptation of the Chay-Keizer dynamical system. This scheme can explain the suspected subjective sensitivity to mobile phone signals under the thermal threshold, in terms of cell calcium regularity mechanisms. Concerning the two kinds of emission, the stronger occupation of the ELF band of last generation UMTS phones is compensated by lower power emitted.

  8. INDIRECT DETERMINATION METHOD OF DYNAMIC FORCEBY USING CEPSTRUM ANALYSIS

    Institute of Scientific and Technical Information of China (English)

    吴淼; 魏任之

    1996-01-01

    The dynamic load spectrum is one of the most important basis of design and dynamic characteristics analysis of machines. But it is difficult to measure it on many occasions, especially for mining machines, due to their bad working circumstances and high cost of measurements. For such situation, the load spectrum has to be obtained by indirect determination methods. A new method to identify the load spectrum, cepstrum analysis method, was presented in this paper.This method can be used to eliminate the filtering influence of transfer function to the response signals so that the load spectrum can be determined indirectly. The experimental and engineering actual examples indicates that this method has the advantages that the calculation is simple and the measurement is easy.

  9. Satellite Aerodynamics and Density Determination from Satellite Dynamic Response

    Science.gov (United States)

    Karr, G. R.

    1972-01-01

    The aerodynamic drag and lift properties of a satellite are first expressed as a function of two parameters associated with gas-surface interaction at the satellite surface. The dynamic response of the satellite as it passes through the atmosphere is then expressed as a function of the two gas-surface interaction parameters, the atmospheric density, the satellite velocity, and the satellite orientation to the high speed flow. By proper correlation of the observed dynamic response with the changing angle of attack of the satellite, it is found that the two unknown gas-surface interaction parameters can be determined. Once the gas-surface interaction parameters are known, the aerodynamic properties of the satellite at all angles of attack are also determined.

  10. Microenvironment-Centred Dynamics in Aggressive B-Cell Lymphomas

    Directory of Open Access Journals (Sweden)

    Matilde Cacciatore

    2012-01-01

    Full Text Available Aggressive B-cell lymphomas share high proliferative and invasive attitudes and dismal prognosis despite heterogeneous biological features. In the interchained sequence of events leading to cancer progression, neoplastic clone-intrinsic molecular events play a major role. Nevertheless, microenvironment-related cues have progressively come into focus as true determinants for this process. The cancer-associated microenvironment is a complex network of nonneoplastic immune and stromal cells embedded in extracellular components, giving rise to a multifarious crosstalk with neoplastic cells towards the induction of a supportive milieu. The immunological and stromal microenvironments have been classically regarded as essential partners of indolent lymphomas, while considered mainly negligible in the setting of aggressive B-cell lymphomas that, by their nature, are less reliant on external stimuli. By this paper we try to delineate the cardinal microenvironment-centred dynamics exerting an influence over lymphoid clone progression in aggressive B-cell lymphomas.

  11. A Bacterial Cell Shape-Determining Inhibitor.

    Science.gov (United States)

    Liu, Yanjie; Frirdich, Emilisa; Taylor, Jennifer A; Chan, Anson C K; Blair, Kris M; Vermeulen, Jenny; Ha, Reuben; Murphy, Michael E P; Salama, Nina R; Gaynor, Erin C; Tanner, Martin E

    2016-04-15

    Helicobacter pylori and Campylobacter jejuni are human pathogens and causative agents of gastric ulcers/cancer and gastroenteritis, respectively. Recent studies have uncovered a series of proteases that are responsible for maintaining the helical shape of these organisms. The H. pylori metalloprotease Csd4 and its C. jejuni homologue Pgp1 cleave the amide bond between meso-diaminopimelate and iso-d-glutamic acid in truncated peptidoglycan side chains. Deletion of either csd4 or pgp1 results in bacteria with a straight rod phenotype, a reduced ability to move in viscous media, and reduced pathogenicity. In this work, a phosphinic acid-based pseudodipeptide inhibitor was designed to act as a tetrahedral intermediate analog against the Csd4 enzyme. The phosphinic acid was shown to inhibit the cleavage of the alternate substrate, Ac-l-Ala-iso-d-Glu-meso-Dap, with a Ki value of 1.5 μM. Structural analysis of the Csd4-inhibitor complex shows that the phosphinic acid displaces the zinc-bound water and chelates the metal in a bidentate fashion. The phosphinate oxygens also interact with the key acid/base residue, Glu222, and the oxyanion-stabilizing residue, Arg86. The results are consistent with the "promoted-water pathway" mechanism for carboxypeptidase A catalysis. Studies on cultured bacteria showed that the inhibitor causes significant cell straightening when incubated with H. pylori at millimolar concentrations. A diminished, yet observable, effect on the morphology of C. jejuni was also apparent. Cell straightening was more pronounced with an acapsular C. jejuni mutant strain compared to the wild type, suggesting that the capsule impaired inhibitor accessibility. These studies demonstrate that a highly polar compound is capable of crossing the outer membrane and altering cell shape, presumably by inhibiting cell shape determinant proteases. Peptidoglycan proteases acting as cell shape determinants represent novel targets for the development of antimicrobials

  12. An Endothelial Planar Cell Model for Imaging Immunological Synapse Dynamics.

    Science.gov (United States)

    Martinelli, Roberta; Carman, Christopher V

    2015-12-24

    Adaptive immunity is regulated by dynamic interactions between T cells and antigen presenting cells ('APCs') referred to as 'immunological synapses'. Within these intimate cell-cell interfaces discrete sub-cellular clusters of MHC/Ag-TCR, F-actin, adhesion and signaling molecules form and remodel rapidly. These dynamics are thought to be critical determinants of both the efficiency and quality of the immune responses that develop and therefore of protective versus pathologic immunity. Current understanding of immunological synapses with physiologic APCs is limited by the inadequacy of the obtainable imaging resolution. Though artificial substrate models (e.g., planar lipid bilayers) offer excellent resolution and have been extremely valuable tools, they are inherently non-physiologic and oversimplified. Vascular and lymphatic endothelial cells have emerged as an important peripheral tissue (or stromal) compartment of 'semi-professional APCs'. These APCs (which express most of the molecular machinery of professional APCs) have the unique feature of forming virtually planar cell surface and are readily transfectable (e.g., with fluorescent protein reporters). Herein a basic approach to implement endothelial cells as a novel and physiologic 'planar cellular APC model' for improved imaging and interrogation of fundamental antigenic signaling processes will be described.

  13. Automated three-dimensional single cell phenotyping of spindle dynamics, cell shape, and volume

    CERN Document Server

    Plumb, Kemp; Pelletier, Vincent; Kilfoil, Maria L

    2015-01-01

    We present feature finding and tracking algorithms in 3D in living cells, and demonstrate their utility to measure metrics important in cell biological processes. We developed a computational imaging hybrid approach that combines automated three-dimensional tracking of point-like features with surface determination from which cell (or nuclear) volume, shape, and planes of interest can be extracted. After validation, we applied the technique to real space context-rich dynamics of the mitotic spindle, and cell volume and its relationship to spindle length, in dividing living cells. These methods are additionally useful for automated segregation of pre-anaphase and anaphase spindle populations in budding yeast. We found that genetic deletion of the yeast kinesin-5 mitotic motor cin8 leads to large mother and daughter cells that were indistinguishable based on size, and that in those cells the spindle length becomes uncorrelated with cell size. The technique can be used to visualize and quantify tracked feature c...

  14. Comprehensive Gravity and Dynamics Model Determination of Binary Asteroid Systems

    Science.gov (United States)

    Fahnestock, Eugene G.

    2009-09-01

    I present the development of additional tools within the framework of JPL's in-house Mirage / Orbit Determination Program (ODP) software to allow the determination of a comprehensive gravity and dynamics model for any binary asteroid system potentially visited by a spacecraft rendezvous mission. This involves a concurrent global solution for the gravity fields of both components, sufficient parametric description of their fully-coupled translational and rotational dynamics, the spacecraft state, and all other relevant force model parameters. This estimation process primarily uses spacecraft radio tracking data (range and Doppler measurements), supplemented by in-situ imaging observations data types. A solution for the gravity field (gravity analysis) and a simultaneous solution for the spacecraft motion and other system properties has been performed before using the ODP for solitary irregular small solar system bodies (e.g. Eros, visited by the NEAR mission), but never for any closely gravitationally bound pair of irregular small solar system bodies. I am expanding NASA's tool set to allow the latter, in preparation for potential future spacecraft rendezvous missions. This is nontrivial, because of the need to incorporate propagation of the binary system's fully-coupled rigid-body dynamical model either along with the spacecraft state within Mirage/ODP or "offline", followed by interpolating an appropriate "binary dynamics ephemeris” representation. Further, this model optionally incorporates formulations for body gravity fields not previously used in this context, and it can be computationally very expensive. However, successfully performing this model determination at a binary asteroid yields valuable science results concerning internal mass distributions and structures of the components and insight into the system's formation and evolution. In this poster I present my current progress in the development of this capability and results for the quality of science

  15. Characterizing motility dynamics in human RPE cells

    Science.gov (United States)

    Liu, Zhuolin; Kurokawa, Kazuhiro; Zhang, Furu; Miller, Donald T.

    2017-02-01

    Retinal pigment epithelium (RPE) cells are vital to health of the outer retina, however, are often compromised in ageing and ocular diseases that lead to blindness. Early manifestation of RPE disruption occurs at the cellular level, but while in vivo biomarkers at this scale hold considerable promise, RPE cells have proven extremely challenging to image in the living human eye. Recently we addressed this problem by using organelle motility as a novel contrast agent to enhance the RPE cell in conjunction with 3D resolution of adaptive optics-optical coherence tomography (AO-OCT) to section the RPE layer. In this study, we expand on the central novelty of our method - organelle motility - by characterizing the dynamics of the motility in individual RPE cells, important because of its direct link to RPE physiology. To do this, AO-OCT videos of the same retinal patch were acquired at approximately 1 min intervals or less, time stamped, and registered in 3D with sub-cellular accuracy. Motility was quantified by an exponential decay time constant, the time for motility to decorrelate the speckle field across an RPE cell. In two normal subjects, we found the decay time constant to be just 3 seconds, thus indicating rapid motility in normal RPE cells.

  16. A system dynamics model to determine products mix

    Directory of Open Access Journals (Sweden)

    Mahtab Hajghasem

    2014-02-01

    Full Text Available This paper presents an implementation of system dynamics model to determine appropriate product mix by considering various factors such as labor, materials, overhead, etc. for an Iranian producer of cosmetic and sanitary products. The proposed model of this paper considers three hypotheses including the relationship between product mix and profitability, optimum production capacity and having minimum amount of storage to take advantage of low cost production. The implementation of system dynamics on VENSIM software package has confirmed all three hypotheses of the survey and suggested that in order to reach better mix product, it is necessary to reach optimum production planning, take advantage of all available production capacities and use inventory management techniques.

  17. Clustering determines the dynamics of complex contagions in multiplex networks

    CERN Document Server

    Zhuang, Yong; Yağan, Osman

    2016-01-01

    We present the mathematical analysis of generalized complex contagions in clustered multiplex networks for susceptible-infected-recovered (SIR)-like dynamics. The model is intended to understand diffusion of influence, or any other spreading process implying a threshold dynamics, in setups of interconnected networks with significant clustering. The contagion is assumed to be general enough to account for a content-dependent linear threshold model, where each link type has a different weight (for spreading influence) that may depend on the content (e.g., product, rumor, political view) that is being spread. Using the generating functions formalism, we determine the conditions, probability, and expected size of the emergent global cascades. This analysis provides a generalization of previous approaches and is specially useful in problems related to spreading and percolation. The results present non trivial dependencies between the clustering coefficient of the networks and its average degree. In particular, sev...

  18. Dynamic metabolic flux analysis of plant cell wall synthesis.

    Science.gov (United States)

    Chen, Xuewen; Alonso, Ana P; Shachar-Hill, Yair

    2013-07-01

    The regulation of plant cell wall synthesis pathways remains poorly understood. This has become a bottleneck in designing bioenergy crops. The goal of this study was to analyze the regulation of plant cell wall precursor metabolism using metabolic flux analysis based on dynamic labeling experiments. Arabidopsis T87 cells were cultured heterotrophically with (13)C labeled sucrose. The time course of ¹³C labeling patterns in cell wall precursors and related sugar phosphates was monitored using liquid chromatography tandem mass spectrometry until steady state labeling was reached. A kinetic model based on mass action reaction mechanisms was developed to simulate the carbon flow in the cell wall synthesis network. The kinetic parameters of the model were determined by fitting the model to the labeling time course data, cell wall composition, and synthesis rates. A metabolic control analysis was performed to predict metabolic regulations that may improve plant biomass composition for biofuel production. Our results describe the routes and rates of carbon flow from sucrose to cell wall precursors. We found that sucrose invertase is responsible for the entry of sucrose into metabolism and UDP-glucose-4-epimerase plays a dominant role in UDP-Gal synthesis in heterotrophic Aradidopsis cells under aerobic conditions. We also predicted reactions that exert strong regulatory influence over carbon flow to cell wall synthesis and its composition.

  19. Clustering determines the dynamics of complex contagions in multiplex networks

    Science.gov (United States)

    Zhuang, Yong; Arenas, Alex; Yaǧan, Osman

    2017-01-01

    We present the mathematical analysis of generalized complex contagions in a class of clustered multiplex networks. The model is intended to understand spread of influence, or any other spreading process implying a threshold dynamics, in setups of interconnected networks with significant clustering. The contagion is assumed to be general enough to account for a content-dependent linear threshold model, where each link type has a different weight (for spreading influence) that may depend on the content (e.g., product, rumor, political view) that is being spread. Using the generating functions formalism, we determine the conditions, probability, and expected size of the emergent global cascades. This analysis provides a generalization of previous approaches and is especially useful in problems related to spreading and percolation. The results present nontrivial dependencies between the clustering coefficient of the networks and its average degree. In particular, several phase transitions are shown to occur depending on these descriptors. Generally speaking, our findings reveal that increasing clustering decreases the probability of having global cascades and their size, however, this tendency changes with the average degree. There exists a certain average degree from which on clustering favors the probability and size of the contagion. By comparing the dynamics of complex contagions over multiplex networks and their monoplex projections, we demonstrate that ignoring link types and aggregating network layers may lead to inaccurate conclusions about contagion dynamics, particularly when the correlation of degrees between layers is high.

  20. Mechanosensing Dynamics of Red blood Cells

    Science.gov (United States)

    Wan, Jiandi

    2015-11-01

    Mechanical stress-induced deformation of human red blood cells (RBCs) plays important physiopathological roles in oxygen delivery, blood rheology, transfusion, and malaria. Recent studies demonstrate that, in response to mechanical deformation, RBCs release adenosine-5'-triphosphate (ATP), suggesting the existence of mechanotransductive pathways in RBCs. Most importantly, the released ATP from RBCs regulates vascular tone and impaired release of ATP from RBCs has been linked to diseases such as type II diabetes and cystic fibrosis. To date, however, the mechanisms of mechanotransductive release of ATP from RBCs remain unclear. Given that RBCs experience shear stresses continuously during the circulation cycle and the released ATP plays a central role in vascular physiopathology, understanding the mechanotransductive release of ATP from RBCs will provide not only fundamental insights to the role of RBCs in vascular homeostasis but also novel therapeutic strategies for red cell dysfunction and vascular disease. This talk describes the main research in my group on integrating microfluidic-based approaches to study the mechanosensing dynamics of RBCs. Specifically, I will introduce a micro?uidic approach that can probe the dynamics of shear-induced ATP release from RBCs with millisecond resolution and provide quantitative understandings of the mechanosensitive ATP release processes in RBCs. Furthermore, I will also describe our recent findings about the roles of the Piezo1 channel, a newly discovered mechanosensitive cation channel in the mechanotransductive ATP release in RBCs. Last, possible functions of RBCs in the regulation of cerebral blood flow will be discussed.

  1. Determination of dynamic fracture toughness using a new experimental technique

    Directory of Open Access Journals (Sweden)

    Cady Carl M.

    2015-01-01

    Full Text Available In other studies dynamic fracture toughness has been measured using Charpy impact and modified Hopkinson Bar techniques. In this paper results will be shown for the measurement of fracture toughness using a new test geometry. The crack propagation velocities range from ∼0.15 mm/s to 2.5 m/s. Digital image correlation (DIC will be the technique used to measure both the strain and the crack growth rates. The boundary of the crack is determined using the correlation coefficient generated during image analysis and with interframe timing the crack growth rate and crack opening can be determined. A comparison of static and dynamic loading experiments will be made for brittle polymeric materials. The analysis technique presented by Sammis et al. [1] is a semi-empirical solution, however, additional Linear Elastic Fracture Mechanics analysis of the strain fields generated as part of the DIC analysis allow for the more commonly used method resembling the crack tip opening displacement (CTOD experiment. It should be noted that this technique was developed because limited amounts of material were available and crack growth rates were to fast for a standard CTOD method.

  2. Sperm Cell Dynamics in Shallow Chambers

    Science.gov (United States)

    Condat, Carlos; Marconi, Veronica; Guidobaldi, Alejandro; Giojalas, Laura; Silhanek, Alejandro; Jeyaram, Yogesh; Moshchalkov, Victor

    2015-03-01

    Self-propelled microorganisms are attracted to surfaces. This makes their dynamic behavior in restricted geometries very different from that observed in the bulk. Here we analyze the motion of spermatozoids confined to shallow chambers, investigating the nature of the cell trajectories and their accumulation near the side boundaries. Observed cell trajectories are composed of a succession of quasi-circular and quasi-linear segments. This suggests that the cells follow a path of intermittent trappings near the top and down surfaces separated by stretches of quasi-free motion near the center of the gap. Use of microstructured petal-shaped edges limits accumulation near the borders and contributes to increase the concentration in the chamber interior. System stabilization occurs over times of the order of minutes, which agrees well with a theoretical estimate that assumes that the cell mean-square displacement is largely due to the quasi-linear segments. Pure quasi-circular trajectories would require several hours to stabilize. Our estimates also indicate that stabilization proceeds 2.5 times faster in the rosette geometries than in the smooth-edged chambers, which is another practical reason to prefer the former.

  3. Imaging Cellular Dynamics with Spectral Relaxation Imaging Microscopy: Distinct Spectral Dynamics in Golgi Membranes of Living Cells

    Science.gov (United States)

    Lajevardipour, Alireza; Chon, James W. M.; Chattopadhyay, Amitabha; Clayton, Andrew H. A.

    2016-11-01

    Spectral relaxation from fluorescent probes is a useful technique for determining the dynamics of condensed phases. To this end, we have developed a method based on wide-field spectral fluorescence lifetime imaging microscopy to extract spectral relaxation correlation times of fluorescent probes in living cells. We show that measurement of the phase and modulation of fluorescence from two wavelengths permit the identification and determination of excited state lifetimes and spectral relaxation correlation times at a single modulation frequency. For NBD fluorescence in glycerol/water mixtures, the spectral relaxation correlation time determined by our approach exhibited good agreement with published dielectric relaxation measurements. We applied this method to determine the spectral relaxation dynamics in membranes of living cells. Measurements of the Golgi-specific C6-NBD-ceramide probe in living HeLa cells revealed sub-nanosecond spectral dynamics in the intracellular Golgi membrane and slower nanosecond spectral dynamics in the extracellular plasma membrane. We interpret the distinct spectral dynamics as a result of structural plasticity of the Golgi membrane relative to more rigid plasma membranes. To the best of our knowledge, these results constitute one of the first measurements of Golgi rotational dynamics.

  4. Imaging Cellular Dynamics with Spectral Relaxation Imaging Microscopy: Distinct Spectral Dynamics in Golgi Membranes of Living Cells.

    Science.gov (United States)

    Lajevardipour, Alireza; Chon, James W M; Chattopadhyay, Amitabha; Clayton, Andrew H A

    2016-11-22

    Spectral relaxation from fluorescent probes is a useful technique for determining the dynamics of condensed phases. To this end, we have developed a method based on wide-field spectral fluorescence lifetime imaging microscopy to extract spectral relaxation correlation times of fluorescent probes in living cells. We show that measurement of the phase and modulation of fluorescence from two wavelengths permit the identification and determination of excited state lifetimes and spectral relaxation correlation times at a single modulation frequency. For NBD fluorescence in glycerol/water mixtures, the spectral relaxation correlation time determined by our approach exhibited good agreement with published dielectric relaxation measurements. We applied this method to determine the spectral relaxation dynamics in membranes of living cells. Measurements of the Golgi-specific C6-NBD-ceramide probe in living HeLa cells revealed sub-nanosecond spectral dynamics in the intracellular Golgi membrane and slower nanosecond spectral dynamics in the extracellular plasma membrane. We interpret the distinct spectral dynamics as a result of structural plasticity of the Golgi membrane relative to more rigid plasma membranes. To the best of our knowledge, these results constitute one of the first measurements of Golgi rotational dynamics.

  5. Dynamic cell culture system (7-IML-1)

    Science.gov (United States)

    Cogoli, Augusto

    1992-01-01

    This experiment is one of the Biorack experiments being flown on the International Microgravity Laboratory 1 (MIL-1) mission as part of an investigation studying cell proliferation and performance in space. One of the objectives of this investigation is to assess the potential benefits of bioprocessing in space with the ultimate goal of developing a bioreactor for continuous cell cultures in space. This experiment will test the operation of an automated culture chamber that was designed for use in a Bioreactor in space. The device to be tested is called the Dynamic Cell Culture System (DCCS). It is a simple device in which media are renewed or chemicals are injected automatically, by means of osmotic pumps. This experiment uses four Type I/O experiment containers. One DCCS unit, which contains a culture chamber with renewal of medium and a second chamber without a medium supply fits in each container. Two DCCS units are maintained under zero gravity conditions during the on-orbit period. The other two units are maintained under 1 gh conditions in a 1 g centrifuge. The schedule for incubator transfer is given.

  6. Determining equilibrium constants for dimerization reactions from molecular dynamics simulations.

    Science.gov (United States)

    De Jong, Djurre H; Schäfer, Lars V; De Vries, Alex H; Marrink, Siewert J; Berendsen, Herman J C; Grubmüller, Helmut

    2011-07-15

    With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices covers sufficiently many dimerization and dissociation events, their binding free energy is readily derived from the fraction of time during which the two helices are observed in dimeric form. Exactly how the correct value for the free energy is to be calculated, however, is unclear, and indeed several different and contradictory approaches have been used. In particular, results obtained via Boltzmann statistics differ from those determined via the law of mass action. Here, we develop a theory that resolves this discrepancy. We show that for simulation systems containing two molecules, the dimerization free energy is given by a formula of the form ΔG ∝ ln(P(1) /P(0) ). Our theory is also applicable to high concentrations that typically have to be used in molecular dynamics simulations to keep the simulation system small, where the textbook dilute approximations fail. It also covers simulations with an arbitrary number of monomers and dimers and provides rigorous error estimates. Comparison with test simulations of a simple Lennard Jones system with various particle numbers as well as with reference free energy values obtained from radial distribution functions show full agreement for both binding free energies and dimerization statistics.

  7. Dynamic determination reserves of the underground gas storage

    Institute of Scientific and Technical Information of China (English)

    谭羽非

    2004-01-01

    One of the key problems in the use of underground gas storage is frequent leakage. It can lead to the actual gas storage amount being less than that accounted for. Combining numerical simulation and parameter auto fit, this paper ascertains the dynamic variation of the pressure in the storage reservoir, adjusts the actual injecting and producing gas to fit the accounted pressure with the tested pressure, obtains the gas leakage of the storage, and then determines the difference between accounted amount and leakage amount. The result is the actual reserves of the storage. The simulation result shows that the method presented can provide a theoretic foundation for estimating the leakage amount, thereby ensuring the actual reserves, searching the leakage route,and reducing leakage by adjusting the storage method.

  8. Beta cell dynamics: beta cell replenishment, beta cell compensation and diabetes.

    Science.gov (United States)

    Cerf, Marlon E

    2013-10-01

    Type 2 diabetes, characterized by persistent hyperglycemia, arises mostly from beta cell dysfunction and insulin resistance and remains a highly complex metabolic disease due to various stages in its pathogenesis. Glucose homeostasis is primarily regulated by insulin secretion from the beta cells in response to prevailing glycemia. Beta cell populations are dynamic as they respond to fluctuating insulin demand. Beta cell replenishment and death primarily regulate beta cell populations. Beta cells, pancreatic cells, and extra-pancreatic cells represent the three tiers for replenishing beta cells. In rodents, beta cell self-replenishment appears to be the dominant source for new beta cells supported by pancreatic cells (non-beta islet cells, acinar cells, and duct cells) and extra-pancreatic cells (liver, neural, and stem/progenitor cells). In humans, beta cell neogenesis from non-beta cells appears to be the dominant source of beta cell replenishment as limited beta cell self-replenishment occurs particularly in adulthood. Metabolic states of increased insulin demand trigger increased insulin synthesis and secretion from beta cells. Beta cells, therefore, adapt to support their physiology. Maintaining physiological beta cell populations is a strategy for targeting metabolic states of persistently increased insulin demand as in diabetes.

  9. Mitochondrial dynamics and the cell cycle

    Directory of Open Access Journals (Sweden)

    Penny M.A. Kianian

    2014-05-01

    Full Text Available Nuclear-mitochondrial (NM communication impacts many aspects of plant development including vigor, sterility and viability. Dynamic changes in mitochondrial number, shape, size, and cellular location takes place during the cell cycle possibly impacting the process itself and leading to distribution of this organelle into daughter cells. The genes that underlie these changes are beginning to be identified in model plants such as Arabidopsis. In animals disruption of the drp1 gene, a homolog to the plant drp3A and drp3B, delays mitochondrial division. This mutation results in increased aneuploidy due to chromosome mis-segregation. It remains to be discovered if a similar outcome is observed in plants. Alloplasmic lines provide an opportunity to understand the communication between the cytoplasmic organelles and the nucleus. Examples of studies in these lines, especially from the extensive collection in wheat, point to the role of mitochondria in chromosome movement, pollen fertility and other aspects of development. Genes involved in NM interaction also are believed to play a critical role in evolution of species and interspecific cross incompatibilities.

  10. Discrete dynamic modeling of T cell survival signaling networks

    Science.gov (United States)

    Zhang, Ranran

    2009-03-01

    Biochemistry-based frameworks are often not applicable for the modeling of heterogeneous regulatory systems that are sparsely documented in terms of quantitative information. As an alternative, qualitative models assuming a small set of discrete states are gaining acceptance. This talk will present a discrete dynamic model of the signaling network responsible for the survival and long-term competence of cytotoxic T cells in the blood cancer T-LGL leukemia. We integrated the signaling pathways involved in normal T cell activation and the known deregulations of survival signaling in leukemic T-LGL, and formulated the regulation of each network element as a Boolean (logic) rule. Our model suggests that the persistence of two signals is sufficient to reproduce all known deregulations in leukemic T-LGL. It also indicates the nodes whose inactivity is necessary and sufficient for the reversal of the T-LGL state. We have experimentally validated several model predictions, including: (i) Inhibiting PDGF signaling induces apoptosis in leukemic T-LGL. (ii) Sphingosine kinase 1 and NFκB are essential for the long-term survival of T cells in T-LGL leukemia. (iii) T box expressed in T cells (T-bet) is constitutively activated in the T-LGL state. The model has identified potential therapeutic targets for T-LGL leukemia and can be used for generating long-term competent CTL necessary for tumor and cancer vaccine development. The success of this model, and of other discrete dynamic models, suggests that the organization of signaling networks has an determining role in their dynamics. Reference: R. Zhang, M. V. Shah, J. Yang, S. B. Nyland, X. Liu, J. K. Yun, R. Albert, T. P. Loughran, Jr., Network Model of Survival Signaling in LGL Leukemia, PNAS 105, 16308-16313 (2008).

  11. Cell-surface translational dynamics of nicotinic acetylcholine receptors

    Directory of Open Access Journals (Sweden)

    Francisco J Barrantes

    2014-11-01

    Full Text Available Synapse efficacy heavily relies on the number of neurotransmitter receptors available at a given time. In addition to the equilibrium between the biosynthetic production, exocytic delivery and recycling of receptors on the one hand, and the endocytic internalization on the other, lateral diffusion and clustering of receptors at the cell membrane play key roles in determining the amount of active receptors at the synapse. Mobile receptors traffic between reservoir compartments and the synapse by thermally driven Brownian motion, and become immobilized at the peri-synaptic region or the synapse by: a clustering mediated by homotropic inter-molecular receptor-receptor associations; b heterotropic associations with non-receptor scaffolding proteins or the subjacent cytoskeletal meshwork, leading to diffusional trapping, and c protein-lipid interactions, particularly with the neutral lipid cholesterol. This review assesses the contribution of some of these mechanisms to the supramolecular organization and dynamics of the paradigm neurotransmitter receptor of muscle and neuronal cells -the nicotinic acetylcholine receptor (nAChR. Currently available information stemming from various complementary biophysical techniques commonly used to interrogate the dynamics of cell-surface components is critically discussed. The translational mobility of nAChRs at the cell surface differs between muscle and neuronal receptors in terms of diffusion coefficients and residence intervals at the synapse, which cover an ample range of time regimes. A peculiar feature of brain 7 nAChR is its ability to spend much of its time confined peri-synaptically, vicinal to glutamatergic (excitatory and GABAergic (inhibitory synapses. An important function of the 7 nAChR may thus be visiting the territories of other neurotransmitter receptors, differentially regulating the dynamic equilibrium between excitation and inhibition, depending on its residence time in each domain.

  12. Computational investigation of epithelial cell dynamic phenotype in vitro

    Directory of Open Access Journals (Sweden)

    Debnath Jayanta

    2009-05-01

    Full Text Available Abstract Background When grown in three-dimensional (3D cultures, epithelial cells typically form cystic organoids that recapitulate cardinal features of in vivo epithelial structures. Characterizing essential cell actions and their roles, which constitute the system's dynamic phenotype, is critical to gaining deeper insight into the cystogenesis phenomena. Methods Starting with an earlier in silico epithelial analogue (ISEA1 that validated for several Madin-Darby canine kidney (MDCK epithelial cell culture attributes, we built a revised analogue (ISEA2 to increase overlap between analogue and cell culture traits. Both analogues used agent-based, discrete event methods. A set of axioms determined ISEA behaviors; together, they specified the analogue's operating principles. A new experimentation framework enabled tracking relative axiom use and roles during simulated cystogenesis along with establishment of the consequences of their disruption. Results ISEA2 consistently produced convex cystic structures in a simulated embedded culture. Axiom use measures provided detailed descriptions of the analogue's dynamic phenotype. Dysregulating key cell death and division axioms led to disorganized structures. Adhering to either axiom less than 80% of the time caused ISEA1 to form easily identified morphological changes. ISEA2 was more robust to identical dysregulation. Both dysregulated analogues exhibited characteristics that resembled those associated with an in vitro model of early glandular epithelial cancer. Conclusion We documented the causal chains of events, and their relative roles, responsible for simulated cystogenesis. The results stand as an early hypothesis–a theory–of how individual MDCK cell actions give rise to consistently roundish, cystic organoids.

  13. Empirical determinants of measles metapopulation dynamics in England and Wales.

    OpenAIRE

    Finkenstädt, B; Grenfell, B.

    1998-01-01

    A key issue in metapopulation dynamics is the relative impact of internal patch dynamics and coupling between patches. This problem can be addressed by analysing large spatiotemporal data sets, recording the local and global dynamics of metapopulations. In this paper, we analyse the dynamics of measles meta-populations in a large spatiotemporal case notification data set, collected during the pre-vaccination era in England and Wales. Specifically, we use generalized linear statistical models ...

  14. Dynamic characteristics of rocks and method of their determine

    Directory of Open Access Journals (Sweden)

    Radoslav Schügerl

    2009-01-01

    Full Text Available This paper presents selected problems of the research of the influence of technical vibrations on rocks. The vibrations are the products of the technological procedure, such as mining blasting, ramming of the piles, using of the drilling-equipment or vibration machines. The vibrations could be also evocated by road or train traffic. The most important dynamic characteristics of rocks are dynamic modulus of elasticity Edyn; dynamic modulus of deformation Edef, dyn; dynamic shear-modulus Gdyn; and especially dynamic Poisson´s ratio νdyn. These parameters were obtained by laboratory testing of conglomerate samples.

  15. Discharging dynamics in an electrolytic cell

    Science.gov (United States)

    Feicht, Sarah E.; Frankel, Alexandra E.; Khair, Aditya S.

    2016-07-01

    We analyze the dynamics of a discharging electrolytic cell comprised of a binary symmetric electrolyte between two planar, parallel blocking electrodes. When a voltage is initially applied, ions in the electrolyte migrate towards the electrodes, forming electrical double layers. After the system reaches steady state and the external current decays to zero, the applied voltage is switched off and the cell discharges, with the ions eventually returning to a uniform spatial concentration. At voltages on the order of the thermal voltage VT=kBT /q ≃25 mV, where kB is Boltzmann's constant, T is temperature, and q is the charge of a proton, experiments on surfactant-doped nonpolar fluids observe that the temporal evolution of the external current during charging and discharging is not symmetric [V. Novotny and M. A. Hopper, J. Electrochem. Soc. 126, 925 (1979), 10.1149/1.2129195; P. Kornilovitch and Y. Jeon, J. Appl. Phys. 109, 064509 (2011), 10.1063/1.3554445]. In fact, at sufficiently large voltages (several VT), the current during discharging is no longer monotonic: it displays a "reverse peak" before decaying in magnitude to zero. We analyze the dynamics of discharging by solving the Poisson-Nernst-Planck equations governing ion transport via asymptotic and numerical techniques in three regimes. First, in the "linear regime" when the applied voltage V is formally much less than VT, the charging and discharging currents are antisymmetric in time; however, the potential and charge density profiles during charging and discharging are asymmetric. The current evolution is on the R C timescale of the cell, λDL /D , where L is the width of the cell, D is the diffusivity of ions, and λD is the Debye length. Second, in the (experimentally relevant) thin-double-layer limit ɛ =λD/L ≪1 , there is a "weakly nonlinear" regime defined by VT≲V ≲VTln(1 /ɛ ) , where the bulk salt concentration is uniform; thus the R C timescale of the evolution of the current magnitude

  16. Sex determination in mammalian germ cells

    Directory of Open Access Journals (Sweden)

    Cassy M Spiller

    2015-06-01

    Full Text Available Germ cells are the precursors of the sperm and oocytes and hence are critical for survival of the species. In mammals, they are specified during fetal life, migrate to the developing gonads and then undergo a critical period during which they are instructed, by the soma, to adopt the appropriate sexual fate. In a fetal ovary, germ cells enter meiosis and commit to oogenesis, whereas in a fetal testis, they avoid entry into meiosis and instead undergo mitotic arrest and mature toward spermatogenesis. Here, we discuss what we know so far about the regulation of sex-specific differentiation of germ cells, considering extrinsic molecular cues produced by somatic cells, as well as critical intrinsic changes within the germ cells. This review focuses almost exclusively on our understanding of these events in the mouse model.

  17. Dynamic behaviour of human neuroepithelial cells in the developing forebrain

    Science.gov (United States)

    Subramanian, Lakshmi; Bershteyn, Marina; Paredes, Mercedes F.; Kriegstein, Arnold R.

    2017-01-01

    To understand how diverse progenitor cells contribute to human neocortex development, we examined forebrain progenitor behaviour using timelapse imaging. Here we find that cell cycle dynamics of human neuroepithelial (NE) cells differ from radial glial (RG) cells in both primary tissue and in stem cell-derived organoids. NE cells undergoing proliferative, symmetric divisions retract their basal processes, and both daughter cells regrow a new process following cytokinesis. The mitotic retraction of the basal process is recapitulated by NE cells in cerebral organoids generated from human-induced pluripotent stem cells. In contrast, RG cells undergoing vertical cleavage retain their basal fibres throughout mitosis, both in primary tissue and in older organoids. Our findings highlight developmentally regulated changes in mitotic behaviour that may relate to the role of RG cells to provide a stable scaffold for neuronal migration, and suggest that the transition in mitotic dynamics can be studied in organoid models. PMID:28139695

  18. Determining cell division symmetry through the dissection of dividing cells using single-cell expression analysis.

    Science.gov (United States)

    Jasnos, Lukasz; Sawado, Tomoyuki

    2014-03-01

    Symmetric cell divisions give rise to two sister cells that are identical to each other, whereas asymmetric divisions produce two sister cells with distinctive phenotypes. Although cell division symmetry is usually determined on the basis of a few markers or biological functions, the overall similarity between sister cells has not been thoroughly examined at a molecular level. Here we provide a protocol to separate sister embryonic stem cells (ESCs) and to conduct multiplexed gene expression analyses at the single-cell level by using 48 ESC genes. The procedure includes the dissection of dividing, paired sister cells by micromanipulation, followed by cell lysis, reverse transcription, gene-specific cDNA amplification and multiplexed quantitative PCR analyses. This protocol can be completed in 10 d, and it can be readily adapted to other cell types that are able to grow in suspension culture.

  19. Changes in cytoskeletal dynamics and nonlinear rheology with metastatic ability in cancer cell lines

    Science.gov (United States)

    Coughlin, Mark F.; Fredberg, Jeffrey J.

    2013-12-01

    Metastatic outcome is impacted by the biophysical state of the primary tumor cell. To determine if changes in cancer cell biophysical properties facilitate metastasis, we quantified cytoskeletal biophysics in well-characterized human skin, bladder, prostate and kidney cell line pairs that differ in metastatic ability. Using magnetic twisting cytometry with optical detection, cytoskeletal dynamics was observed through spontaneous motion of surface bound marker beads and nonlinear rheology was characterized through large amplitude forced oscillations of probe beads. Measurements of cytoskeletal dynamics and nonlinear rheology differed between strongly and weakly metastatic cells. However, no set of biophysical parameters changed systematically with metastatic ability across all cell lines. Compared to their weakly metastatic counterparts, the strongly metastatic kidney cancer cells exhibited both increased cytoskeletal dynamics and stiffness at large deformation which are thought to facilitate the process of vascular invasion.

  20. Sex determination in mammalian germ cells

    OpenAIRE

    Spiller, Cassy M; Josephine Bowles

    2015-01-01

    Germ cells are the precursors of the sperm and oocytes and hence are critical for survival of the species. In mammals, they are specified during fetal life, migrate to the developing gonads and then undergo a critical period during which they are instructed, by the soma, to adopt the appropriate sexual fate. In a fetal ovary, germ cells enter meiosis and commit to oogenesis, whereas in a fetal testis, they avoid entry into meiosis and instead undergo mitotic arrest and mature toward spermatog...

  1. Determinants of leader cells in collective cell migration.

    NARCIS (Netherlands)

    Khalil, A.; Friedl, P.H.A.

    2010-01-01

    Collective migration is a basic mechanism of cell translocation during morphogenesis, wound repair and cancer invasion. Collective movement requires cells to retain cell-cell contacts, exhibit group polarization with defined front-rear asymmetry, and consequently move as one multicellular unit. Depe

  2. Understanding dynamic changes in live cell adhesion with neutron reflectometry

    Science.gov (United States)

    Junghans, Ann

    Understanding the structure and functionality of biological systems on a nanometer-resolution and short temporal scales is important for solving complex biological problems, developing innovative treatment, and advancing the design of highly functionalized biomimetic materials. For example, adhesion of cells to an underlying substrate plays a crucial role in physiology and disease development, and has been investigated with great interest for several decades. In the talk, we would like to highlight recent advances in utilizing neutron scattering to study bio-related structures in dynamic conditions (e . g . under the shear flow) including in-situ investigations of the interfacial properties of living cells. The strength of neutron reflectometry is its non-pertubative nature, the ability to probe buried interfaces with nanometer resolution and its sensitivity to light elements like hydrogen and carbon. That allows us to study details of cell - substrate interfaces that are not accessible with any other standard techniques. We studied the adhesion of human brain tumor cells (U251) to quartz substrates and their responses to the external mechanical forces. Such cells are isolated within the central nervous system which makes them difficult to reach with conventional therapies and therefore making them highly invasive. Our results reveal changes in the thickness and composition of the adhesion layer (a layer between the cell lipid membrane and the quartz substrate), largely composed of hyaluronic acid and associated proteoglycans, when the cells were subjected to shear stress. Further studies will allow us to determine more conditions triggering changes in the composition of the bio-material in the adhesion layer. This, in turn, can help to identify changes that correlate with tumor invasiveness, which can have significant medical impact for the development of targeted anti-invasive therapies.

  3. Determination of Dynamics of Plant Plasma Membrane Proteins with Fluorescence Recovery and Raster Image Correlation Spectroscopy.

    Science.gov (United States)

    Laňková, Martina; Humpolíčková, Jana; Vosolsobě, Stanislav; Cit, Zdeněk; Lacek, Jozef; Čovan, Martin; Čovanová, Milada; Hof, Martin; Petrášek, Jan

    2016-04-01

    A number of fluorescence microscopy techniques are described to study dynamics of fluorescently labeled proteins, lipids, nucleic acids, and whole organelles. However, for studies of plant plasma membrane (PM) proteins, the number of these techniques is still limited because of the high complexity of processes that determine the dynamics of PM proteins and the existence of cell wall. Here, we report on the usage of raster image correlation spectroscopy (RICS) for studies of integral PM proteins in suspension-cultured tobacco cells and show its potential in comparison with the more widely used fluorescence recovery after photobleaching method. For RICS, a set of microscopy images is obtained by single-photon confocal laser scanning microscopy (CLSM). Fluorescence fluctuations are subsequently correlated between individual pixels and the information on protein mobility are extracted using a model that considers processes generating the fluctuations such as diffusion and chemical binding reactions. As we show here using an example of two integral PM transporters of the plant hormone auxin, RICS uncovered their distinct short-distance lateral mobility within the PM that is dependent on cytoskeleton and sterol composition of the PM. RICS, which is routinely accessible on modern CLSM instruments, thus represents a valuable approach for studies of dynamics of PM proteins in plants.

  4. Dynamic regulation of Schwann cell enhancers after peripheral nerve injury.

    Science.gov (United States)

    Hung, Holly A; Sun, Guannan; Keles, Sunduz; Svaren, John

    2015-03-13

    Myelination of the peripheral nervous system is required for axonal function and long term stability. After peripheral nerve injury, Schwann cells transition from axon myelination to a demyelinated state that supports neuronal survival and ultimately remyelination of axons. Reprogramming of gene expression patterns during development and injury responses is shaped by the actions of distal regulatory elements that integrate the actions of multiple transcription factors. We used ChIP-seq to measure changes in histone H3K27 acetylation, a mark of active enhancers, to identify enhancers in myelinating rat peripheral nerve and their dynamics after demyelinating nerve injury. Analysis of injury-induced enhancers identified enriched motifs for c-Jun, a transcription factor required for Schwann cells to support nerve regeneration. We identify a c-Jun-bound enhancer in the gene for Runx2, a transcription factor induced after nerve injury, and we show that Runx2 is required for activation of other induced genes. In contrast, enhancers that lose H3K27ac after nerve injury are enriched for binding sites of the Sox10 and early growth response 2 (Egr2/Krox20) transcription factors, which are critical determinants of Schwann cell differentiation. Egr2 expression is lost after nerve injury, and many Egr2-binding sites lose H3K27ac after nerve injury. However, the majority of Egr2-bound enhancers retain H3K27ac, indicating that other transcription factors maintain active enhancer status after nerve injury. The global epigenomic changes in H3K27ac deposition pinpoint dynamic changes in enhancers that mediate the effects of transcription factors that control Schwann cell myelination and peripheral nervous system responses to nerve injury.

  5. Nonequilibrium population dynamics of phenotype conversion of cancer cells.

    Directory of Open Access Journals (Sweden)

    Joseph Xu Zhou

    Full Text Available Tumorigenesis is a dynamic biological process that involves distinct cancer cell subpopulations proliferating at different rates and interconverting between them. In this paper we proposed a mathematical framework of population dynamics that considers both distinctive growth rates and intercellular transitions between cancer cell populations. Our mathematical framework showed that both growth and transition influence the ratio of cancer cell subpopulations but the latter is more significant. We derived the condition that different cancer cell types can maintain distinctive subpopulations and we also explain why there always exists a stable fixed ratio after cell sorting based on putative surface markers. The cell fraction ratio can be shifted by changing either the growth rates of the subpopulations (Darwinism selection or by environment-instructed transitions (Lamarckism induction. This insight can help us to understand the dynamics of the heterogeneity of cancer cells and lead us to new strategies to overcome cancer drug resistance.

  6. Cycle length restitution in sinoatrial node cells: a theory for understanding spontaneous action potential dynamics.

    Directory of Open Access Journals (Sweden)

    Patric Glynn

    Full Text Available Normal heart rhythm (sinus rhythm is governed by the sinoatrial node, a specialized and highly heterogeneous collection of spontaneously active myocytes in the right atrium. Sinoatrial node dysfunction, characterized by slow and/or asynchronous pacemaker activity and even failure, is associated with cardiovascular disease (e.g. heart failure, atrial fibrillation. While tremendous progress has been made in understanding the molecular and ionic basis of automaticity in sinoatrial node cells, the dynamics governing sinoatrial nodel cell synchrony and overall pacemaker function remain unclear. Here, a well-validated computational model of the mouse sinoatrial node cell is used to test the hypothesis that sinoatrial node cell dynamics reflect an inherent restitution property (cycle length restitution that may give rise to a wide range of behavior from regular periodicity to highly complex, irregular activation. Computer simulations are performed to determine the cycle length restitution curve in the computational model using a newly defined voltage pulse protocol. The ability of the restitution curve to predict sinoatrial node cell dynamics (e.g., the emergence of irregular spontaneous activity and susceptibility to termination is evaluated. Finally, ionic and tissue level factors (e.g. ion channel conductances, ion concentrations, cell-to-cell coupling that influence restitution and sinoatrial node cell dynamics are explored. Together, these findings suggest that cycle length restitution may be a useful tool for analyzing cell dynamics and dysfunction in the sinoatrial node.

  7. Cycle length restitution in sinoatrial node cells: a theory for understanding spontaneous action potential dynamics.

    Science.gov (United States)

    Glynn, Patric; Onal, Birce; Hund, Thomas J

    2014-01-01

    Normal heart rhythm (sinus rhythm) is governed by the sinoatrial node, a specialized and highly heterogeneous collection of spontaneously active myocytes in the right atrium. Sinoatrial node dysfunction, characterized by slow and/or asynchronous pacemaker activity and even failure, is associated with cardiovascular disease (e.g. heart failure, atrial fibrillation). While tremendous progress has been made in understanding the molecular and ionic basis of automaticity in sinoatrial node cells, the dynamics governing sinoatrial nodel cell synchrony and overall pacemaker function remain unclear. Here, a well-validated computational model of the mouse sinoatrial node cell is used to test the hypothesis that sinoatrial node cell dynamics reflect an inherent restitution property (cycle length restitution) that may give rise to a wide range of behavior from regular periodicity to highly complex, irregular activation. Computer simulations are performed to determine the cycle length restitution curve in the computational model using a newly defined voltage pulse protocol. The ability of the restitution curve to predict sinoatrial node cell dynamics (e.g., the emergence of irregular spontaneous activity) and susceptibility to termination is evaluated. Finally, ionic and tissue level factors (e.g. ion channel conductances, ion concentrations, cell-to-cell coupling) that influence restitution and sinoatrial node cell dynamics are explored. Together, these findings suggest that cycle length restitution may be a useful tool for analyzing cell dynamics and dysfunction in the sinoatrial node.

  8. Stochastic dynamics of actin filaments in guard cells regulating chloroplast localization during stomatal movement.

    Science.gov (United States)

    Wang, Xiu-Ling; Gao, Xin-Qi; Wang, Xue-Chen

    2011-08-01

    Actin filaments and chloroplasts in guard cells play roles in stomatal function. However, detailed actin dynamics vary, and the roles that they play in chloroplast localization during stomatal movement remain to be determined. We examined the dynamics of actin filaments and chloroplast localization in transgenic tobacco expressing green fluorescent protein (GFP)-mouse talin in guard cells by time-lapse imaging. Actin filaments showed sliding, bundling and branching dynamics in moving guard cells. During stomatal movement, long filaments can be severed into small fragments, which can form longer filaments by end-joining activities. With chloroplast movement, actin filaments near chloroplasts showed severing and elongation activity in guard cells during stomatal movement. Cytochalasin B treatment abolished elongation, bundling and branching activities of actin filaments in guard cells, and these changes of actin filaments, and as a result, more chloroplasts were localized at the centre of guard cells. However, chloroplast turning to avoid high light, and sliding of actin fragments near the chloroplast, was unaffected following cytochalasin B treatment in guard cells. We suggest that the sliding dynamics of actin may play roles in chloroplast turning in guard cells. Our results indicate that the stochastic dynamics of actin filaments in guard cells regulate chloroplast localization during stomatal movement.

  9. Desmosome dynamics in migrating epithelial cells requires the actin cytoskeleton

    Science.gov (United States)

    Roberts, Brett J.; Pashaj, Anjeza; Johnson, Keith R.; Wahl, James K.

    2011-01-01

    Re-modeling of epithelial tissues requires that the cells in the tissue rearrange their adhesive contacts in order to allow cells to migrate relative to neighboring cells. Desmosomes are prominent adhesive structures found in a variety of epithelial tissues that are believed to inhibit cell migration and invasion. Mechanisms regulating desmosome assembly and stability in migrating cells are largely unknown. In this study we established a cell culture model to examine the fate of desmosomal components during scratch wound migration. Desmosomes are rapidly assembled between epithelial cells at the lateral edges of migrating cells and structures are transported in a retrograde fashion while the structures become larger and mature. Desmosome assembly and dynamics in this system are dependent on the actin cytoskeleton prior to being associated with the keratin intermediate filament cytoskeleton. These studies extend our understanding of desmosome assembly and provide a system to examine desmosome assembly and dynamics during epithelial cell migration. PMID:21945137

  10. Role of finite populations in determining evolutionary dynamics

    Science.gov (United States)

    Ray, Tane S.; Payne, Karl A.; Moseley, L. Leo

    2008-02-01

    The connection between the finite size of an evolving population and its dynamical behavior is examined through analytical and computational studies of a simple model of evolution. The infinite population limit of the model is shown to be governed by a special case of the quasispecies equations. A flat fitness landscape yields identical results for the dynamics of infinite and finite populations. On the other hand, a monotonically increasing fitness landscape shows “epochs” in the dynamics of finite populations that become more pronounced as the rate of mutation decreases. The details of the dynamics are profoundly different for any two simulation runs in that events arising from the stochastic noise in the pseudorandom number sequence are amplified. As the population size is increased or, equivalently, the mutation rate is increased, these epochs become smaller but do not entirely disappear.

  11. Empirical determinants of measles metapopulation dynamics in England and Wales.

    Science.gov (United States)

    Finkenstädt, B; Grenfell, B

    1998-02-07

    A key issue in metapopulation dynamics is the relative impact of internal patch dynamics and coupling between patches. This problem can be addressed by analysing large spatiotemporal data sets, recording the local and global dynamics of metapopulations. In this paper, we analyse the dynamics of measles meta-populations in a large spatiotemporal case notification data set, collected during the pre-vaccination era in England and Wales. Specifically, we use generalized linear statistical models to quantify the relative importance of local influences (birth rate and population size) and regional coupling on local epidemic dynamics. Apart from the proportional effect of local population size on case totals, the models indicate patterns of local and regional dynamic influences which depend on the current state of epidemics. Birth rate and geographic coupling are not associated with the size of major epidemics. By contrast, minor epidemics--and especially the incidence of local extinction of infection--are influenced both by birth rate and geographical coupling. Birth rate at a lag of four years provides the best fit, reflecting the delayed recruitment of susceptibles to school cohorts. A hierarchical index of spatial coupling to large centres provides the best spatial model. The model also indicates that minor epidemics and extinction patterns are more strongly influenced by this regional effect than the local impact of birth rate.

  12. Emergent structures and dynamics of cell colonies by contact inhibition of locomotion.

    Science.gov (United States)

    Smeets, Bart; Alert, Ricard; Pešek, Jiří; Pagonabarraga, Ignacio; Ramon, Herman; Vincent, Romaric

    2016-12-20

    Cells in tissues can organize into a broad spectrum of structures according to their function. Drastic changes of organization, such as epithelial-mesenchymal transitions or the formation of spheroidal aggregates, are often associated either to tissue morphogenesis or to cancer progression. Here, we study the organization of cell colonies by means of simulations of self-propelled particles with generic cell-like interactions. The interplay between cell softness, cell-cell adhesion, and contact inhibition of locomotion (CIL) yields structures and collective dynamics observed in several existing tissue phenotypes. These include regular distributions of cells, dynamic cell clusters, gel-like networks, collectively migrating monolayers, and 3D aggregates. We give analytical predictions for transitions between noncohesive, cohesive, and 3D cell arrangements. We explicitly show how CIL yields an effective repulsion that promotes cell dispersal, thereby hindering the formation of cohesive tissues. Yet, in continuous monolayers, CIL leads to collective cell motion, ensures tensile intercellular stresses, and opposes cell extrusion. Thus, our work highlights the prominent role of CIL in determining the emergent structures and dynamics of cell colonies.

  13. Development and dynamics of cell polarity at a glance.

    Science.gov (United States)

    Campanale, Joseph P; Sun, Thomas Y; Montell, Denise J

    2017-04-01

    Cells exhibit morphological and molecular asymmetries that are broadly categorized as cell polarity. The cell polarity established in early embryos prefigures the macroscopic anatomical asymmetries characteristic of adult animals. For example, eggs and early embryos have polarized distributions of RNAs and proteins that generate global anterior/posterior and dorsal/ventral axes. The molecular programs that polarize embryos are subsequently reused in multiple contexts. Epithelial cells require apical/basal polarity to establish their barrier function. Migrating cells polarize in the direction of movement, creating distinct leading and trailing structures. Asymmetrically dividing stem cells partition different molecules between themselves and their daughter cells. Cell polarity can develop de novo, be maintained through rounds of cell division and be dynamically remodeled. In this Cell Science at a Glance review and poster, we describe molecular asymmetries that underlie cell polarity in several cellular contexts. We highlight multiple developmental systems that first establish cell/developmental polarity, and then maintain it. Our poster showcases repeated use of the Par, Scribble and Crumbs polarity complexes, which drive the development of cell polarity in many cell types and organisms. We then briefly discuss the diverse and dynamic changes in cell polarity that occur during cell migration, asymmetric cell division and in planar polarized tissues.

  14. Cell fate determination in the Caenorhabditis elegans epidermal lineages

    NARCIS (Netherlands)

    Soete, G.A.J.

    2007-01-01

    The starting point for this work was to use the hypodermal seam of C. elegans as a model system to study cell fate determination. Even though the seam is a relatively simple developmental system, the mechanisms that control cell fate determination in the seam lineages are connected in a highly compl

  15. Cell fate determination in the Caenorhabditis elegans epidermal lineages

    NARCIS (Netherlands)

    Soete, G.A.J.

    2007-01-01

    The starting point for this work was to use the hypodermal seam of C. elegans as a model system to study cell fate determination. Even though the seam is a relatively simple developmental system, the mechanisms that control cell fate determination in the seam lineages are connected in a highly compl

  16. Exploring Neural Cell Dynamics with Digital Holographic Microscopy

    KAUST Repository

    Marquet, Pierre

    2013-04-21

    In this talk, I will present how digital holographic microscopy, as a powerful quantitative phase technique, can non-invasively measure cell dynamics and especially resolve local neuronal network activity through simultaneous multiple site optical recording.

  17. The interaction of intrinsic dynamics and network topology in determining network burst synchrony.

    Science.gov (United States)

    Gaiteri, Chris; Rubin, Jonathan E

    2011-01-01

    The pre-Bötzinger complex (pre-BötC), within the mammalian respiratory brainstem, represents an ideal system for investigating the synchronization properties of complex neuronal circuits via the interaction of cell-type heterogeneity and network connectivity. In isolation, individual respiratory neurons from the pre-BötC may be tonically active, rhythmically bursting, or quiescent. Despite this intrinsic heterogeneity, coupled networks of pre-BötC neurons en bloc engage in synchronized bursting that can drive inspiratory motor neuron activation. The region's connection topology has been recently characterized and features dense clusters of cells with occasional connections between clusters. We investigate how the dynamics of individual neurons (quiescent/bursting/tonic) and the betweenness centrality of neurons' positions within the network connectivity graph interact to govern network burst synchrony, by simulating heterogeneous networks of computational model pre-BötC neurons. Furthermore, we compare the prevalence and synchrony of bursting across networks constructed with a variety of connection topologies, analyzing the same collection of heterogeneous neurons in small-world, scale-free, random, and regularly structured networks. We find that several measures of network burst synchronization are determined by interactions of network topology with the intrinsic dynamics of neurons at central network positions and by the strengths of synaptic connections between neurons. Surprisingly, despite the functional role of synchronized bursting within the pre-BötC, we find that synchronized network bursting is generally weakest when we use its specific connection topology, which leads to synchrony within clusters but poor coordination across clusters. Overall, our results highlight the relevance of interactions between topology and intrinsic dynamics in shaping the activity of networks and the concerted effects of connectivity patterns and dynamic heterogeneities.

  18. Extracellular Regulation of the Mitotic Spindle and Fate Determinants Driving Asymmetric Cell Division.

    Science.gov (United States)

    Smith, Prestina; Azzam, Mark; Hinck, Lindsay

    2017-01-01

    Stem cells use mode of cell division, symmetric (SCD) versus asymmetric (ACD), to balance expansion with self-renewal and the generation of daughter cells with different cell fates. Studies in model organisms have identified intrinsic mechanisms that govern this process, which involves partitioning molecular components between daughter cells, frequently through the regulation of the mitotic spindle. Research performed in vertebrate tissues is revealing both conservation of these intrinsic mechanisms and crucial roles for extrinsic cues in regulating the frequency of these divisions. Morphogens and positional cues, including planar cell polarity proteins and guidance molecules, regulate key signaling pathways required to organize cell/ECM contacts and spindle pole dynamics. Noncanonical WNT7A/VANGL2 signaling governs asymmetric cell division and the acquisition of cell fates through spindle pole orientation in satellite stem cells of regenerating muscle fibers. During cortical neurogenesis, the same pathway regulates glial cell fate determination by regulating spindle size, independent of its orientation. Sonic hedgehog (SHH) stimulates the symmetric expansion of cortical stem and cerebellar progenitor cells and contributes to cell fate acquisition in collaboration with Notch and Wnt signaling pathways. SLIT2 also contributes to stem cell homeostasis by restricting ACD frequency through the regulation of spindle orientation. The capacity to influence stem cells makes these secreted factors excellent targets for therapeutic strategies designed to enhance cell populations in degenerative disease or restrict cell proliferation in different types of cancers.

  19. Protein dynamics in individual human cells: experiment and theory.

    Directory of Open Access Journals (Sweden)

    Ariel Aharon Cohen

    Full Text Available A current challenge in biology is to understand the dynamics of protein circuits in living human cells. Can one define and test equations for the dynamics and variability of a protein over time? Here, we address this experimentally and theoretically, by means of accurate time-resolved measurements of endogenously tagged proteins in individual human cells. As a model system, we choose three stable proteins displaying cell-cycle-dependant dynamics. We find that protein accumulation with time per cell is quadratic for proteins with long mRNA life times and approximately linear for a protein with short mRNA lifetime. Both behaviors correspond to a classical model of transcription and translation. A stochastic model, in which genes slowly switch between ON and OFF states, captures measured cell-cell variability. The data suggests, in accordance with the model, that switching to the gene ON state is exponentially distributed and that the cell-cell distribution of protein levels can be approximated by a Gamma distribution throughout the cell cycle. These results suggest that relatively simple models may describe protein dynamics in individual human cells.

  20. Dynamic 3D cell culture via a chemoselective photoactuated ligand.

    Science.gov (United States)

    Westcott, Nathan P; Luo, Wei; Goldstein, Jeffrey; Yousaf, Muhammad N

    2014-09-01

    A new strategy to create a dynamic scaffold for three-dimensional (3D) cell experiments based on a photo-activated cell adhesive peptide ligand is described. After polymerization, the inert matrix becomes cell adhesive by chemoselective modification through the conjugation of oxyamine-terminated ligands. Furthermore, spatial and temporal control of cell culture within the 3D matrix was achieved by the use of a biospecific photoprotected peptide and visualized by confocal microscopy.

  1. Dynamics of cell degradation. [nickel cadmium batteries

    Science.gov (United States)

    Mcdermott, P. P.

    1978-01-01

    The use of chemical and physical data as a supplement to linear regression models in the prediction of cell failure is discussed. Principal factors to be considered are the positive thickness and weight, and the negative thickness. A model for cell degradation and failure in accelerated life test cells is presented and predictions based on a teardown analysis are included.

  2. New Dynamic Spin Rig Capabilities Used to Determine Rotating Blade Dynamics

    Science.gov (United States)

    Provenza, Andrew J.

    2004-01-01

    The Dynamic Spin Rig Facility at the NASA Glenn Research Center is used to determine the structural response of rotating engine components without the effects of aerodynamic loading. Recently, this rig's capabilities were enhanced through the replacement of grease-lubricated ball bearings with magnetic bearings. Magnetic bearings offer a number of advantages--the most important here being that they not only fully support the rotor system, but excite it as well. Three magnetic bearings support the rotor and provide five axes of controlled motion: an x- and y-axis translation at each of two radial bearings and a z-axis translation in the vertical or axial direction. Sinusoidal excitation (most commonly used) can be imparted on the rotor through the radial magnetic bearings in either a fixed or rotating frame of reference. This excitation is added directly to the magnetic bearing control output. Since the rotor is fully levitated, large translations and rotations of the rotor system can be achieved. Some of the capabilities of this excitation system were determined and reported. The accelerations obtained at the tip of a titanium flat plate test article versus the swept sine excitation sent to both radial bearings in phase and perpendicular to the plane containing the two blades are shown. Recent tests required the excitation of fundamental bending and torsional blade resonances at rotor speeds up to 10,000 rpm. Successful fixed synchronous rotation of the excitation signal provided the best detectable blade resonant vibrations at excitation frequencies up to 1100 Hz for the particular blades of interest. A noncontacting laser measurement system was used to collect blade-tip motions. From these data, the amplitude and frequency of the motion could be determined as well as the blade damping properties. Damping could be determined using two methods: (1) free decay and (2) curve fitting the vibration amplitude as a function of frequency in and around the resonance of

  3. Mitochondrial dynamics and morphology in beta-cells.

    Science.gov (United States)

    Stiles, Linsey; Shirihai, Orian S

    2012-12-01

    Mitochondrial dynamics contribute to the regulation of mitochondrial shape as well as various mitochondrial functions and quality control. This is of particular interest in the beta-cell because of the key role mitochondria play in the regulation of beta-cell insulin secretion function. Moreover, mitochondrial dysfunction has been suggested to contribute to the development of Type 2 Diabetes. Genetic tools that shift the balance of mitochondrial fusion and fission result in alterations to beta-cell function and viability. Additionally, conditions that induce beta-cell dysfunction, such as exposure to a high nutrient environment, disrupt mitochondrial morphology and dynamics. While it has been shown that mitochondria display a fragmented morphology in islets of diabetic patients and animal models, the mechanism behind this is currently unknown. Here, we review the current literature on mitochondrial morphology and dynamics in the beta-cell as well as some of the unanswered question in this field.

  4. Dynamics of epileptic phenomena determined from statistics of ictal transitions

    NARCIS (Netherlands)

    Suffczynski, P.; Silva, F.H.L. da; Parra, J.; Velis, D.N.; Bouwman, B.M.; Rijn, C.M. van; Hese, P. van; Boon, P.; Khosravani, H.; Derchansky, M.; Carlen, P.; Kalitzin, S.

    2006-01-01

    In this paper, we investigate the dynamical scenarios of transitions between normal and paroxysmal state in epilepsy. We assume that some epileptic neural network are bistable i.e., they feature two operational states, ictal and interictal that co-exist. The transitions between these two states may

  5. Brownian dynamics determine universality of charge transport in ionic liquids

    Energy Technology Data Exchange (ETDEWEB)

    Sangoro, Joshua R [ORNL; Iacob, Ciprian [University of Leipzig; Mierzwa, Michal [University of Silesia, Uniwersytecka, Katowice, Poland; Paluch, Marian [University of Silesia, Uniwersytecka, Katowice, Poland; Kremer, Friedrich [University of Leipzig

    2012-01-01

    Broadband dielectric spectroscopy is employed to investigate charge transport in a variety of glass-forming ionic liquids over wide frequency, temperature and pressure ranges. Using a combination of Einstein, Einstein-Smoluchowski, and Langevin relations, the observed universal scaling of charge transport in ionic liquids is traced back to the dominant role of Brownian dynamics.

  6. Determining Equilibrium Constants for Dimerization Reactions from Molecular Dynamics Simulations

    NARCIS (Netherlands)

    De Jong, Djurre H.; Schafer, Lars V.; De Vries, Alex H.; Marrink, Siewert J.; Berendsen, Herman J. C.; Grubmueller, Helmut

    2011-01-01

    With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices c

  7. Cell Polarity Determinants Establish Asymmetry in MEN Signaling

    OpenAIRE

    Monje-Casas, Fernando; Amon, Angelika

    2009-01-01

    Components of the Mitotic Exit Network (MEN), a signaling pathway that triggers exit from mitosis, localize to the spindle pole body (SPB) that migrates into the daughter cell during anaphase but are largely absent from the SPB that remains in the mother cell. Through the analysis of one of the determinants of this asymmetry, Bfa1, we find that the machinery responsible for establishing cell polarity and cytoplasmic microtubules collaborate to establish MEN asymmetry. In cells defective in th...

  8. Cell shape dynamics: from waves to migration.

    Directory of Open Access Journals (Sweden)

    Meghan K Driscoll

    Full Text Available We observe and quantify wave-like characteristics of amoeboid migration. Using the amoeba Dictyostelium discoideum, a model system for the study of chemotaxis, we demonstrate that cell shape changes in a wave-like manner. Cells have regions of high boundary curvature that propagate from the leading edge toward the back, usually along alternating sides of the cell. Curvature waves are easily seen in cells that do not adhere to a surface, such as cells that are electrostatically repelled from surfaces or cells that extend over the edge of micro-fabricated cliffs. Without surface contact, curvature waves travel from the leading edge to the back of a cell at -35 µm/min. Non-adherent myosin II null cells do not exhibit these curvature waves. At the leading edge of adherent cells, curvature waves are associated with protrusive activity. Like regions of high curvature, protrusive activity travels along the boundary in a wave-like manner. Upon contact with a surface, the protrusions stop moving relative to the surface, and the boundary shape thus reflects the history of protrusive motion. The wave-like character of protrusions provides a plausible mechanism for the zig-zagging of pseudopods and for the ability of cells both to swim in viscous fluids and to navigate complex three dimensional topography.

  9. Local Nucleosome Dynamics Facilitate Chromatin Accessibility in Living Mammalian Cells

    Directory of Open Access Journals (Sweden)

    Saera Hihara

    2012-12-01

    Full Text Available Genome information, which is three-dimensionally organized within cells as chromatin, is searched and read by various proteins for diverse cell functions. Although how the protein factors find their targets remains unclear, the dynamic and flexible nature of chromatin is likely crucial. Using a combined approach of fluorescence correlation spectroscopy, single-nucleosome imaging, and Monte Carlo computer simulations, we demonstrate local chromatin dynamics in living mammalian cells. We show that similar to interphase chromatin, dense mitotic chromosomes also have considerable chromatin accessibility. For both interphase and mitotic chromatin, we observed local fluctuation of individual nucleosomes (∼50 nm movement/30 ms, which is caused by confined Brownian motion. Inhibition of these local dynamics by crosslinking impaired accessibility in the dense chromatin regions. Our findings show that local nucleosome dynamics drive chromatin accessibility. We propose that this local nucleosome fluctuation is the basis for scanning genome information.

  10. Why Do CD8 + T Cells Become Indifferent To Tumors: A Dynamic Modeling Approach

    Directory of Open Access Journals (Sweden)

    Colin eCampbell

    2011-07-01

    Full Text Available CD8+ T cells have the potential to influence the outcome of cancer pathogenesis, including complete tumor eradication or selection of malignant tumor escape variants. The Simian virus 40 large T-antigen oncoprotein promotes tumor formation in T-antigen transgenic mice and also provides multiple target determinants (sites for responding CD8+ T cells in C57BL/6 (H-2b mice. To understand the in vivo quantitative dynamics of CD8+ T cells after encountering T-antigen, we constructed a dynamic model from in vivo-generated data to simulate the interactions between T-antigen expressing cells and CD8+ T cells in distinct scenarios including immunization of wild type C57BL/6 mice and of T-antigen transgenic mice that develop various tumors. In these scenarios the model successfully reproduces the dynamics of both the T-antigen-expressing cells and antigen specific CD8+ T cell responses. The model predicts that the tolerance of the site-specific T cells is dependent on their apoptosis rates and that the net growth of CD8+ T cells is altered in transgenic mice. We experimentally validate both predictions. Our results indicate that site-specific CD8+ T cells have tissue-specific apoptosis rates affecting their tolerance to the tumor antigen. Moreover, the model highlights differences in apoptosis rates that contribute to compromised CD8+ T cell responses and tumor progression, knowledge of which is essential for development of cancer immunotherapy.

  11. Fluids as Dynamic Templates for Cytoskeletal Proteins in Plant Cells

    CERN Document Server

    Lofthouse, J T

    2008-01-01

    The Dynamic Template model of biological cell membranes and the cytoplasm as spatially organised fluid layers is extended to plant cells, and is shown to offer a feasible shear driven mechanism for the co-alignment of internal and external fibres observed during growth and tropic responses

  12. Dynamic determinants of the uncontrolled manifold during human quiet stance

    Directory of Open Access Journals (Sweden)

    Yasuyuki Suzuki

    2016-12-01

    Full Text Available Human postural sway during stance arises from coordinated multi-joint movements. Thus, a sway trajectory represented by a time-varying postural vector in the multiple-joint-angle-space tends to be constrained to a low-dimensional subspace. It has been proposed that the subspace corresponds to a manifold defined by a kinematic constraint, such that the position of the center of mass (CoM of the whole body is constant in time, referred to as the kinematic uncontrolled manifold (kinematic-UCM. A control strategy related to this hypothesis (CoM-control-strategy claims that the central nervous system (CNS aims to keep the posture close to the kinematic-UCM using a continuous feedback controller, leading to sway patterns that mostly occur within the kinematic-UCM, where no corrective control is exerted. An alternative strategy proposed by the authors (intermittent control-strategy claims that the CNS stabilizes posture by intermittently suspending the active feedback controller, in such a way to allow the CNS to exploit a stable manifold of the saddle-type upright equilibrium in the state-space of the system, referred to as the dynamic-UCM, when the state point is on or near the manifold. Although the mathematical definitions of the kinematic- and dynamic-UCM are completely different, both UCMs play similar roles in the stabilization of multi-joint upright posture. The purpose of this study was to compare the dynamic performance of the two control strategies. In particular, we considered a double-inverted-pendulum-model of postural control, and analyzed the two UCMs defined above. We first showed that the geometric configurations of the two UCMs are almost identical. We then investigated whether the UCM-component of experimental sway could be considered as passive dynamics with no active control, and showed that such UCM-component mainly consists of high frequency oscillations above 1 Hz, corresponding to anti-phase coordination between the ankle and

  13. Macromolecular Dynamics in Red Blood Cells Investigated Using Neutron Spectroscopy

    CERN Document Server

    Stadler, Andreas Maximilian; Demmel, Franz; Artmann, Gerhard; 10.1098/rsif.2010.0306

    2011-01-01

    We present neutron scattering measurements on the dynamics of hemoglobin (Hb) in human red blood cells in vivo. Global and internal Hb dynamics were measured in the ps to ns time- and {\\AA} length-scale using quasielastic neutron backscattering spectroscopy. We observed the cross-over from global Hb short-time to long-time self-diffusion. Both short- and long-time diffusion coefficients agree quantitatively with predicted values from hydrodynamic theory of non-charged hard-sphere suspensions when a bound water fraction of around 0.23g H2O/ g Hb is taken into account. The higher amount of water in the cells facilitates internal protein fluctuations in the ps time-scale when compared to fully hydrated Hb powder. Slower internal dynamics of Hb in red blood cells in the ns time-range were found to be rather similar to results obtained with fully hydrated protein powders, solutions and E. coli cells.

  14. Relation Between the Cell Volume and the Cell Cycle Dynamics in Mammalian cell

    Science.gov (United States)

    Magno, A. C. G.; Oliveira, I. L.; Hauck, J. V. S.

    2016-08-01

    The main goal of this work is to add and analyze an equation that represents the volume in a dynamical model of the mammalian cell cycle proposed by Gérard and Goldbeter (2011) [1]. The cell division occurs when the cyclinB/Cdkl complex is totally degraded (Tyson and Novak, 2011)[2] and it reaches a minimum value. At this point, the cell is divided into two newborn daughter cells and each one will contain the half of the cytoplasmic content of the mother cell. The equations of our base model are only valid if the cell volume, where the reactions occur, is constant. Whether the cell volume is not constant, that is, the rate of change of its volume with respect to time is explicitly taken into account in the mathematical model, then the equations of the original model are no longer valid. Therefore, every equations were modified from the mass conservation principle for considering a volume that changes with time. Through this approach, the cell volume affects all model variables. Two different dynamic simulation methods were accomplished: deterministic and stochastic. In the stochastic simulation, the volume affects every model's parameters which have molar unit, whereas in the deterministic one, it is incorporated into the differential equations. In deterministic simulation, the biochemical species may be in concentration units, while in stochastic simulation such species must be converted to number of molecules which are directly proportional to the cell volume. In an effort to understand the influence of the new equation a stability analysis was performed. This elucidates how the growth factor impacts the stability of the model's limit cycles. In conclusion, a more precise model, in comparison to the base model, was created for the cell cycle as it now takes into consideration the cell volume variation

  15. ζ-potential determination using a ZetaMeter-Dynamic Speckle assembly

    Science.gov (United States)

    González-Peña, Rolando J.; Sánchez-Muñoz, Orlando L.; Martínez-Celorio, René A.; Cibrián, Rosa M.; Salvador-Palmer, Rosario; Salgado, Jesús

    2012-10-01

    Electrophoretic mobility and ζ-potential are important physical parameters for the characterization of micro- and nanosystems. In this communication we describe a new method for determining the ζ-potential through the assembly of two well known techniques: free electrophoresis and Dynamic Speckle. When coherent light passes through a fluid having scattering centres, the far field interference originates a speckled image. If the scattering centres are contained within the cylindrical electrophoresis cell of a ZetaMeter and are forced to move in an orderly way under the action of an external electric field, the time variation of the light intensity in the far field speckle images follows a temporal autocorrelation function g(τ). The corresponding correlation time can then be obtained and related with the velocity, from which the electrophoretic mobility and the ζ-potential of the scattering centres can be determined. We have applied this method to microparticles, like natural air-floated silica and two classes of bioceramics, hydroxyapatite and biphasic calcium phosphate. For comparison, we analysed the same samples in parallel using a commercial Zetasizer Nano from Malvern Instruments. The values of ζ-potential determined using the two techniques were the same within ~3% error. These results validate our new method as a useful and efficient alternative for ζ-potential determination of particles, at least within the micrometer scale.

  16. Spatial stochastic dynamics enable robust cell polarization.

    Directory of Open Access Journals (Sweden)

    Michael J Lawson

    Full Text Available Although cell polarity is an essential feature of living cells, it is far from being well-understood. Using a combination of computational modeling and biological experiments we closely examine an important prototype of cell polarity: the pheromone-induced formation of the yeast polarisome. Focusing on the role of noise and spatial heterogeneity, we develop and investigate two mechanistic spatial models of polarisome formation, one deterministic and the other stochastic, and compare the contrasting predictions of these two models against experimental phenotypes of wild-type and mutant cells. We find that the stochastic model can more robustly reproduce two fundamental characteristics observed in wild-type cells: a highly polarized phenotype via a mechanism that we refer to as spatial stochastic amplification, and the ability of the polarisome to track a moving pheromone input. Moreover, we find that only the stochastic model can simultaneously reproduce these characteristics of the wild-type phenotype and the multi-polarisome phenotype of a deletion mutant of the scaffolding protein Spa2. Significantly, our analysis also demonstrates that higher levels of stochastic noise results in increased robustness of polarization to parameter variation. Furthermore, our work suggests a novel role for a polarisome protein in the stabilization of actin cables. These findings elucidate the intricate role of spatial stochastic effects in cell polarity, giving support to a cellular model where noise and spatial heterogeneity combine to achieve robust biological function.

  17. The F-Landscape: Dynamically Determining The Multiverse

    Science.gov (United States)

    Li, Tianjun; Maxin, James A.; Nanopoulos, Dimitri V.; Walker, Joel W.

    2012-09-01

    We evolve our Multiverse Blueprints to characterize our local neighborhood of the String Landscape and the Multiverse of plausible string, M- and F-theory vacua. Building upon the tripodal foundations of (i) the Flipped SU(5) Grand Unified Theory (GUT), (ii) extra TeV-Scale vector-like multiplets derived out of F-theory, and (iii) the dynamics of No-Scale supergravity, together dubbed No-Scale F-SU(5), we demonstrate the existence of a continuous family of solutions which might adeptly describe the dynamics of distinctive universes. This Multiverse landscape of F-SU(5) solutions, which we shall refer to as the F-Landscape, accommodates a subset of universes compatible with the presently known experimental uncertainties of our own universe. We show that by secondarily minimizing the minimum of the scalar Higgs potential of each solution within the F-Landscape, a continuous hypervolume of distinct minimum minimorum can be engineered which comprise a regional dominion of universes, with our own universe cast as the bellwether. We conjecture that an experimental signal at the LHC of the No-Scale F-SU(5) framework's applicability to our own universe might sensibly be extrapolated as corroborating evidence for the role of string, M- and F-theory as a master theory of the Multiverse, with No-Scale supergravity as a crucial and pervasive reinforcing structure.

  18. The F-Landscape: Dynamically Determining the Multiverse

    CERN Document Server

    Li, Tianjun; Nanopoulos, Dimitri V; Walker, Joel W

    2011-01-01

    We evolve our Multiverse Blueprints to characterize our local neighborhood of the String Landscape and the Multiverse of plausible string, M- and F-theory vacua. Building upon the tripodal foundations of i) the Flipped SU(5) Grand Unified Theory (GUT), ii) extra TeV-Scale vector-like multiplets derived out of F-theory, and iii) the dynamics of No-Scale Supergravity, together dubbed No-Scale F-SU(5), we demonstrate the existence of a continuous family of solutions which might adeptly describe the dynamics of distinctive universes. This Multiverse landscape of F-SU(5) solutions, which we shall refer to as the F-Landscape, accommodates a subset of universes compatible with the presently known experimental uncertainties of our own universe. We show that by secondarily minimizing the minimum of the scalar Higgs potential of each solution within the F-Landscape, a continuous hypervolume of distinct minimum minimorum can be engineered which comprise a regional dominion of universes, with our own universe cast as the...

  19. Cell differentiation and development in Arabidopsis are associated with changes in histone dynamics at the single-cell level.

    Science.gov (United States)

    Rosa, Stefanie; Ntoukakis, Vardis; Ohmido, Nobuko; Pendle, Ali; Abranches, Rita; Shaw, Peter

    2014-12-01

    The mechanism whereby the same genome can give rise to different cell types with different gene expression profiles is a fundamental problem in biology. Chromatin organization and dynamics have been shown to vary with altered gene expression in different cultured animal cell types, but there is little evidence yet from whole organisms linking chromatin dynamics with development. Here, we used both fluorescence recovery after photobleaching and two-photon photoactivation to show that in stem cells from Arabidopsis thaliana roots the mobility of the core histone H2B, as judged by exchange dynamics, is lower than in the surrounding cells of the meristem. However, as cells progress from meristematic to fully differentiated, core histones again become less mobile and more strongly bound to chromatin. We show that these transitions are largely mediated by changes in histone acetylation. We further show that altering histone acetylation levels, either in a mutant or by drug treatment, alters both the histone mobility and markers of development and differentiation. We propose that plant stem cells have relatively inactive chromatin, but they keep the potential to divide and differentiate into more dynamic states, and that these states are at least in part determined by histone acetylation levels. © 2014 American Society of Plant Biologists. All rights reserved.

  20. Entrainment of cell division in phytoplankton with dynamic energy budgets

    Science.gov (United States)

    Muller, Erik B.; Ananthasubramaniam, Bharath; Klanjšček, Tin; Nisbet, Roger M.

    2011-11-01

    We explore the entrainment behavior of cell division in phytoplankton in the context of Dynamic Energy Budget (DEB) theory. In particular, we explore the range of DEB and environmental parameter values within which a cell divides at regular intervals in a periodic light environment with abundant nutrients and investigate the impact of parameter values on the phase of cell division. We consider three types of cells that differ in the evolution of surface area to volume ratio during the cell cycle: cells with a constant shape (isomorphs), cells with a constant surface area (V0-morphs) and cells with a constant surface area to volume ratio (V1-morphs), the latter being the default choice in studies on the population dynamics of unicellular organisms because of its desirable mathematical implications. Only in isomorphs and V0-morphs, however, cell division can be entrained to a periodic light. Regular cell division in V1 is purely coincidental, as it depends on exact choices for parameter values. We attribute this to the fact that V1-morphs lack the negative feedback of size on the dynamics of reserves in V0-morphs and isomorphs. Because entrained isomorphs and V0-morphs divide during the dark hours in our simulations, these two shapes can represent the division behavior of phytoplankton species that complete the cell cycle during the night, such as dinoflagellates and coccolithophores. A description of the division behavior of species completing the cell cycle during the day, such as silicon dependent diatoms and cyanobacteria, requires a more complex model than used in this paper. Furthermore, we explore the robustness of our findings by randomizing model parameters and introducing unevenness in biomass separation between daughter cells during cell division. We conclude that especially the entrainment in V0-morphs is relatively insensitive to perturbations.

  1. Determination of Scaling Parameter and Dynamical Resonances in Complex-Rotated Hamiltonian Ⅱ: Numerical Analysis

    Institute of Scientific and Technical Information of China (English)

    LIU Zong-Liang; ZHAO Fang; LI Shao-Hua; ZHAO Mei-Shan; CHEN Chang-Yong

    2008-01-01

    This paper is concerned with the determination of a unique scaling parameter in complex scaling analysis and with accurate calculation of dynamics resonances. In the preceding paper we have presented a theoretical analysis and provided a formalism for dynamical resonance calculations. In this paper we present accurate numerical results for two non-trivial dynamical processes, namely, models of diatomie molecular predissoeiation and of barrier potential scattering for resonances. The results presented in this paper confirm our theoretical analysis, remove a theoretical ambiguity on determination of the complex scaling parameter, and provide an improved understanding for dynamical resonance calculations in rigged Hilbert space.

  2. Cell fate determination in zebrafish embryonic and adult muscle development

    NARCIS (Netherlands)

    Tee, J.M.

    2010-01-01

    We are interested in how the genetic basis of muscle precursor cells determines the outcome of the muscle cell fate, and thus leading to disruption in muscle formation and maintenance. We utilized the zebrafish carrying mutations in both Axin1 and Apc1, resulting in overactivation of the Wnt/beta-ca

  3. Antigen Processing by Autoreactive B Cells Promotes Determinant Spreading

    Institute of Scientific and Technical Information of China (English)

    Yang D.Dai; George Carayanniotis; Eli Sercarz

    2005-01-01

    Acute primary immune responses tend to focus on few immunodominant determinants using a very limited number of T cell clones for expansion, whereas chronic inflammatory responses generally recruit a large number of different T cell clones to attack a broader range of determinants of the invading pathogens or the inflamed tissues.In T cell-mediated organ-specific autoimmune disease, a transition from the acute to the chronic phase contributes to pathogenesis, and the broadening process is called determinant spreading. The cellular components catalyzing the spreading reaction are not identified. It has been suggested that autoreactive B cells may play a central role in diversifying autoreactive T cell responses, possibly through affecting antigen processing and presentation. The clonal identity and diversity of the B cells and antibodies seem critical in regulating T cell activity and subsequent tissue damage or repair. Here, we use two autoimmune animal models, experimental autoimmune thyroiditis (EAT)and type 1 diabetes (T1D), to discuss how autoreactive B cells or antibodies alter the processing and presentation of autoantigens to regulate specific T cell response.

  4. Nanofiber density determines endothelial cell behavior on hydrogel matrix

    Energy Technology Data Exchange (ETDEWEB)

    Berti, Fernanda V., E-mail: fernanda@intelab.ufsc.br [Department of Chemical and Food Engineering, Federal University of Santa Catarina, 88040-900 Florianópolis, SC (Brazil); Rambo, Carlos R. [Department of Electrical Engineering, Federal University of Santa Catarina, 88040-900 Florianópolis, SC (Brazil); Dias, Paulo F. [Department of Cell Biology, Embryology and Genetics, Federal University of Santa Catarina, 88040-900 Florianópolis, SC (Brazil); Porto, Luismar M. [Department of Chemical and Food Engineering, Federal University of Santa Catarina, 88040-900 Florianópolis, SC (Brazil)

    2013-12-01

    When cultured under static conditions, bacterial cellulose pellicles, by the nature of the polymer synthesis that involves molecular oxygen, are characterized by two distinct surface sides. The upper surface is denser in fibers (entangled) than the lower surface that shows greater surface porosity. Human umbilical vein endothelial cells (HUVECs) were used to exploit how the microarchitecture (i.e., surface porosity, fiber network structure, surface topology, and fiber density) of bacterial cellulose pellicle surfaces influence cell–biomaterial interaction and therefore cell behavior. Adhesion, cell ingrowth, proliferation, viability and cell death mechanisms were evaluated on the two pellicle surface sides. Cell behavior, including secondary necrosis, is influenced only by the microarchitecture of the surface, since the biomaterial is extremely pure (constituted of cellulose and water only). Cell–cellulose fiber interaction is the determinant signal in the cell–biomaterial responses, isolated from other frequently present interferences such as protein and other chemical traces usually present in cell culture matrices. Our results suggest that microarchitecture of hydrogel materials might determine the performance of biomedical products, such as bacterial cellulose tissue engineering constructs (BCTECs). - Highlights: • Topography of BC pellicle is relevant to determine endothelial cells' fate. • Cell–biomaterial response is affected by the topography of BC-pellicle surface. • Endothelial cells exhibit different behavior depending on the BC topography. • Apoptosis and necrosis of endothelial cells were affected by the BC topography.

  5. A human cell model for dynamic testing of MR contrast agents.

    Science.gov (United States)

    Aulanier, Anne-Lise; Doiron, Amber L; Shepherd, Robert D; Rinker, Kristina D; Frayne, Richard; Andersen, Linda B

    2011-02-01

    To determine the initial feasibility of using magnetic resonance (MR) imaging to detect early atherosclerosis, we investigated inflammatory cells labeled with a positive contrast agent in an endothelial cell-based testing system. The human monocytic cell line THP-1 was labeled by overnight incubation with a gadolinium colloid (Gado CELLTrack) prior to determination of the in vitro release profile from T1-weighted MR images. Next, MR signals arising from both a synthetic model of THP-1/human umbilical vein endothelial cell (HUVEC) accumulation and the dynamic adhesion of THP-1 cells to activated HUVECs under flow were obtained. THP-1 cells were found to be successfully--but not optimally--labeled with gadolinium colloid, and MR images demonstrated increased signal from labeled cells in both the synthetic and dynamic THP-1/HUVEC models. The observed THP-1 contrast release profile was rapid, suggesting the need for an agent that is optimized for retention in the target cells for use in further studies. Detection of labeled THP-1 cells was accomplished with no signal enhancement from unlabeled cells. These achievements demonstrate the feasibility of targeting early atherosclerosis with MR imaging, and suggest that using an in vitro system like the one described provides a rapid, efficient, and cost-effective way to support the development and evaluation of novel MR contrast agents.

  6. Accurate determination of heteroclinic orbits in chaotic dynamical systems

    Science.gov (United States)

    Li, Jizhou; Tomsovic, Steven

    2017-03-01

    Accurate calculation of heteroclinic and homoclinic orbits can be of significant importance in some classes of dynamical system problems. Yet for very strongly chaotic systems initial deviations from a true orbit will be magnified by a large exponential rate making direct computational methods fail quickly. In this paper, a method is developed that avoids direct calculation of the orbit by making use of the well-known stability property of the invariant unstable and stable manifolds. Under an area-preserving map, this property assures that any initial deviation from the stable (unstable) manifold collapses onto them under inverse (forward) iterations of the map. Using a set of judiciously chosen auxiliary points on the manifolds, long orbit segments can be calculated using the stable and unstable manifold intersections of the heteroclinic (homoclinic) tangle. Detailed calculations using the example of the kicked rotor are provided along with verification of the relation between action differences and certain areas bounded by the manifolds.

  7. Inverse problem of HIV cell dynamics using Genetic Algorithms

    Science.gov (United States)

    González, J. A.; Guzmán, F. S.

    2017-01-01

    In order to describe the cell dynamics of T-cells in a patient infected with HIV, we use a flavour of Perelson's model. This is a non-linear system of Ordinary Differential Equations that describes the evolution of healthy, latently infected, infected T-cell concentrations and the free viral cells. Different parameters in the equations give different dynamics. Considering the concentration of these types of cells is known for a particular patient, the inverse problem consists in estimating the parameters in the model. We solve this inverse problem using a Genetic Algorithm (GA) that minimizes the error between the solutions of the model and the data from the patient. These errors depend on the parameters of the GA, like mutation rate and population, although a detailed analysis of this dependence will be described elsewhere.

  8. Formative cell divisions: principal determinants of plant morphogenesis.

    Science.gov (United States)

    Smolarkiewicz, Michalina; Dhonukshe, Pankaj

    2013-03-01

    Formative cell divisions utilizing precise rotations of cell division planes generate and spatially place asymmetric daughters to produce different cell layers. Therefore, by shaping tissues and organs, formative cell divisions dictate multicellular morphogenesis. In animal formative cell divisions, the orientation of the mitotic spindle and cell division planes relies on intrinsic and extrinsic cortical polarity cues. Plants lack known key players from animals, and cell division planes are determined prior to the mitotic spindle stage. Therefore, it appears that plants have evolved specialized mechanisms to execute formative cell divisions. Despite their profound influence on plant architecture, molecular players and cellular mechanisms regulating formative divisions in plants are not well understood. This is because formative cell divisions in plants have been difficult to track owing to their submerged positions and imprecise timings of occurrence. However, by identifying a spatiotemporally inducible cell division plane switch system applicable for advanced microscopy techniques, recent studies have begun to uncover molecular modules and mechanisms for formative cell divisions. The identified molecular modules comprise developmentally triggered transcriptional cascades feeding onto microtubule regulators that now allow dissection of the hierarchy of the events at better spatiotemporal resolutions. Here, we survey the current advances in understanding of formative cell divisions in plants in the context of embryogenesis, stem cell functionality and post-embryonic organ formation.

  9. Bone Cells Dynamics during Peri-Implantitis: a Theoretical Analysis

    Directory of Open Access Journals (Sweden)

    Maria Helena Fernandes

    2016-09-01

    Full Text Available Objectives: The present manuscript aims a detailed characterization of the bone cells dynamics during physiological bone remodelling and, subsequently, to address the cellular and molecular mechanisms that play a fundamental role in the immune-inflammatory-induced uncoupled bone remodelling observed in peri-implantitis. Results: An intimate relationship between the immune system and bone is acknowledged to be determinant for bone tissue remodelling and integrity. Due to the close interaction of immune and bone cells, the two systems share a number of surface receptors, cytokines, signalling pathways and transcription factors that are involved in mutual regulatory mechanisms. This physiological equilibrium is disturbed in pathological conditions, as verified in peri-implantitis establishment and development. Activation of the innate and adaptive immune response, challenged by the local bacterial infection, induces the synthesis of high levels of a variety of pro- and anti-inflammatory cytokines that disturb the normal functioning of the bone cells, by uncoupling bone resorption and formation, ending up with a net alveolar bone loss and subsequent implant failure. Most data points to an immune-inflammatory induced osteoclast differentiation and function, as the major underlying mechanism to the uncoupled bone resorption to bone formation. Further, the disturbed functioning of osteoblasts, reflected by the possible expression of a fibro-osteoblastic phenotype, may also play a role. Conclusions: Alveolar bone loss is a hallmark of peri-implantitis. A great deal of data is still needed on the cellular and humoral crosstalk in the context of an integrated view of the osteoimmunologic interplay occurring in the peri-implantitis environment subjacent to the bone loss outcome.

  10. Blood cell telomere length is a dynamic feature.

    Directory of Open Access Journals (Sweden)

    Ulrika Svenson

    Full Text Available There is a considerable heterogeneity in blood cell telomere length (TL for individuals of similar age and recent studies have revealed that TL changes by time are dependent on TL at baseline. TL is partly inherited, but results from several studies indicate that e.g. life style and/or environmental factors can affect TL during life. Collectively, these studies imply that blood cell TL might fluctuate during a life time and that the actual TL at a defined time point is the result of potential regulatory mechanism(s and environmental factors. We analyzed relative TL (RTL in subsequent blood samples taken six months apart from 50 individuals and found significant associations between RTL changes and RTL at baseline. Individual RTL changes per month were more pronounced than the changes recorded in a previously studied population analyzed after 10 years' follow up. The data argues for an oscillating TL pattern which levels out at longer follow up times. In a separate group of five blood donors, a marked telomere loss was demonstrated within a six month period for one donor where after TL was stabilized. PCR determined RTL changes were verified by Southern blotting and STELA (single telomere elongation length analysis. The STELA demonstrated that for the donor with a marked telomere loss, the heterogeneity of the telomere distribution decreased considerably, with a noteworthy loss of the largest telomeres. In summary, the collected data support the concept that individual blood cell telomere length is a dynamic feature and this will be important to recognize in future studies of human telomere biology.

  11. QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells.

    Science.gov (United States)

    Fisher, Ciarán P; Plant, Nicholas J; Moore, J Bernadette; Kierzek, Andrzej M

    2013-12-15

    Dynamic simulation of genome-scale molecular interaction networks will enable the mechanistic prediction of genotype-phenotype relationships. Despite advances in quantitative biology, full parameterization of whole-cell models is not yet possible. Simulation methods capable of using available qualitative data are required to develop dynamic whole-cell models through an iterative process of modelling and experimental validation. We formulate quasi-steady state Petri nets (QSSPN), a novel method integrating Petri nets and constraint-based analysis to predict the feasibility of qualitative dynamic behaviours in qualitative models of gene regulation, signalling and whole-cell metabolism. We present the first dynamic simulations including regulatory mechanisms and a genome-scale metabolic network in human cell, using bile acid homeostasis in human hepatocytes as a case study. QSSPN simulations reproduce experimentally determined qualitative dynamic behaviours and permit mechanistic analysis of genotype-phenotype relationships. The model and simulation software implemented in C++ are available in supplementary material and at http://sysbio3.fhms.surrey.ac.uk/qsspn/.

  12. Phosphorylation site dynamics of early T-cell receptor signaling

    DEFF Research Database (Denmark)

    Chylek, Lily A; Akimov, Vyacheslav; Dengjel, Jörn

    2014-01-01

    a systems-level understanding of how these components cooperate to control signaling dynamics, especially during the crucial first seconds of stimulation. Here, we used quantitative proteomics to characterize reshaping of the T-cell phosphoproteome in response to TCR/CD28 co-stimulation, and found...... that diverse dynamic patterns emerge within seconds. We detected phosphorylation dynamics as early as 5 s and observed widespread regulation of key TCR signaling proteins by 30 s. Development of a computational model pointed to the presence of novel regulatory mechanisms controlling phosphorylation of sites...

  13. Charge carrier dynamics in thin film solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Strothkaemper, Christian

    2013-06-24

    This work investigates the charge carrier dynamics in three different technological approaches within the class of thin film solar cells: radial heterojunctions, the dye solar cell, and microcrystalline CuInSe{sub 2}, focusing on charge transport and separation at the electrode, and the relaxation of photogenerated charge carriers due to recombination and energy dissipation to the phonon system. This work relies mostly on optical-pump terahertz-probe (OPTP) spectroscopy, followed by transient absorption (TA) and two-photon photoemission (2PPE). The charge separation in ZnO-electrode/In{sub 2}S{sub 3}-absorber core/shell nanorods, which represent a model system of a radial heterojunction, is analyzed by OPTP. It is concluded, that the dynamics in the absorber are determined by multiple trapping, which leads to a dispersive charge transport to the electrode that lasts over hundreds of picoseconds. The high trap density on the order of 10{sup 19}/cm{sup 3} is detrimental for the injection yield, which exhibits a decrease with increasing shell thickness. The heterogeneous electron transfer from a series of model dyes into ZnO proceeds on a time-scale of 200 fs. However, the photoconductivity builds up just on a 2-10 ps timescale, and 2PPE reveals that injected electrons are meanwhile localized spatially and energetically at the interface. It is concluded that the injection proceeds through adsorbate induced interface states. This is an important result because the back reaction from long lived interface states can be expected to be much faster than from bulk states. While the charge transport in stoichiometric CuInSe{sub 2} thin films is indicative of free charge carriers, CuInSe{sub 2} with a solar cell grade composition (Cu-poor) exhibits signs of carrier localization. This detrimental effect is attributed to a high density of charged defects and a high degree of compensation, which together create a spatially fluctuating potential that inhibits charge transport. On

  14. Determination of boron over a large dynamic range by prompt-gamma activation analysis

    Energy Technology Data Exchange (ETDEWEB)

    Harrison, R.K. [University of Texas at Austin, Nuclear Engineering Teaching Lab., Pickle Research Campus, R-9000 Austin, TX 78712 (United States); Landsberger, S. [University of Texas at Austin, Nuclear Engineering Teaching Lab., Pickle Research Campus, R-9000 Austin, TX 78712 (United States)], E-mail: s.landsberger@mail.utexas.edu

    2009-02-15

    An evaluation of the PGAA method for the determination of boron across a wide dynamic range of concentrations was performed for trace levels up to 5 wt.% boron. This range encompasses a transition from neutron transparency to significant self- shielding conditions. To account for self-shielding, several PGAA techniques were employed. First, a calibration curve was developed in which a set of boron standards was tested and the count rate to boron mass curve was determined. This set of boron measurements was compared with an internal standard self-shielding correction method and with a method for determining composition using PGAA peak ratios. The advantages and disadvantages of each method are analyzed. The boron concentrations of several laboratory-grade chemicals and standard reference materials were measured with each method and compared. The evaluation of the boron content of nanocrystalline transition metals prepared with a boron-containing reducing agent was also performed with each of the methods tested. Finally, the k{sub 0} method was used for non-destructive measurement of boron in catalyst materials for the characterization of new non-platinum fuel cell catalysts.

  15. Cell wall elongation mode in Gram-negative bacteria is determined by peptidoglycan architecture.

    Science.gov (United States)

    Turner, Robert D; Hurd, Alexander F; Cadby, Ashley; Hobbs, Jamie K; Foster, Simon J

    2013-01-01

    Cellular integrity and morphology of most bacteria is maintained by cell wall peptidoglycan, the target of antibiotics essential in modern healthcare. It consists of glycan strands, cross-linked by peptides, whose arrangement determines cell shape, prevents lysis due to turgor pressure and yet remains dynamic to allow insertion of new material, and hence growth. The cellular architecture and insertion pattern of peptidoglycan have remained elusive. Here we determine the peptidoglycan architecture and dynamics during growth in rod-shaped Gram-negative bacteria. Peptidoglycan is made up of circumferentially oriented bands of material interspersed with a more porous network. Super-resolution fluorescence microscopy reveals an unexpected discontinuous, patchy synthesis pattern. We present a consolidated model of growth via architecture-regulated insertion, where we propose only the more porous regions of the peptidoglycan network that are permissive for synthesis.

  16. Long term charge retention dynamics of SONOS cells

    Science.gov (United States)

    Arreghini, A.; Akil, N.; Driussi, F.; Esseni, D.; Selmi, L.; van Duuren, M. J.

    2008-09-01

    We present a model for charge retention dynamics in SONOS non volatile memory cells which accounts for the space and energy distributions of the trapped charge in the silicon nitride, self consistently with the potential. Long term retention measurements (beyond 106 s) versus temperature allowed us to decouple two charge loss mechanisms, to calibrate the model parameters and then to reproduce a large set of measurements on devices featuring different gate stacks, initial threshold voltages (including negative ones) and operation temperatures. A detailed analysis has been also carried out to compare the retention dynamics of cells featuring thin or thick tunnel oxide barriers.

  17. Analysis and Report on SD2000: A Workshop to Determine Structural Dynamics Research for the Millenium

    Science.gov (United States)

    2007-11-02

    This ONR grant was to facilitate the meeting of an international group of researchers to examine the future of structural dynamics . A group of about...promptly dismissed it as an intellectual pursuit not useful in structural dynamics . In reflecting back over his career, he now views this as a mistake...smart materials, mechatronics, etc.) and determining the appropriate interaction between these new advances and structural dynamics was one of the

  18. Experimental determination of dynamic parameters of an industrial robot

    Science.gov (United States)

    Banas, W.; Cwikła, G.; Foit, K.; Gwiazda, A.; Monica, Z.; Sekala, A.

    2017-08-01

    In an industry increasingly used are industrial robots. Commonly used are two basic methods of programming, on-line programming and off-line programming. In both cases, the programming consists in getting to the selected points record this position, and set the order of movement of the robot, and the introduction of logical tests. Such a program is easy to write, and it is suitable for most industrial applications. Especially when the process is known, respectively slow and unchanging. In this case, the program is being prepared for a universal model of the robot with the appropriate geometry and are checked only collisions. Is not taken into account the dynamics of the robot and how it will really behave while in motion. For this reason, the robot programmed to be tested at a reduced speed, which is raised gradually to the final value. Depending on the complexity of the move and the proximity of the elements it takes a lot of time. It is easy to notice that the robot at different speeds have different trajectories and behaves differently.

  19. Determining tumor blood flow parameters from dynamic image measurements

    Science.gov (United States)

    Libertini, Jessica M.

    2008-11-01

    Many recent cancer treatments focus on preventing angiogenesis, the process by which a tumor promotes the growth of large and efficient capillary beds for the increased nourishment required to support the tumor's rapid growth[l]. To measure the efficacy of these treatments in a timely fashion, there is an interest in using data from dynamic sequences of contrast-enhanced medical imaging, such as MRI and CT, to measure blood flow parameters such as perfusion, permeability-surface-area product, and the relative volumes of the plasma and extracellular-extravascular space. Starting with a two compartment model presented by the radiology community[2], this work challenges the application of a simplification to this problem, which was originally developed to model capillary reuptake[3]. While the primary result of this work is the demonstration of the inaccuracy of this simplification, the remainder of the paper is dedicated to presenting alternative methods for calculating the perfusion and plasma volume coefficients. These methods are applied to model data sets based on real patient data, and preliminary results are presented.

  20. Determining tumor blood flow parameters from dynamic image measurements

    Energy Technology Data Exchange (ETDEWEB)

    Libertini, Jessica M [Division of Applied Mathematics, Brown University, Providence, Rhode Island 02906 (United States)], E-mail: Jessica_Libertini@brown.edu

    2008-11-01

    Many recent cancer treatments focus on preventing angiogenesis, the process by which a tumor promotes the growth of large and efficient capillary beds for the increased nourishment required to support the tumor's rapid growth. To measure the efficacy of these treatments in a timely fashion, there is an interest in using data from dynamic sequences of contrast-enhanced medical imaging, such as MRI and CT, to measure blood flow parameters such as perfusion, permeability-surface-area product, and the relative volumes of the plasma and extracellular-extravascular space. Starting with a two compartment model presented by the radiology community, this work challenges the application of a simplification to this problem, which was originally developed to model capillary reuptake. While the primary result of this work is the demonstration of the inaccuracy of this simplification, the remainder of the paper is dedicated to presenting alternative methods for calculating the perfusion and plasma volume coefficients. These methods are applied to model data sets based on real patient data, and preliminary results are presented.

  1. Experimental determination of the dynamics of an acoustically levitated sphere

    Energy Technology Data Exchange (ETDEWEB)

    Pérez, Nicolás, E-mail: nico@fisica.edu.uy [Centro Universitario de Paysandú, Universidad de la República, Paysandú (Uruguay); Andrade, Marco A. B. [Institute of Physics, University of São Paulo, São Paulo (Brazil); Canetti, Rafael [Facultad de Ingeniería, Universidad de la República, Montevideo (Uruguay); Adamowski, Julio C. [Department of Mechatronics and Mechanical Systems Engineering, Escola Politécnica, University of São Paulo, São Paulo (Brazil)

    2014-11-14

    Levitation of solids and liquids by ultrasonic standing waves is a promising technique to manipulate materials without contact. When a small particle is introduced in certain areas of a standing wave field, the acoustic radiation force pushes the particle to the pressure node. This movement is followed by oscillations of the levitated particle. Aiming to investigate the particle oscillations in acoustic levitation, this paper presents the experimental and numerical characterization of the dynamic behavior of a levitated sphere. To obtain the experimental response, a small sphere is lifted by the acoustic radiation force. After the sphere lift, it presents a damped oscillatory behavior, which is recorded by a high speed camera. To model this behavior, a mass-spring-damper system is proposed. In this model, the acoustic radiation force that acts on the sphere is theoretically predicted by the Gor'kov theory and the viscous forces are modeled by two damping terms, one term proportional to the square of the velocity and another term proportional to the particle velocity. The proposed model was experimentally verified by using different values of sound pressure amplitude. The comparison between numerical and experimental results shows that the model can accurately describe the oscillatory behavior of the sphere in an acoustic levitator.

  2. A dynamical phyllotaxis model to determine floral organ number.

    Directory of Open Access Journals (Sweden)

    Miho S Kitazawa

    2015-05-01

    Full Text Available How organisms determine particular organ numbers is a fundamental key to the development of precise body structures; however, the developmental mechanisms underlying organ-number determination are unclear. In many eudicot plants, the primordia of sepals and petals (the floral organs first arise sequentially at the edge of a circular, undifferentiated region called the floral meristem, and later transition into a concentric arrangement called a whorl, which includes four or five organs. The properties controlling the transition to whorls comprising particular numbers of organs is little explored. We propose a development-based model of floral organ-number determination, improving upon earlier models of plant phyllotaxis that assumed two developmental processes: the sequential initiation of primordia in the least crowded space around the meristem and the constant growth of the tip of the stem. By introducing mutual repulsion among primordia into the growth process, we numerically and analytically show that the whorled arrangement emerges spontaneously from the sequential initiation of primordia. Moreover, by allowing the strength of the inhibition exerted by each primordium to decrease as the primordium ages, we show that pentamerous whorls, in which the angular and radial positions of the primordia are consistent with those observed in sepal and petal primordia in Silene coeli-rosa, Caryophyllaceae, become the dominant arrangement. The organ number within the outmost whorl, corresponding to the sepals, takes a value of four or five in a much wider parameter space than that in which it takes a value of six or seven. These results suggest that mutual repulsion among primordia during growth and a temporal decrease in the strength of the inhibition during initiation are required for the development of the tetramerous and pentamerous whorls common in eudicots.

  3. Automated live cell imaging systems reveal dynamic cell behavior.

    Science.gov (United States)

    Chirieleison, Steven M; Bissell, Taylor A; Scelfo, Christopher C; Anderson, Jordan E; Li, Yong; Koebler, Doug J; Deasy, Bridget M

    2011-07-01

    Automated time-lapsed microscopy provides unique research opportunities to visualize cells and subcellular components in experiments with time-dependent parameters. As accessibility to these systems is increasing, we review here their use in cell science with a focus on stem cell research. Although the use of time-lapsed imaging to answer biological questions dates back nearly 150 years, only recently have the use of an environmentally controlled chamber and robotic stage controllers allowed for high-throughput continuous imaging over long periods at the cell and subcellular levels. Numerous automated imaging systems are now available from both companies that specialize in live cell imaging and from major microscope manufacturers. We discuss the key components of robots used for time-lapsed live microscopic imaging, and the unique data that can be obtained from image analysis. We show how automated features enhance experimentation by providing examples of uniquely quantified proliferation and migration live cell imaging data. In addition to providing an efficient system that drastically reduces man-hours and consumes fewer laboratory resources, this technology greatly enhances cell science by providing a unique dataset of temporal changes in cell activity. Copyright © 2011 American Institute of Chemical Engineers (AIChE).

  4. Determination of the viscoelastic properties of elastomeric materials by the dynamic indentation method

    NARCIS (Netherlands)

    Vriend, Nathalie M.; Kren, Alexander P.

    2004-01-01

    In this paper the dynamic indentation test method, which is not often used, is discussed. The goal of the paper is to consider the possibility of applying a dynamic indentation test method to investigate rubber materials. The basic equations for the determination of the viscoelastic characteristics

  5. A quantitative and dynamic model for plant stem cell regulation.

    Directory of Open Access Journals (Sweden)

    Florian Geier

    Full Text Available Plants maintain pools of totipotent stem cells throughout their entire life. These stem cells are embedded within specialized tissues called meristems, which form the growing points of the organism. The shoot apical meristem of the reference plant Arabidopsis thaliana is subdivided into several distinct domains, which execute diverse biological functions, such as tissue organization, cell-proliferation and differentiation. The number of cells required for growth and organ formation changes over the course of a plants life, while the structure of the meristem remains remarkably constant. Thus, regulatory systems must be in place, which allow for an adaptation of cell proliferation within the shoot apical meristem, while maintaining the organization at the tissue level. To advance our understanding of this dynamic tissue behavior, we measured domain sizes as well as cell division rates of the shoot apical meristem under various environmental conditions, which cause adaptations in meristem size. Based on our results we developed a mathematical model to explain the observed changes by a cell pool size dependent regulation of cell proliferation and differentiation, which is able to correctly predict CLV3 and WUS over-expression phenotypes. While the model shows stem cell homeostasis under constant growth conditions, it predicts a variation in stem cell number under changing conditions. Consistent with our experimental data this behavior is correlated with variations in cell proliferation. Therefore, we investigate different signaling mechanisms, which could stabilize stem cell number despite variations in cell proliferation. Our results shed light onto the dynamic constraints of stem cell pool maintenance in the shoot apical meristem of Arabidopsis in different environmental conditions and developmental states.

  6. Preparation of cell lines for single-cell analysis of transcriptional activation dynamics.

    Science.gov (United States)

    Rafalska-Metcalf, Ilona U; Janicki, Susan M

    2013-01-01

    Imaging molecularly defined regions of chromatin in single living cells during transcriptional activation has the potential to provide new insight into gene regulatory mechanisms. Here, we describe a method for isolating cell lines with multi-copy arrays of reporter transgenes, which can be used for real-time high-resolution imaging of transcriptional activation dynamics in single cells.

  7. Cell fate determination by ubiquitin-dependent regulation of translation

    Science.gov (United States)

    Werner, Achim; Iwasaki, Shintaro; McGourty, Colleen; Medina-Ruiz, Sofia; Teerikorpi, Nia; Fedrigo, Indro; Ingolia, Nicholas T.; Rape, Michael

    2015-01-01

    Metazoan development depends on accurate execution of differentiation programs that allow pluripotent stem cells to adopt specific fates 1. Differentiation requires changes to chromatin architecture and transcriptional networks, yet whether other regulatory events support cell fate determination is less well understood. Here, we have identified the vertebrate-specific ubiquitin ligase CUL3KBTBD8 as an essential regulator of neural crest specification. CUL3KBTBD8 monoubiquitylates NOLC1 and its paralog TCOF1, whose mutation underlies the neurocristopathy Treacher Collins Syndrome 2,3. Ubiquitylation drives formation of a TCOF1-NOLC1 platform that connects RNA polymerase I with ribosome modification enzymes and remodels the translational program of differentiating cells in favor of neural crest specification. We conclude that ubiquitin-dependent regulation of translation is an important feature of cell fate determination. PMID:26399832

  8. Determination of the Orientation and Dynamics of Ergosterol in Model Membranes Using Uniform 13C Labeling and Dynamically Averaged 13C Chemical Shift Anisotropies as Experimental Restraints

    Science.gov (United States)

    Soubias, O.; Jolibois, F.; Massou, S.; Milon, A.; Réat, V.

    2005-01-01

    A new strategy was established to determine the average orientation and dynamics of ergosterol in dimyristoylphosphatidylcholine model membranes. It is based on the analysis of chemical shift anisotropies (CSAs) averaged by the molecular dynamics. Static 13C CSA tensors were computed by quantum chemistry, using the gauge-including atomic-orbital approach within Hartree-Fock theory. Uniformly 13C-labeled ergosterol was purified from Pichia pastoris cells grown on labeled methanol. After reconstitution into dimyristoylphosphatidylcholine lipids, the complete 1H and 13C assignment of ergosterol's resonances was performed using a combination of magic-angle spinning two-dimensional experiments. Dynamically averaged CSAs were determined by standard side-band intensity analysis for isolated 13C resonances (C3 and ethylenic carbons) and by off-magic-angle spinning experiments for other carbons. A set of 18 constraints was thus obtained, from which the sterol's molecular order parameter and average orientation could be precisely defined. The validity of using computed CSAs in this strategy was verified on cholesterol model systems. This new method allowed us to quantify ergosterol's dynamics at three molar ratios: 16 mol % (Ld phase), 30 mol % (Lo phase), and 23 mol % (mixed phases). Contrary to cholesterol, ergosterol's molecular diffusion axis makes an important angle (14°) with the inertial axis of the rigid four-ring system. PMID:15923221

  9. Dynamic heterogeneity and DNA methylation in embryonic stem cells.

    KAUST Repository

    Singer, Zakary S

    2014-07-01

    Cell populations can be strikingly heterogeneous, composed of multiple cellular states, each exhibiting stochastic noise in its gene expression. A major challenge is to disentangle these two types of variability and to understand the dynamic processes and mechanisms that control them. Embryonic stem cells (ESCs) provide an ideal model system to address this issue because they exhibit heterogeneous and dynamic expression of functionally important regulatory factors. We analyzed gene expression in individual ESCs using single-molecule RNA-FISH and quantitative time-lapse movies. These data discriminated stochastic switching between two coherent (correlated) gene expression states and burst-like transcriptional noise. We further showed that the "2i" signaling pathway inhibitors modulate both types of variation. Finally, we found that DNA methylation plays a key role in maintaining these metastable states. Together, these results show how ESC gene expression states and dynamics arise from a combination of intrinsic noise, coherent cellular states, and epigenetic regulation.

  10. Sperm cell surface dynamics during activation and fertilization

    NARCIS (Netherlands)

    Boerke, A.

    2013-01-01

    Before the sperm cell can reach the oocyte it needs to be activated and to undergo a series of preparative steps. The sperm surface dynamics was studied in relation to this activation process and the modifications and removal of sperm surface components havebeen investigated. Bicarbonate-induced rad

  11. Transcription closed and open complex dynamics studies reveal balance between genetic determinants and co-factors.

    Science.gov (United States)

    Sala, Adrien; Shoaib, Muhammad; Anufrieva, Olga; Mutharasu, Gnanavel; Jahan Hoque, Rawnak; Yli-Harja, Olli; Kandhavelu, Meenakshisundaram

    2015-05-19

    In E. coli, promoter closed and open complexes are key steps in transcription initiation, where magnesium-dependent RNA polymerase catalyzes RNA synthesis. However, the exact mechanism of initiation remains to be fully elucidated. Here, using single mRNA detection and dual reporter studies, we show that increased intracellular magnesium concentration affects Plac initiation complex formation resulting in a highly dynamic process over the cell growth phases. Mg2+ regulates transcription transition, which modulates bimodality of mRNA distribution in the exponential phase. We reveal that Mg2+ regulates the size and frequency of the mRNA burst by changing the open complex duration. Moreover, increasing magnesium concentration leads to higher intrinsic and extrinsic noise in the exponential phase. RNAP-Mg2+ interaction simulation reveals critical movements creating a shorter contact distance between aspartic acid residues and Nucleotide Triphosphate residues and increasing electrostatic charges in the active site. Our findings provide unique biophysical insights into the balanced mechanism of genetic determinants and magnesium ion in transcription initiation regulation during cell growth.

  12. Dynamic simulation of a direct carbonate fuel cell power plant

    Energy Technology Data Exchange (ETDEWEB)

    Ernest, J.B. [Fluor Daniel, Inc., Irvine, CA (United States); Ghezel-Ayagh, H.; Kush, A.K. [Fuel Cell Engineering, Danbury, CT (United States)

    1996-12-31

    Fuel Cell Engineering Corporation (FCE) is commercializing a 2.85 MW Direct carbonate Fuel Cell (DFC) power plant. The commercialization sequence has already progressed through construction and operation of the first commercial-scale DFC power plant on a U.S. electric utility, the 2 MW Santa Clara Demonstration Project (SCDP), and the completion of the early phases of a Commercial Plant design. A 400 kW fuel cell stack Test Facility is being built at Energy Research Corporation (ERC), FCE`s parent company, which will be capable of testing commercial-sized fuel cell stacks in an integrated plant configuration. Fluor Daniel, Inc. provided engineering, procurement, and construction services for SCDP and has jointly developed the Commercial Plant design with FCE, focusing on the balance-of-plant (BOP) equipment outside of the fuel cell modules. This paper provides a brief orientation to the dynamic simulation of a fuel cell power plant and the benefits offered.

  13. Determination of cell electroporation in small-volume samples.

    Science.gov (United States)

    Saulis, Gintautas; Praneviciŭte, Rita

    2007-01-01

    Expose of cells to electric field pulses increases the cell membrane permeability. Intracellular potassium ions leak out of the cells through aqueous pores created in the membrane. This release is used here for the determination of the fraction of electroporated cells. To determine cell membrane electroporation in small-volume samples (40-50 miacrol), mini both potassium ion-selective and reference electrodes, with tip diameters of 1-1.5 mm and minimum immersion depths of 1 mm, were utilized. The obtained calibration graph was linear within the concentration range 0.2-100 mM. The slope was 50-51 and 53-56 mV per concentration order at 10-11 and 19-21 degrees C, respectively. Detection limit of the electrode was determined to be 0.05-0.08 mM, however, it was possible to work down to concentrations in the range of 0.01 mM. Experiments have been carried out on human erythrocytes exposed to a square-wave electric pulse with the duration of 0.1-2 ms. The extracellular potassium concentrations were in the range between 0.04-0.08 mM (intact cells) and 3-5 mM (100% electroporation). The obtained dependences of the fraction of electroporated cells on the pulse intensity were of a sigmoid shape. The dependence of the pulse amplitude required to electroporate 50% of cells on the pulse duration, obtained from the release of intracellular potassium ions, coincided with the one determined from the extent of hemolysis after 24 h-incubation at low temperature.

  14. CFD Based Determination of Dynamic Stability Derivatives in Yaw for a Bird

    Institute of Scientific and Technical Information of China (English)

    M. A. Moelyadi; G. Sachs

    2007-01-01

    Dynamic yaw stability derivatives of a gull bird are determined using Computational Fluid Dynamics(CFD) method. Two kinds of motions are applied for calculating the dynamic yaw stability derivatives CNr and CNβ. The first one relates to a lateral translation and, separately, to a yaw rotation. The second one consists of a combined translational and rotational motion. To determine dynamic yaw stability derivatives, the simulation of an unsteady flow with a bird model showing a harmonic motion is performed. The flow solution for each time step is obtained by solving unsteady Euler equations based on a finite volume approach for a small reduced frequency. Then, an evaluation of unsteady forces and moments for one cycle is conducted using harmonic Fourier analysis. The results of the dynamic yaw stability derivatives for both simulations of the model show a good agreement.

  15. Biomaterial surface proteomic signature determines interaction with epithelial cells.

    Science.gov (United States)

    Abdallah, Mohamed-Nur; Tran, Simon D; Abughanam, Ghada; Laurenti, Marco; Zuanazzi, David; Mezour, Mohamed A; Xiao, Yizhi; Cerruti, Marta; Siqueira, Walter L; Tamimi, Faleh

    2017-03-01

    Cells interact with biomaterials indirectly through extracellular matrix (ECM) proteins adsorbed onto their surface. Accordingly, it could be hypothesized that the surface proteomic signature of a biomaterial might determine its interaction with cells. Here, we present a surface proteomic approach to test this hypothesis in the specific case of biomaterial-epithelial cell interactions. In particular, we determined the surface proteomic signature of different biomaterials exposed to the ECM of epithelial cells (basal lamina). We revealed that the biomaterial surface chemistry determines the surface proteomic profile, and subsequently the interaction with epithelial cells. In addition, we found that biomaterials with surface chemistries closer to that of percutaneous tissues, such as aminated PMMA and aminated PDLLA, promoted higher selective adsorption of key basal lamina proteins (laminins, nidogen-1) and subsequently improved their interactions with epithelial cells. These findings suggest that mimicking the surface chemistry of natural percutaneous tissues can improve biomaterial-epithelial integration, and thus provide a rationale for the design of improved biomaterial surfaces for skin regeneration and percutaneous medical devices.

  16. Stochastic dynamics of interacting haematopoietic stem cell niche lineages.

    Directory of Open Access Journals (Sweden)

    Tamás Székely

    2014-09-01

    Full Text Available Since we still know very little about stem cells in their natural environment, it is useful to explore their dynamics through modelling and simulation, as well as experimentally. Most models of stem cell systems are based on deterministic differential equations that ignore the natural heterogeneity of stem cell populations. This is not appropriate at the level of individual cells and niches, when randomness is more likely to affect dynamics. In this paper, we introduce a fast stochastic method for simulating a metapopulation of stem cell niche lineages, that is, many sub-populations that together form a heterogeneous metapopulation, over time. By selecting the common limiting timestep, our method ensures that the entire metapopulation is simulated synchronously. This is important, as it allows us to introduce interactions between separate niche lineages, which would otherwise be impossible. We expand our method to enable the coupling of many lineages into niche groups, where differentiated cells are pooled within each niche group. Using this method, we explore the dynamics of the haematopoietic system from a demand control system perspective. We find that coupling together niche lineages allows the organism to regulate blood cell numbers as closely as possible to the homeostatic optimum. Furthermore, coupled lineages respond better than uncoupled ones to random perturbations, here the loss of some myeloid cells. This could imply that it is advantageous for an organism to connect together its niche lineages into groups. Our results suggest that a potential fruitful empirical direction will be to understand how stem cell descendants communicate with the niche and how cancer may arise as a result of a failure of such communication.

  17. Topological defects control collective dynamics in neural progenitor cell cultures

    Science.gov (United States)

    Kawaguchi, Kyogo; Kageyama, Ryoichiro; Sano, Masaki

    2017-04-01

    Cultured stem cells have become a standard platform not only for regenerative medicine and developmental biology but also for biophysical studies. Yet, the characterization of cultured stem cells at the level of morphology and of the macroscopic patterns resulting from cell-to-cell interactions remains largely qualitative. Here we report on the collective dynamics of cultured murine neural progenitor cells (NPCs), which are multipotent stem cells that give rise to cells in the central nervous system. At low densities, NPCs moved randomly in an amoeba-like fashion. However, NPCs at high density elongated and aligned their shapes with one another, gliding at relatively high velocities. Although the direction of motion of individual cells reversed stochastically along the axes of alignment, the cells were capable of forming an aligned pattern up to length scales similar to that of the migratory stream observed in the adult brain. The two-dimensional order of alignment within the culture showed a liquid-crystalline pattern containing interspersed topological defects with winding numbers of +1/2 and -1/2 (half-integer due to the nematic feature that arises from the head-tail symmetry of cell-to-cell interaction). We identified rapid cell accumulation at +1/2 defects and the formation of three-dimensional mounds. Imaging at the single-cell level around the defects allowed us to quantify the velocity field and the evolving cell density; cells not only concentrate at +1/2 defects, but also escape from -1/2 defects. We propose a generic mechanism for the instability in cell density around the defects that arises from the interplay between the anisotropic friction and the active force field.

  18. Dynamically constrained pipeline for tracking neural progenitor cells

    DEFF Research Database (Denmark)

    Vestergaard, Jacob Schack; Dahl, Anders; Holm, Peter

    2013-01-01

    . A mitosis detector constructed from empirical observations of cells in a pre-mitotic state interacts with the graph formulation to dynamically allow for cell mitosis when appropriate. Track consistency is ensured by introducing pragmatic constraints and the notion of blob states. We validate the proposed...... tracking methods are fundamental building blocks of setting up multi purpose pipelines. Segmentation by discriminative dictionary learning and a graph formulated tracking method constraining the allowed topology changes are combined here to accommodate for highly irregular cell shapes and movement patterns...

  19. Determination of thermal properties of commercial Ni-MH cells

    Science.gov (United States)

    Darcy, Eric C.

    1994-01-01

    The test objectives were to evaluate the electrical and thermal performance of commercial Ni-MH cells, evaluate the effectiveness of commercial charge control circuits, assess the abuse tolerance of these cells, and correlate performance and abuse tolerances to cell design via disassembly. Design objectives were to determine which cell designs are most suitable for scale-up and to guide the design of future shuttle and space station based battery chargers. Results, displayed in viewgraph format, include: reflex charging with ICS circuit resulted in premature charge termination; Ni-MH cells appear very tolerant to overcharge at low rates; Enstore's charger is more electrically and thermally efficient at high rates; and Ni-MH cycles much more efficiently than Ni-Cd with the delta-V/delta-t termination.

  20. Nonlinear Dynamic Theory of Acute Cell Injuries and Brain Ischemia

    Science.gov (United States)

    Taha, Doaa; Anggraini, Fika; Degracia, Donald; Huang, Zhi-Feng

    2015-03-01

    Cerebral ischemia in the form of stroke and cardiac arrest brain damage affect over 1 million people per year in the USA alone. In spite of close to 200 clinical trials and decades of research, there are no treatments to stop post-ischemic neuron death. We have argued that a major weakness of current brain ischemia research is lack of a deductive theoretical framework of acute cell injury to guide empirical studies. A previously published autonomous model based on the concept of nonlinear dynamic network was shown to capture important facets of cell injury, linking the concept of therapeutic to bistable dynamics. Here we present an improved, non-autonomous formulation of the nonlinear dynamic model of cell injury that allows multiple acute injuries over time, thereby allowing simulations of both therapeutic treatment and preconditioning. Our results are connected to the experimental data of gene expression and proteomics of neuron cells. Importantly, this new model may be construed as a novel approach to pharmacodynamics of acute cell injury. The model makes explicit that any pro-survival therapy is always a form of sub-lethal injury. This insight is expected to widely influence treatment of acute injury conditions that have defied successful treatment to date. This work is supported by NIH NINDS (NS081347) and Wayne State University President's Research Enhancement Award.

  1. Determinism and probability in the development of the cell theory.

    Science.gov (United States)

    Duchesneau, François

    2012-09-01

    A return to Claude Bernard's original use of the concept of 'determinism' displays the fact that natural laws were presumed to rule over all natural processes. In a more restricted sense, the term boiled down to a mere presupposition of constant determinant causes for those processes, leaving aside any particular ontological principle, even stochastic. The history of the cell theory until around 1900 was dominated by a twofold conception of determinant causes. Along a reductionist trend, cells' structures and processes were supposed to be accounted for through their analysis into detailed partial mechanisms. But a more holistic approach tended to subsume those analytic means and the mechanism involved under a program of global functional determinations. When mitotic and meiotic sequences in nuclear replication were being unveiled and that neo-Mendelian genetics was being grafted onto cytology and embryology, a conception of strict determinism at the nuclear level, principally represented by Wilhelm Roux and August Weismann, would seem to rule unilaterally over the mosaic interpretation of the cleavage of blastomeres. But, as shown by E.B. Wilson, in developmental processes there occur contingent outcomes of cell division which observations and experiments reveal. This induces the need to admit 'epigenetic' determinants and relativize the presumed 'preformation' of thedevelopmental phases by making room for an emergent order which the accidental circumstances of gene replication would trigger on.

  2. Direct Visualization of DNA Replication Dynamics in Zebrafish Cells.

    Science.gov (United States)

    Kuriya, Kenji; Higashiyama, Eriko; Avşar-Ban, Eriko; Tamaru, Yutaka; Ogata, Shin; Takebayashi, Shin-ichiro; Ogata, Masato; Okumura, Katsuzumi

    2015-12-01

    Spatiotemporal regulation of DNA replication in the S-phase nucleus has been extensively studied in mammalian cells because it is tightly coupled with the regulation of other nuclear processes such as transcription. However, little is known about the replication dynamics in nonmammalian cells. Here, we analyzed the DNA replication processes of zebrafish (Danio rerio) cells through the direct visualization of replicating DNA in the nucleus and on DNA fiber molecules isolated from the nucleus. We found that zebrafish chromosomal DNA at the nuclear interior was replicated first, followed by replication of DNA at the nuclear periphery, which is reminiscent of the spatiotemporal regulation of mammalian DNA replication. However, the relative duration of interior DNA replication in zebrafish cells was longer compared to mammalian cells, possibly reflecting zebrafish-specific genomic organization. The rate of replication fork progression and ori-to-ori distance measured by the DNA combing technique were ∼ 1.4 kb/min and 100 kb, respectively, which are comparable to those in mammalian cells. To our knowledge, this is a first report that measures replication dynamics in zebrafish cells.

  3. Modeling dynamics of HIV infected cells using stochastic cellular automaton

    Science.gov (United States)

    Precharattana, Monamorn; Triampo, Wannapong

    2014-08-01

    Ever since HIV was first diagnosed in human, a great number of scientific works have been undertaken to explore the biological mechanisms involved in the infection and progression of the disease. Several cellular automata (CA) models have been introduced to gain insights into the dynamics of the disease progression but none of them has taken into account effects of certain immune cells such as the dendritic cells (DCs) and the CD8+ T lymphocytes (CD8+ T cells). In this work, we present a CA model, which incorporates effects of the HIV specific immune response focusing on the cell-mediated immunities, and investigate the interaction between the host immune response and the HIV infected cells in the lymph nodes. The aim of our work is to propose a model more realistic than the one in Precharattana et al. (2010) [10], by incorporating roles of the DCs, the CD4+ T cells, and the CD8+ T cells into the model so that it would reproduce the HIV infection dynamics during the primary phase of HIV infection.

  4. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

    Science.gov (United States)

    Yoo, Jejoong; Aksimentiev, Aleksei

    2013-12-10

    The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

  5. The determination of the attitude and attitude dynamics of TeamSat

    DEFF Research Database (Denmark)

    Betto, Maurizio; Jørgensen, John Leif; Riis, Troels

    1999-01-01

    , in space, multiple autonomous processes intended for spacecraft applications such as autonomous star identification, attitude determination and identification and tracking of non-stellar objects, imaging and real-time compression of image and science data for further ground analysis. AVS successfully...... determined the attitude and attitude dynamics of TeamSat....

  6. The Dynamics of Interactions Among Immune and Glioblastoma Cells.

    Science.gov (United States)

    Eder, Katalin; Kalman, Bernadette

    2015-12-01

    Glioblastoma is the most common intracranial malignancy that constitutes about 50 % of all gliomas. Despite aggressive, multimodal therapy consisting of surgery, radiation, and chemotherapy, the outcome of patients with glioblastoma remains poor with 5-year survival rates of immune mediators may represent a critical contributor to this resistance. The tumor microenvironment contains innate and adaptive immune cells in addition to the cancer cells and their surrounding stroma. These various cells communicate with each other by means of direct cell-cell contact or by soluble factors including cytokines and chemokines, and act in autocrine and paracrine manners to modulate tumor growth. There are dynamic interactions among the local immune elements and the tumor cells, where primarily the protective immune cells attempt to overcome the malignant cells. However, by developing somatic mutations and epigenetic modifications, the glioblastoma tumor cells acquire the capability of counteracting the local immune responses, and even exploit the immune cells and products for their own growth benefits. In this review, we survey those immune mechanisms that likely contribute to glioblastoma pathogenesis and may serve as a basis for novel treatment strategies.

  7. Galvanic Cells and the Determination of Equilibrium Constants

    Science.gov (United States)

    Brosmer, Jonathan L.; Peters, Dennis G.

    2012-01-01

    Readily assembled mini-galvanic cells can be employed to compare their observed voltages with those predicted from the Nernst equation and to determine solubility products for silver halides and overall formation constants for metal-ammonia complexes. Results obtained by students in both an honors-level first-year course in general chemistry and…

  8. Galvanic Cells and the Determination of Equilibrium Constants

    Science.gov (United States)

    Brosmer, Jonathan L.; Peters, Dennis G.

    2012-01-01

    Readily assembled mini-galvanic cells can be employed to compare their observed voltages with those predicted from the Nernst equation and to determine solubility products for silver halides and overall formation constants for metal-ammonia complexes. Results obtained by students in both an honors-level first-year course in general chemistry and…

  9. Mitochondrial dynamics and inheritance during cell division, development and disease.

    Science.gov (United States)

    Mishra, Prashant; Chan, David C

    2014-10-01

    During cell division, it is critical to properly partition functional sets of organelles to each daughter cell. The partitioning of mitochondria shares some common features with that of other organelles, particularly in the use of interactions with cytoskeletal elements to facilitate delivery to the daughter cells. However, mitochondria have unique features - including their own genome and a maternal mode of germline transmission - that place additional demands on this process. Consequently, mechanisms have evolved to regulate mitochondrial segregation during cell division, oogenesis, fertilization and tissue development, as well as to ensure the integrity of these organelles and their DNA, including fusion-fission dynamics, organelle transport, mitophagy and genetic selection of functional genomes. Defects in these processes can lead to cell and tissue pathologies.

  10. Shape and Dynamics of Adhesive Cells: Mechanical Response of Open Systems

    Science.gov (United States)

    Yang, Yuehua; Jiang, Hongyuan

    2017-05-01

    Cell adhesion is an essential biological process. However, previous theoretical and experimental studies ignore a key variable, the changes of cellular volume and pressure, during the dynamic adhesion process. Here, we treat cells as open systems and propose a theoretical framework to investigate how the exchange of water and ions with the environment affects the shape and dynamics of cells adhered between two adhesive surfaces. We show that adherent cells can be either stable (convex or concave) or unstable (spontaneous rupture or collapse) depending on the adhesion energy density, the cell size, the separation of two adhesive surfaces, and the stiffness of the flexible surface. Strikingly, we find that the unstable states vanish when cellular volume and pressure are constant. We further show that the detachments of convex and concave cells are very different. The mechanical response of adherent cells is mainly determined by the competition between the loading rate and the regulation of the cellular volume and pressure. Finally, we show that as an open system the detachment of adherent cells is also significantly influenced by the loading history. Thus, our findings reveal a major difference between living cells and nonliving materials.

  11. Dynamic expression of the Robo ligand Slit2 in bone marrow cell populations.

    Science.gov (United States)

    Smith-Berdan, Stephanie; Schepers, Koen; Ly, Alan; Passegué, Emmanuelle; Forsberg, E Camilla

    2012-02-15

    The bone marrow (BM) niche is essential for lifelong hematopoietic stem cell (HSC) maintenance, proliferation and differentiation. Several BM cell types, including osteoblast lineage cells (OBC), mesenchymal stem cells (MSC) and endothelial cells (EC) have been implicated in supporting HSC location and function, but the relative importance of these cell types and their secreted ligands remain controversial. We recently found that the cell surface receptors Robo4 and CXCR4 cooperate to localize HSC to BM niches. We hypothesized that Slit2, a putative ligand for Robo4, cooperates with the CXCR4 ligand SDF1 to direct HSC to specific BM niche sites. Here, we have isolated OBC, MSC and EC by flow cytometry and determined their frequency within the bone marrow and the relative mRNA levels of Slit2, SDF1 and Robo4. We found that expression of Slit2 and SDF1 were dynamically regulated in MSC and OBC-like populations following radiation, while Robo4 expression was restricted to EC. Radiation also significantly affected the cellularity and frequency of both the non-adherent and adherent cells within the BM stroma. These data support a physiological role for Slit2 in regulating the dynamic function of Robo-expressing cells within BM niches at steady state and following radiation.

  12. Sendai virus utilizes specific sialyloligosaccharides as host cell receptor determinants.

    Science.gov (United States)

    Markwell, M A; Paulson, J C

    1980-10-01

    Purified sialyltransferases (CMP-N-acetyl-neuraminate:D-galactosyl-glycoprotein N-acetylneuraminyl-transferase, EC 2.4.99.1) in conjunction with neuraminidase (acylneuraminyl hydrolase, EC 3.2.1.18) were used to produce cell surface sialyloligosaccharides of defined sequence to investigate their role in paramyxovirus infection of host cells. Infection of Madin-Darby bovine kidney cells by Sendai virus was monitored by hemagglutination titer of the virus produced and by changes in morphological characteristics. By either criterion, treatment of the cells with Vibrio cholerae neuraminidase to remove cell surface sialic acids rendered them resistant to infection by Sendai virus. Endogenous replacement of receptors by the cell occurred slowly but supported maximal levels of infection within 6 hr. In contrast, sialylation during a 20-min incubation with CMP-sialic acid and beta-galactoside alpha 2,3-sialytransferase restored full susceptibility to infection. This enzyme elaborates the NeuAc alpha 2,3Gal beta 1,3GalNAc (NeuAc, N-acetylneuraminic acid) sequence on glycoproteins and glycolipids. No restoration of infectivity was observed when neuraminidase-treated cells were sialylated by using beta-galactoside alpha 2,6-sialytransferase, which elaborates the NeuAc-alpha 2,6Gal beta 1,4GlcNAc sequence. These results suggest that sialyloligosaccharide receptor determinants of defined sequence are required for Sendai virus infection of host cells.

  13. Direct determination of phosphatase activity from physiological substrates in cells.

    Directory of Open Access Journals (Sweden)

    Zhongyuan Ren

    Full Text Available A direct and continuous approach to determine simultaneously protein and phosphate concentrations in cells and kinetics of phosphate release from physiological substrates by cells without any labeling has been developed. Among the enzymes having a phosphatase activity, tissue non-specific alkaline phosphatase (TNAP performs indispensable, multiple functions in humans. It is expressed in numerous tissues with high levels detected in bones, liver and neurons. It is absolutely required for bone mineralization and also necessary for neurotransmitter synthesis. We provided the proof of concept that infrared spectroscopy is a reliable assay to determine a phosphatase activity in the osteoblasts. For the first time, an overall specific phosphatase activity in cells was determined in a single step by measuring simultaneously protein and substrate concentrations. We found specific activities in osteoblast like cells amounting to 116 ± 13 nmol min(-1 mg(-1 for PPi, to 56 ± 11 nmol min(-1 mg(-1 for AMP, to 79 ± 23 nmol min(-1 mg(-1 for beta-glycerophosphate and to 73 ± 15 nmol min(-1 mg(-1 for 1-alpha-D glucose phosphate. The assay was also effective to monitor phosphatase activity in primary osteoblasts and in matrix vesicles. The use of levamisole--a TNAP inhibitor--served to demonstrate that a part of the phosphatase activity originated from this enzyme. An IC50 value of 1.16 ± 0.03 mM was obtained for the inhibition of phosphatase activity of levamisole in osteoblast like cells. The infrared assay could be extended to determine any type of phosphatase activity in other cells. It may serve as a metabolomic tool to monitor an overall phosphatase activity including acid phosphatases or other related enzymes.

  14. Dynamic Pax6 expression during the neurogenic cell cycle influences proliferation and cell fate choices of retinal progenitors

    Directory of Open Access Journals (Sweden)

    Yang Xian-Jie

    2009-08-01

    Full Text Available Abstract Background The paired homeobox protein Pax6 is essential for proliferation and pluripotency of retinal progenitors. However, temporal changes in Pax6 protein expression associated with the generation of various retinal neurons have not been characterized with regard to the cell cycle. Here, we examine the dynamic changes of Pax6 expression among chicken retinal progenitors as they progress through the neurogenic cell cycle, and determine the effects of altered Pax6 levels on retinogenesis. Results We provide evidence that during the preneurogenic to neurogenic transition, Pax6 protein levels in proliferating progenitor cells are down-regulated. Neurogenic retinal progenitors retain a relatively low level of Pax6 protein, whereas postmitotic neurons either elevate or extinguish Pax6 expression in a cell type-specific manner. Cell imaging and cell cycle analyses show that neurogenic progenitors in the S phase of the cell cycle contain low levels of Pax6 protein, whereas a subset of progenitors exhibits divergent levels of Pax6 protein upon entering the G2 phase of the cell cycle. We also show that M phase cells contain varied levels of Pax6, and some correlate with the onset of early neuronal marker expression, forecasting cell cycle exit and cell fate commitment. Furthermore, either elevating or knocking down Pax6 attenuates cell proliferation and results in increased cell death. Reducing Pax6 decreases retinal ganglion cell genesis and enhances cone photoreceptor and amacrine interneuron production, whereas elevating Pax6 suppresses cone photoreceptor and amacrine cell fates. Conclusion These studies demonstrate for the first time quantitative changes in Pax6 protein expression during the preneurogenic to neurogenic transition and during the neurogenic cell cycle. The results indicate that Pax6 protein levels are stringently controlled in proliferating progenitors. Maintaining a relatively low Pax6 protein level is necessary for S phase

  15. On the role of CD8+ T cells in determining recovery time from influenza virus infection

    Directory of Open Access Journals (Sweden)

    Pengxing Cao

    2016-12-01

    Full Text Available Myriad experiments have identified an important role for CD8+ T cell response mechanisms in determining recovery from influenza A virus infection. Animal models of influenza infection further implicate multiple elements of the immune response in defining the dynamical characteristics of viral infection. To date, influenza virus models, while capturing particular aspects of the natural infection history, have been unable to reproduce the full gamut of observed viral kinetic behaviour in a single coherent framework. Here, we introduce a mathematical model of influenza viral dynamics incorporating innate, humoral and cellular immune components and explore its properties with a particular emphasis on the role of cellular immunity. Calibrated against a range of murine data, our model is capable of recapitulating observed viral kinetics from a multitude of experiments. Importantly, the model predicts a robust exponential relationship between the level of effector CD8+ T cells and recovery time, whereby recovery time rapidly decreases to a fixed minimum recovery time with an increasing level of effector CD8+ T cells. We find support for this relationship in recent clinical data from influenza A(H7N9 hospitalized patients. The exponential relationship implies that people with a lower level of naive CD8+ T cells may receive significantly more benefit from induction of additional effector CD8+ T cells arising from immunological memory, itself established through either previous viral infection or T cell-based vaccines.

  16. cellGPU: Massively parallel simulations of dynamic vertex models

    Science.gov (United States)

    Sussman, Daniel M.

    2017-10-01

    Vertex models represent confluent tissue by polygonal or polyhedral tilings of space, with the individual cells interacting via force laws that depend on both the geometry of the cells and the topology of the tessellation. This dependence on the connectivity of the cellular network introduces several complications to performing molecular-dynamics-like simulations of vertex models, and in particular makes parallelizing the simulations difficult. cellGPU addresses this difficulty and lays the foundation for massively parallelized, GPU-based simulations of these models. This article discusses its implementation for a pair of two-dimensional models, and compares the typical performance that can be expected between running cellGPU entirely on the CPU versus its performance when running on a range of commercial and server-grade graphics cards. By implementing the calculation of topological changes and forces on cells in a highly parallelizable fashion, cellGPU enables researchers to simulate time- and length-scales previously inaccessible via existing single-threaded CPU implementations. Program Files doi:http://dx.doi.org/10.17632/6j2cj29t3r.1 Licensing provisions: MIT Programming language: CUDA/C++ Nature of problem: Simulations of off-lattice "vertex models" of cells, in which the interaction forces depend on both the geometry and the topology of the cellular aggregate. Solution method: Highly parallelized GPU-accelerated dynamical simulations in which the force calculations and the topological features can be handled on either the CPU or GPU. Additional comments: The code is hosted at https://gitlab.com/dmsussman/cellGPU, with documentation additionally maintained at http://dmsussman.gitlab.io/cellGPUdocumentation

  17. A Versatile Bioreactor for Dynamic Suspension Cell Culture. Application to the Culture of Cancer Cell Spheroids.

    Science.gov (United States)

    Massai, Diana; Isu, Giuseppe; Madeddu, Denise; Cerino, Giulia; Falco, Angela; Frati, Caterina; Gallo, Diego; Deriu, Marco A; Falvo D'Urso Labate, Giuseppe; Quaini, Federico; Audenino, Alberto; Morbiducci, Umberto

    2016-01-01

    A versatile bioreactor suitable for dynamic suspension cell culture under tunable shear stress conditions has been developed and preliminarily tested culturing cancer cell spheroids. By adopting simple technological solutions and avoiding rotating components, the bioreactor exploits the laminar hydrodynamics establishing within the culture chamber enabling dynamic cell suspension in an environment favourable to mass transport, under a wide range of tunable shear stress conditions. The design phase of the device has been supported by multiphysics modelling and has provided a comprehensive analysis of the operating principles of the bioreactor. Moreover, an explanatory example is herein presented with multiphysics simulations used to set the proper bioreactor operating conditions for preliminary in vitro biological tests on a human lung carcinoma cell line. The biological results demonstrate that the ultralow shear dynamic suspension provided by the device is beneficial for culturing cancer cell spheroids. In comparison to the static suspension control, dynamic cell suspension preserves morphological features, promotes intercellular connection, increases spheroid size (2.4-fold increase) and number of cycling cells (1.58-fold increase), and reduces double strand DNA damage (1.5-fold reduction). It is envisioned that the versatility of this bioreactor could allow investigation and expansion of different cell types in the future.

  18. Dynamics of frontal extension of an amoeboid cell

    Science.gov (United States)

    Baumgarten, Werner; Hauser, Marcus J. B.

    2014-12-01

    The acellular slime mould Physarum polycephalum forms giant plasmodia that consist of an apical zone, which is succeeded by a vast network of veins where protoplasm is periodically transported back and forth. The apical zone is formed by a dense layer of viscoelastic cell material, whose leading edge is characterized by the development of undulations, which are called fingers. The dynamics of finger formation and evolution was studied. The front is characterized by alternating events of front advancement and stagnation, which are reflected in the development of the fingers. Therefore, the dynamics of the front was divided into two distinct, periodically alternating regimes. The dispersion relations, i.e., the growth rates of fingers of different wavelengths, observed in these two regimes were found to be symmetric, except for the sign of the growth rates. Furthermore, finger splitting occurred once the fingers reached a critical curvature. Our findings are discussed in terms of the intracellular dynamics of this slime mould.

  19. Evaluation of experimental methods for determining dynamic stiffness and damping of composite materials

    Science.gov (United States)

    Bert, C. W.; Clary, R. R.

    1974-01-01

    Various methods potentially usable for determining dynamic stiffness and damping of composite materials are reviewed. Of these, the following most widely used techniques are singled out for more detailed discussion: free vibration, pulse propagation, and forced vibration response. To illustrate the usefulness and validity of dynamic property data, their application in dynamic analyses and comparison with measured structural response are described for the following composite-material structures: free-free sandwich beam with glass-epoxy facings, clamped-edge sandwich plate with similar facings, free-end sandwich conical shell with similar facings, and boron-epoxy free plate with layers arranged at various orientations.

  20. Reinterpretation of Dynamic Vibrational Spectroscopy to Determine the Molecular Structure and Dynamics of Ferrocene.

    Science.gov (United States)

    Best, Stephen P; Wang, Feng; Islam, M Tauhidul; Islam, Shawkat; Appadoo, Dominique; Trevorah, Ryan M; Chantler, Christopher T

    2016-12-12

    Molecular distortion of dynamic molecules gives a clear signature in the vibrational spectra, which can be modeled to give estimates of the energy barrier and the sensitivity of the frequencies of the vibrational modes to the reaction coordinate. The reaction coordinate method (RCM) utilizes ab initio-calculated spectra of the molecule in its ground and transition states together with their relative energies to predict the temperature dependence of the vibrational spectra. DFT-calculated spectra of the eclipsed (D5h ) and staggered (D5d ) forms of ferrocene (Fc), and its deuterated analogue, within RCM explain the IR spectra of Fc in gas (350 K), solution (300 K), solid solution (7-300 K), and solid (7-300 K) states. In each case the D5h rotamer is lowest in energy but with the barrier to interconversion between rotamers higher for solution-phase samples (ca. 6 kJ mol(-1) ) than for the gas-phase species (1-3 kJ mol(-1) ). The generality of the approach is demonstrated with application to tricarbonyl(η(4) -norbornadiene)iron(0), Fe(NBD)(CO)3 . The temperature-dependent coalescence of the ν(CO) bands of Fe(NBD)(CO)3 is well explained by the RCM without recourse to NMR-like rapid exchange. The RCM establishes a clear link between the calculated ground and transition states of dynamic molecules and the temperature-dependence of their vibrational spectra. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Exploring neural cell dynamics with digital holographic microscopy

    KAUST Repository

    Marquet, Pierre

    2013-07-11

    In this review, we summarize how the new concept of digital optics applied to the field of holographic microscopy has allowed the development of a reliable and flexible digital holographic quantitative phase microscopy (DH-QPM) technique at the nanoscale particularly suitable for cell imaging. Particular emphasis is placed on the original biological ormation provided by the quantitative phase signal. We present the most relevant DH-QPM applications in the field of cell biology, including automated cell counts, recognition, classification, three-dimensional tracking, discrimination between physiological and pathophysiological states, and the study of cell membrane fluctuations at the nanoscale. In the last part, original results show how DH-QPM can address two important issues in the field of neurobiology, namely, multiple-site optical recording of neuronal activity and noninvasive visualization of dendritic spine dynamics resulting from a full digital holographic microscopy tomographic approach. Copyright © 2013 by Annual Reviews.

  2. Germ cell dynamics in the testis of the postnatal common marmoset monkey (Callithrix jacchus).

    Science.gov (United States)

    Albert, S; Ehmcke, J; Wistuba, J; Eildermann, K; Behr, R; Schlatt, S; Gromoll, J

    2010-11-01

    The seminiferous epithelium in the nonhuman primate Callithrix jacchus is similarly organized to man. This monkey has therefore been used as a preclinical model for spermatogenesis and testicular stem cell physiology. However, little is known about the developmental dynamics of germ cells in the postnatal primate testis. In this study, we analyzed testes of newborn, 8-week-old, and adult marmosets employing immunohistochemistry using pluripotent stem cell and germ cell markers DDX4 (VASA), POU5F1 (OCT3/4), and TFAP2C (AP-2γ). Stereological and morphometric techniques were applied for quantitative analysis of germ cell populations and testicular histological changes. Quantitative RT-PCR (qRT-PCR) of testicular mRNA was applied using 16 marker genes establishing the corresponding profiles during postnatal testicular development. Testis size increased during the first 8 weeks of life with the main driver being longitudinal outgrowth of seminiferous cords. The number of DDX4-positive cells per testis doubled between birth and 8 weeks of age whereas TFAP2C- and POU5F1-positive cells remained unchanged. This increase in DDX4-expressing cells indicates dynamic growth of the differentiated A-spermatogonial population. The presence of cells expressing POU5F1 and TFAP2C after 8 weeks reveals the persistence of less differentiated germ cells. The mRNA and protein profiles determined by qRT-PCR and western blot in newborn, 8-week-old, and adult marmosets corroborated the immunohistochemical findings. In conclusion, we demonstrated the presence of distinct spermatogonial subpopulations in the primate testis exhibiting different dynamics during early testicular development. Our study demonstrates the suitability of the marmoset testis as a model for human testicular development.

  3. Hydrodynamic determinants of cell necrosis and molecular delivery produced by pulsed laser microbeam irradiation of adherent cells.

    Science.gov (United States)

    Compton, Jonathan L; Hellman, Amy N; Venugopalan, Vasan

    2013-11-05

    Time-resolved imaging, fluorescence microscopy, and hydrodynamic modeling were used to examine cell lysis and molecular delivery produced by picosecond and nanosecond pulsed laser microbeam irradiation in adherent cell cultures. Pulsed laser microbeam radiation at λ = 532 nm was delivered to confluent monolayers of PtK2 cells via a 40×, 0.8 NA microscope objective. Using laser microbeam pulse durations of 180-1100 ps and pulse energies of 0.5-10.5 μJ, we examined the resulting plasma formation and cavitation bubble dynamics that lead to laser-induced cell lysis, necrosis, and molecular delivery. The cavitation bubble dynamics are imaged at times of 0.5 ns to 50 μs after the pulsed laser microbeam irradiation, and fluorescence assays assess the resulting cell viability and molecular delivery of 3 kDa dextran molecules. Reductions in both the threshold laser microbeam pulse energy for plasma formation and the cavitation bubble energy are observed with decreasing pulse duration. These energy reductions provide for increased precision of laser-based cellular manipulation including cell lysis, cell necrosis, and molecular delivery. Hydrodynamic analysis reveals critical values for the shear-stress impulse generated by the cavitation bubble dynamics governs the location and spatial extent of cell necrosis and molecular delivery independent of pulse duration and pulse energy. Specifically, cellular exposure to a shear-stress impulse J≳0.1 Pa s ensures cell lysis or necrosis, whereas exposures in the range of 0.035≲J≲0.1 Pa s preserve cell viability while also enabling molecular delivery of 3 kDa dextran. Exposure to shear-stress impulses of J≲0.035 Pa s leaves the cells unaffected. Hydrodynamic analysis of these data, combined with data from studies of 6 ns microbeam irradiation, demonstrates the primacy of shear-stress impulse in determining cellular outcome resulting from pulsed laser microbeam irradiation spanning a nearly two-orders-of-magnitude range of

  4. Dynamic analysis of magnetic nanoparticles crossing cell membrane

    Science.gov (United States)

    Pedram, Maysam Z.; Shamloo, Amir; Ghafar-Zadeh, Ebrahim; Alasty, Aria

    2017-01-01

    Nowadays, nanoparticles (NPs) are used in a variety of biomedical applications including brain disease diagnostics and subsequent treatments. Among the various types of NPs, magnetic nanoparticles (MNPs) have been implemented by many research groups for an array of life science applications. In this paper, we studied MNPs controlled delivery into the endothelial cells using a magnetic field. Dynamics equations of MNPs were defined in the continuous domain using control theory methods and were applied to crossing the cell membrane. This study, dedicated to clinical and biomedical research applications, offers a guideline for the generation of a magnetic field required for the delivery of MNPs.

  5. Stochastic and coherent dynamics of single and coupled beta cells

    DEFF Research Database (Denmark)

    phenomenon, modeled by a slow-fast nonlinear system of ordinary differential equations (ODEs). The single cell oscillations are complex as the dynamical behavior is a result of traversing a series of saddle node and homoclinic bifurcations, controlled by the slow variable. We shall present results...... is the simplest reaction-diffusion partial differential equation....... on the burst period as function of an external applied stochastic term and use a technique for reducing the stochastic differential equations to ODEs for the average and higher order moments. The later method is approximate and we shall discuss the limits of validity. The individual beta cells are coupled...

  6. Dynamics of Traction Stress Field during Cell Division

    Science.gov (United States)

    Tanimoto, Hirokazu; Sano, Masaki

    2012-12-01

    We report a quantitative measurement of traction stress exerted by dividing eukaryotic cells. The stress field was highly dynamic and sequentially changed as follows: (1) strong and localized as two spots, (2) weak and broadly distributed, and (3) strong and localized as four spots. At the final stage of cytokinesis, the dividing cells exerted strong tensile force on the intercellular bridge. The asymmetry of the traction stress and the orientation of the division axis matched throughout the division process, suggesting the possible role of the mechanical force as a “store” of the orientational information.

  7. Dynamic Response during PEM Fuel Cell Loading-up

    OpenAIRE

    Jun Gou; Pengcheng Li; Xing Yuan; Pucheng Pei

    2009-01-01

    A study on the effects of controlling and operating parameters for a Proton Exchange Membrane (PEM) fuel cell on the dynamic phenomena during the loading-up process is presented. The effect of the four parameters of load-up amplitudes and rates, operating pressures and current levels on gas supply or even starvation in the flow field is analyzed based accordingly on the transient characteristics of current output and voltage. Experiments are carried out in a single fuel cell with an active ar...

  8. Improved generalized cell mapping for global analysis of dynamical systems

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Three main parts of generalized cell mapping are improved for global analysis. A simple method, which is not based on the theory of digraphs, is presented to locate complete self-cycling sets that corre- spond to attractors and unstable invariant sets involving saddle, unstable periodic orbit and chaotic saddle. Refinement for complete self-cycling sets is developed to locate attractors and unstable in- variant sets with high degree of accuracy, which can start with a coarse cell structure. A nonuniformly interior-and-boundary sampling technique is used to make the refinement robust. For homeomorphic dissipative dynamical systems, a controlled boundary sampling technique is presented to make gen- eralized cell mapping method with refinement extremely accurate to obtain invariant sets. Recursive laws of group absorption probability and expected absorption time are introduced into generalized cell mapping, and then an optimal order for quantitative analysis of transient cells is established, which leads to the minimal computational work. The improved method is applied to four examples to show its effectiveness in global analysis of dynamical systems.

  9. Improved generalized cell mapping for global analysis of dynamical systems

    Institute of Scientific and Technical Information of China (English)

    ZOU HaiLin; XU JianXue

    2009-01-01

    Three main parts of generalized cell mapping are improved for global analysis. A simple method, whichis not based on the theory of digraphs, is presented to locate complete self-cycling sets that corre-spond to attractors and unstable invariant sets involving saddle, unstable periodic orbit and chaotic saddle. Refinement for complete self-cycling sets is developed to locate attractors and unstable in-variant sets with high degree of accuracy, which can start with a coarse cell structure. A nonuniformly interior-and-boundary sampling technique is used to make the refinement robust. For homeomorphic dissipative dynamical systems, a controlled boundary sampling technique is presented to make gen-eralized cell mapping method with refinement extremely accurate to obtain invariant sets. Recursive laws of group absorption probability and expected absorption time are introduced into generalized cell mapping, and then an optimal order for quantitative analysis of transient cells is established, which leads to the minimal computational work. The improved method is applied to four examples to show its effectiveness in global analysis of dynamical systems.

  10. Modelling the dynamics of stem cells in colonic crypts

    Science.gov (United States)

    Sirio, Orozco-Fuentes; Barrio, Rafael A.

    2017-02-01

    We present a theoretical and computational framework to model the colonic crypt organisation in the human intestine. We construct a theoretical and computational framework to model the colonic crypt behaviour, using a Voronoi tessellation to represent each cell and elastic forces between them we addressed how their dynamical disfunction can lead to tumour masses and cancer. Our results indicate that for certain parameters the crypt is in a homeostatic state, but slight changes on their values can disrupt this behaviour.

  11. Nanodomain stabilization dynamics in plasma membranes of biological cells

    Science.gov (United States)

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

    2011-02-01

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

  12. Hybrid bright-field and hologram imaging of cell dynamics

    Science.gov (United States)

    Byeon, Hyeokjun; Lee, Jaehyun; Doh, Junsang; Lee, Sang Joon

    2016-09-01

    Volumetric observation is essential for understanding the details of complex biological phenomena. In this study, a bright-field microscope, which provides information on a specific 2D plane, and a holographic microscope, which provides information spread over 3D volumes, are integrated to acquire two complementary images simultaneously. The developed system was successfully applied to capture distinct T-cell adhesion dynamics on inflamed endothelial layers, including capture, rolling, crawling, transendothelial migration, and subendothelial migration.

  13. Illuminating the dynamics of signal integration in Natural Killer cells

    Directory of Open Access Journals (Sweden)

    Sophie Victoria Pageon

    2012-10-01

    Full Text Available Natural Killer (NK cell responses are shaped by the integration of signals transduced from multiple activating and inhibitory receptors at their surface. Biochemical and genetic approaches have identified most of the key proteins involved in signal integration but a major challenge remains in understanding how the spatial and temporal dynamics of their interactions lead to NK cells responding appropriately when encountering ligands on target cells. Well over a decade of research using fluorescence microscopy has revealed much about the architecture of the NK cell immune synapse – the structured interface between NK cells and target cells - and how it varies when inhibition or activation is the outcome of signal integration. However, key questions – such as the proximity of individual activating and inhibitory receptors – have remained unanswered because the resolution of optical microscopy has been insufficient, being limited by diffraction. Recent developments in fluorescence microscopy have broken this limit, seeding new opportunities for studying the nanometre-scale organisation of the NK cell immune synapse. Here, we discuss how these new imaging technologies, including super-resolution imaging and other novel light-based methods, can illuminate our understanding of NK cell biology.

  14. The scale-free dynamics of eukaryotic cells.

    Directory of Open Access Journals (Sweden)

    Miguel A Aon

    Full Text Available Temporal organization of biological processes requires massively parallel processing on a synchronized time-base. We analyzed time-series data obtained from the bioenergetic oscillatory outputs of Saccharomyces cerevisiae and isolated cardiomyocytes utilizing Relative Dispersional (RDA and Power Spectral (PSA analyses. These analyses revealed broad frequency distributions and evidence for long-term memory in the observed dynamics. Moreover RDA and PSA showed that the bioenergetic dynamics in both systems show fractal scaling over at least 3 orders of magnitude, and that this scaling obeys an inverse power law. Therefore we conclude that in S. cerevisiae and cardiomyocytes the dynamics are scale-free in vivo. Applying RDA and PSA to data generated from an in silico model of mitochondrial function indicated that in yeast and cardiomyocytes the underlying mechanisms regulating the scale-free behavior are similar. We validated this finding in vivo using single cells, and attenuating the activity of the mitochondrial inner membrane anion channel with 4-chlorodiazepam to show that the oscillation of NAD(PH and reactive oxygen species (ROS can be abated in these two evolutionarily distant species. Taken together these data strongly support our hypothesis that the generation of ROS, coupled to redox cycling, driven by cytoplasmic and mitochondrial processes, are at the core of the observed rhythmicity and scale-free dynamics. We argue that the operation of scale-free bioenergetic dynamics plays a fundamental role to integrate cellular function, while providing a framework for robust, yet flexible, responses to the environment.

  15. Flow cytometry analysis of cell population dynamics and cell cycle during HIV-1 envelope-mediated formation of syncytia in vitro.

    Science.gov (United States)

    Torres-Castro, Israel; Cortés-Rubio, César N; Sandoval, Guadalupe; Lamoyi, Edmundo; Larralde, Carlos; Huerta, Leonor

    2014-01-01

    Cell fusion occurs in physiological and pathological conditions and plays a role in regulation of cell fate. The analysis of cell population dynamics and cell cycle in cell-cell fusion experiments is necessary to determine changes in the quantitative equilibrium of cell populations and to identify potential bystander effects. Here, using cocultures of Jurkat HIV-1 envelope expressing cells and CD4(+) cells as a model system and flow cytometry for the analysis, the number, viability, and cell cycle status of the populations participating in fusion were determined. In 3-day cocultures, a sustained reduction of the number of CD4(+) cells was observed while they showed high viability and normal cell cycle progression; fusion, but not inhibition of proliferation or death, accounted for their decrease. In contrast, the number of Env(+) cells decreased in cocultures due to fusion, death, and an inherent arrest at G1. Most of syncytia formed in the first 6 h of coculture showed DNA synthesis activity, indicating that the efficient recruitment of proliferating cells contributed to amplify the removal of CD4(+) cells by syncytia formation. Late in cocultures, approximately 50% of syncytia were viable and a subpopulation still underwent DNA synthesis, even when the recruitment of additional cells was prevented by the addition of the fusion inhibitor T-20, indicating that a population of syncytia may progress into the cell cycle. These results show that the quantitative analysis of cellular outcomes of cell-cell fusion can be performed by flow cytometry.

  16. Mathematical determination of cell population doubling times for multiple cell lines.

    Science.gov (United States)

    Daukste, Liene; Basse, Britta; Baguley, Bruce C; Wall, David J N

    2012-10-01

    Cell cycle times are vital parameters in cancer research, and short cell cycle times are often related to poor survival of cancer patients. A method for experimental estimation of cell cycle times, or doubling times of cultured cancer cell populations, based on addition of paclitaxel (an inhibitor of cell division) has been proposed in literature. We use a mathematical model to investigate relationships between essential parameters of the cell division cycle following inhibition of cell division. The reduction in the number of cells engaged in DNA replication reaches a plateau as the concentration of paclitaxel is increased; this can be determined experimentally. From our model we have derived a plateau log reduction formula for proliferating cells and established that there are linear relationships between the plateau log reduction values and the reciprocal of doubling times (i.e. growth rates of the populations). We have therefore provided theoretical justification of an important experimental technique to determine cell doubling times. Furthermore, we have applied Monte Carlo experiments to justify the suggested linear relationships used to estimate doubling time from 5-day cell culture assays. We show that our results are applicable to cancer cell populations with cell loss present.

  17. Cell Stability Analysis of Conventional 6T Dynamic 8T SRAM Cell in 45NM Technology

    Directory of Open Access Journals (Sweden)

    K. Dhanumjaya

    2012-04-01

    Full Text Available A SRAM cell must meet requirements for operation in submicron/nano ranges. The scaling of CMOS technology has significant impact on SRAM cell -- random fluctuation of electrical characteristics and substantial leakage current. In this paper we present dynamic column based power supply 8 T SRAM cell and comparing the proposed SRAM cell with respect to conventional SRAM 6T in various aspects. To verify read stability and write ability analysis we use N-curve metric. Simulation results affirmed that proposed 8T SRAM cell achieved improved read stability, read current, and leakage current in 45nm Technology comparing with conventional 6T SRAM using cadence virtuoso tool.

  18. Cell Stability Analysis of Conventional 6T Dynamic 8T SRAM Cell in 45NM Technology

    Directory of Open Access Journals (Sweden)

    K.Padmaraju

    2012-05-01

    Full Text Available A SRAM cell must meet requirements for operation in submicron/nano ranges. The scaling of CMOS technology has significant impact on SRAM cell -- random fluctuation of electrical characteristics andsubstantial leakage current. In this paper we present dynamic column based power supply 8T SRAM cell and comparing the proposed SRAM cell with respect to conventional SRAM 6T in various aspects. To verify read stability and write ability analysis we use N-curve metric. Simulation results affirmed that proposed 8T SRAM cell achieved improved read stability, read current, and leakage current in 45nm Technology comparing with conventional 6T SRAM using cadence virtuoso tool.

  19. The application of virtual prototyping methods to determine the dynamic parameters of mobile robot

    Science.gov (United States)

    Kurc, Krzysztof; Szybicki, Dariusz; Burghardt, Andrzej; Muszyńska, Magdalena

    2016-04-01

    The paper presents methods used to determine the parameters necessary to build a mathematical model of an underwater robot with a crawler drive. The parameters present in the dynamics equation will be determined by means of advanced mechatronic design tools, including: CAD/CAE software andMES modules. The virtual prototyping process is described as well as the various possible uses (design adaptability) depending on the optional accessories added to the vehicle. A mathematical model is presented to show the kinematics and dynamics of the underwater crawler robot, essential for the design stage.

  20. Dynamics and molecular determinants of cytoplasmic lipid droplet clustering and dispersion.

    Directory of Open Access Journals (Sweden)

    David J Orlicky

    Full Text Available Perilipin-1 (Plin1, a prominent cytoplasmic lipid droplet (CLD binding phosphoprotein and key physiological regulator of triglyceride storage and lipolysis in adipocytes, is thought to regulate the fragmentation and dispersion of CLD that occurs in response to β-adrenergic activation of adenylate cyclase. Here we investigate the dynamics and molecular determinants of these processes using cell lines stably expressing recombinant forms of Plin1 and/or other members of the perilipin family. Plin1 and a C-terminal CLD-binding fragment of Plin1 (Plin1CT induced formation of single dense CLD clusters near the microtubule organizing center, whereas neither an N-terminal CLD-binding fragment of Plin1, nor Plin2 or Plin3 induced clustering. Clustered CLD coated by Plin1, or Plin1CT, dispersed in response to isoproterenol, or other agents that activate adenylate cyclase, in a process inhibited by the protein kinase A inhibitor, H89, and blocked by microtubule disruption. Isoproterenol-stimulated phosphorylation of CLD-associated Plin1 on serine 492 preceded their dispersion, and live cell imaging showed that cluster dispersion involved initial fragmentation of tight clusters into multiple smaller clusters, which then fragmented into well-dispersed individual CLD. siRNA knockdown of the cortical actin binding protein, moesin, induced disaggregation of tight clusters into multiple smaller clusters, and inhibited the reaggregation of dispersed CLD into tight clusters. Together these data suggest that the clustering and dispersion processes involve a complex orchestration of phosphorylation-dependent, microtubule-dependent and independent, and microfilament dependent steps.

  1. Dynamics and Molecular Determinants of Cytoplasmic Lipid Droplet Clustering and Dispersion

    Science.gov (United States)

    Stefanski, Adrianne L.; McManaman, James L.

    2013-01-01

    Perilipin-1 (Plin1), a prominent cytoplasmic lipid droplet (CLD) binding phosphoprotein and key physiological regulator of triglyceride storage and lipolysis in adipocytes, is thought to regulate the fragmentation and dispersion of CLD that occurs in response to β-adrenergic activation of adenylate cyclase. Here we investigate the dynamics and molecular determinants of these processes using cell lines stably expressing recombinant forms of Plin1 and/or other members of the perilipin family. Plin1 and a C-terminal CLD-binding fragment of Plin1 (Plin1CT) induced formation of single dense CLD clusters near the microtubule organizing center, whereas neither an N-terminal CLD-binding fragment of Plin1, nor Plin2 or Plin3 induced clustering. Clustered CLD coated by Plin1, or Plin1CT, dispersed in response to isoproterenol, or other agents that activate adenylate cyclase, in a process inhibited by the protein kinase A inhibitor, H89, and blocked by microtubule disruption. Isoproterenol-stimulated phosphorylation of CLD-associated Plin1 on serine 492 preceded their dispersion, and live cell imaging showed that cluster dispersion involved initial fragmentation of tight clusters into multiple smaller clusters, which then fragmented into well-dispersed individual CLD. siRNA knockdown of the cortical actin binding protein, moesin, induced disaggregation of tight clusters into multiple smaller clusters, and inhibited the reaggregation of dispersed CLD into tight clusters. Together these data suggest that the clustering and dispersion processes involve a complex orchestration of phosphorylation-dependent, microtubule-dependent and independent, and microfilament dependent steps. PMID:23825572

  2. Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components

    DEFF Research Database (Denmark)

    Alabert, Constance; Bukowski-Wills, Jimi-Carlo; Lee, Sung-Po

    2014-01-01

    To maintain genome function and stability, DNA sequence and its organization into chromatin must be duplicated during cell division. Understanding how entire chromosomes are copied remains a major challenge. Here, we use nascent chromatin capture (NCC) to profile chromatin proteome dynamics durin...

  3. Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions

    Energy Technology Data Exchange (ETDEWEB)

    Fattebert, J.-L. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Richards, D.F. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Glosli, J.N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2012-12-01

    We present a new algorithm for automatic parallel load balancing in classical molecular dynamics. It assumes a spatial domain decomposition of particles into Voronoi cells. It is a gradient method which attempts to minimize a cost function by displacing Voronoi sites associated with each processor/sub-domain along steepest descent directions. Excellent load balance has been obtained for quasi-2D and 3D practical applications, with up to 440·106 particles on 65,536 MPI tasks.

  4. Galvanic cell without liquid junction for potentiometric determination of copper.

    Science.gov (United States)

    Migdalski, Jan; Błaz, Teresa; Zrałka, Barbara; Lewenstam, Andrzej

    2007-07-01

    This paper describes potentiometric measurements in an integrated galvanic cell with both indicator and reference electrodes. Both electrodes are conducting polymer-based. The copper-sensitive indicator electrode is made by using poly(3,4-ethylenedioxythiophene) (PEDOT) doped with 2-(o-arsenophenylazo)-1,8-dihydroxynaphthalene-3,6-disulphonic sodium salt (Arsenazo-I) as the electroactive substance in the film, while the reference electrode is based on PEDOT doped by 2-morpholineoethanesulfonic acid (MES). It is shown that the galvanic cell can be used for determination of copper both in non-aqueous media (where all PVC-based membranes failed) and in the presence of chloride ions, which disturb the signal of conventional copper ion-selective electrodes with solid-state membranes. It is further shown that the titration of copper ions can be successfully monitored using the described electrochemical cell.

  5. Global Dynamics of a Virus Dynamical Model with Cell-to-Cell Transmission and Cure Rate

    Directory of Open Access Journals (Sweden)

    Tongqian Zhang

    2015-01-01

    Full Text Available The cure effect of a virus model with both cell-to-cell transmission and cell-to-virus transmission is studied. By the method of next generation matrix, the basic reproduction number is obtained. The locally asymptotic stability of the virus-free equilibrium and the endemic equilibrium is considered by investigating the characteristic equation of the model. The globally asymptotic stability of the virus-free equilibrium is proved by constructing suitable Lyapunov function, and the sufficient condition for the globally asymptotic stability of the endemic equilibrium is obtained by constructing suitable Lyapunov function and using LaSalle invariance principal.

  6. Determination of phase equilibria in confined systems by open pore cell Monte Carlo method.

    Science.gov (United States)

    Miyahara, Minoru T; Tanaka, Hideki

    2013-02-28

    We present a modification of the molecular dynamics simulation method with a unit pore cell with imaginary gas phase [M. Miyahara, T. Yoshioka, and M. Okazaki, J. Chem. Phys. 106, 8124 (1997)] designed for determination of phase equilibria in nanopores. This new method is based on a Monte Carlo technique and it combines the pore cell, opened to the imaginary gas phase (open pore cell), with a gas cell to measure the equilibrium chemical potential of the confined system. The most striking feature of our new method is that the confined system is steadily led to a thermodynamically stable state by forming concave menisci in the open pore cell. This feature of the open pore cell makes it possible to obtain the equilibrium chemical potential with only a single simulation run, unlike existing simulation methods, which need a number of additional runs. We apply the method to evaluate the equilibrium chemical potentials of confined nitrogen in carbon slit pores and silica cylindrical pores at 77 K, and show that the results are in good agreement with those obtained by two conventional thermodynamic integration methods. Moreover, we also show that the proposed method can be particularly useful for determining vapor-liquid and vapor-solid coexistence curves and the triple point of the confined system.

  7. Modeling universal dynamics of cell spreading on elastic substrates.

    Science.gov (United States)

    Fan, Houfu; Li, Shaofan

    2015-11-01

    A three-dimensional (3D) multiscale moving contact line model is combined with a soft matter cell model to study the universal dynamics of cell spreading over elastic substrates. We have studied both the early stage and the late stage cell spreading by taking into account the actin tension effect. In this work, the cell is modeled as an active nematic droplet, and the substrate is modeled as a St. Venant Kirchhoff elastic medium. A complete 3D simulation of cell spreading has been carried out. The simulation results show that the spreading area versus spreading time at different stages obeys specific power laws, which is in good agreement with experimental data and theoretical prediction reported in the literature. Moreover, the simulation results show that the substrate elasticity may affect force dipole distribution inside the cell. The advantage of this approach is that it combines the hydrodynamics of actin retrograde flow with moving contact line model so that it can naturally include actin tension effect resulting from actin polymerization and actomyosin contraction, and thus it might be capable of simulating complex cellular scale phenomenon, such as cell spreading or even crawling.

  8. Determination of metal ions by fluorescence anisotropy exhibits a broad dynamic range

    Science.gov (United States)

    Thompson, Richard B.; Maliwal, Badri P.; Fierke, Carol A.

    1998-05-01

    Recently, we have shown that metal ions free in solution may be determined at low levels by fluorescence anisotropy (polarization) measurements. Anisotropy measurements enjoy the advantages of wavelength ratiometric techniques for determining metal ions such as calcium, because anisotropy measurements are ratiometric as well. Furthermore, fluorescence anisotropy may be imaged in the microscope. An advantage of anisotropy not demonstrated for wavelength ratiometric approaches using indicators such as Fura-2 and Indo-1 is that under favorable circumstances anisotropy-based determinations exhibit a much broader dynamic range in metal ion concentration. Determinations of free Zn(II) in the picomolar range are demonstrated.

  9. Computational fluid dynamics vs. inverse dynamics methods to determine passive drag in two breaststroke glide positions.

    Science.gov (United States)

    Costa, L; Mantha, V R; Silva, A J; Fernandes, R J; Marinho, D A; Vilas-Boas, J P; Machado, L; Rouboa, A

    2015-07-16

    Computational fluid dynamics (CFD) plays an important role to quantify, understand and "observe" the water movements around the human body and its effects on drag (D). We aimed to investigate the flow effects around the swimmer and to compare the drag and drag coefficient (CD) values obtained from experiments (using cable velocimetry in a swimming pool) with those of CFD simulations for the two ventral gliding positions assumed during the breaststroke underwater cycle (with shoulders flexed and upper limbs extended above the head-GP1; with shoulders in neutral position and upper limbs extended along the trunk-GP2). Six well-trained breaststroke male swimmers (with reasonable homogeneity of body characteristics) participated in the experimental tests; afterwards a 3D swimmer model was created to fit within the limits of the sample body size profile. The standard k-ε turbulent model was used to simulate the fluid flow around the swimmer model. Velocity ranged from 1.30 to 1.70 m/s for GP1 and 1.10 to 1.50 m/s for GP2. Values found for GP1 and GP2 were lower for CFD than experimental ones. Nevertheless, both CFD and experimental drag/drag coefficient values displayed a tendency to jointly increase/decrease with velocity, except for GP2 CD where CFD and experimental values display opposite tendencies. Results suggest that CFD values obtained by single model approaches should be considered with caution due to small body shape and dimension differences to real swimmers. For better accuracy of CFD studies, realistic individual 3D models of swimmers are required, and specific kinematics respected.

  10. Just Look! Intravital Microscopy as the Best Means to Study Kidney Cell Death Dynamics.

    Science.gov (United States)

    Schießl, Ina Maria; Hammer, Anna; Riquier-Brison, Anne; Peti-Peterdi, Janos

    2016-05-01

    Kidney cell death plays a key role in the progression of life-threatening renal diseases, such as acute kidney injury and chronic kidney disease. Injured and dying epithelial and endothelial cells take part in complex communication with the innate immune system, which drives the progression of cell death and the decrease in renal function. To improve our understanding of kidney cell death dynamics and its impact on renal disease, a study approach is needed that facilitates the visualization of renal function and morphology in real time. Intravital multiphoton microscopy of the kidney has been used for more than a decade and made substantial contributions to our understanding of kidney physiology and pathophysiology. It is a unique tool that relates renal structure and function in a time- and spatial-dependent manner. Basic renal function, such as microvascular blood flow regulation and glomerular filtration, can be determined in real time and homeostatic alterations, which are linked inevitably to cell death and can be depicted down to the subcellular level. This review provides an overview of the available techniques to study kidney dysfunction and inflammation in terms of cell death in vivo, and addresses how this novel approach can be used to improve our understanding of cell death dynamics in renal disease.

  11. Implementing dynamic clamp with synaptic and artificial conductances in mouse retinal ganglion cells.

    Science.gov (United States)

    Huang, Jin Y; Stiefel, Klaus M; Protti, Dario A

    2013-05-16

    Ganglion cells are the output neurons of the retina and their activity reflects the integration of multiple synaptic inputs arising from specific neural circuits. Patch clamp techniques, in voltage clamp and current clamp configurations, are commonly used to study the physiological properties of neurons and to characterize their synaptic inputs. Although the application of these techniques is highly informative, they pose various limitations. For example, it is difficult to quantify how the precise interactions of excitatory and inhibitory inputs determine response output. To address this issue, we used a modified current clamp technique, dynamic clamp, also called conductance clamp (1, 2, 3) and examined the impact of excitatory and inhibitory synaptic inputs on neuronal excitability. This technique requires the injection of current into the cell and is dependent on the real-time feedback of its membrane potential at that time. The injected current is calculated from predetermined excitatory and inhibitory synaptic conductances, their reversal potentials and the cell's instantaneous membrane potential. Details on the experimental procedures, patch clamping cells to achieve a whole-cell configuration and employment of the dynamic clamp technique are illustrated in this video article. Here, we show the responses of mouse retinal ganglion cells to various conductance waveforms obtained from physiological experiments in control conditions or in the presence of drugs. Furthermore, we show the use of artificial excitatory and inhibitory conductances generated using alpha functions to investigate the responses of the cells.

  12. The six determinants of gait and the inverted pendulum analogy: A dynamic walking perspective.

    Science.gov (United States)

    Kuo, Arthur D

    2007-08-01

    We examine two prevailing, yet surprisingly contradictory, theories of human walking. The six determinants of gait are kinematic features of gait proposed to minimize the energetic cost of locomotion by reducing the vertical displacement of the body center of mass (COM). The inverted pendulum analogy proposes that it is beneficial for the stance leg to behave like a pendulum, prescribing a more circular arc, rather than a horizontal path, for the COM. Recent literature presents evidence against the six determinants theory, and a simple mathematical analysis shows that a flattened COM trajectory in fact increases muscle work and force requirements. A similar analysis shows that the inverted pendulum fares better, but paradoxically predicts no work or force requirements. The paradox may be resolved through the dynamic walking approach, which refers to periodic gaits produced almost entirely by the dynamics of the limbs alone. Demonstrations include passive dynamic walking machines that descend a gentle slope, and active dynamic walking robots that walk on level ground. Dynamic walking takes advantage of the inverted pendulum mechanism, but requires mechanical work to transition from one pendular stance leg to the next. We show how the step-to-step transition is an unavoidable energetic consequence of the inverted pendulum gait, and gives rise to predictions that are experimentally testable on humans and machines. The dynamic walking approach provides a new perspective, focusing on mechanical work rather than the kinematics or forces of gait. It is helpful for explaining human gait features in a constructive rather than interpretive manner.

  13. Structure and dynamics of metalloproteins in live cells.

    Science.gov (United States)

    Cook, Jeremy D; Penner-Hahn, James E; Stemmler, Timothy L

    2008-01-01

    X-ray absorption spectroscopy (XAS) has emerged as one of the premier tools for investigating the structure and dynamic properties of metals in cells and in metal containing biomolecules. Utilizing the high flux and broad energy range of X-rays supplied by synchrotron light sources, one can selectively excite core electronic transitions in each metal. Spectroscopic signals from these electronic transitions can be used to dissect the chemical architecture of metals in cells, in cellular components, and in biomolecules at varying degrees of structural resolution. With the development of ever-brighter X-ray sources, X-ray methods have grown into applications that can be utilized to provide both a cellular image of the relative distribution of metals throughout the cell as well as a high-resolution picture of the structure of the metal. As these techniques continue to grow in their capabilities and ease of use, so too does the demand for their application by chemists and biochemists interested in studying the structure and dynamics of metals in cells, in cellular organelles, and in metalloproteins.

  14. Growth dynamics and cyclin expression in cutaneous T-cell lymphoma cell lines

    Directory of Open Access Journals (Sweden)

    Edyta Biskup

    2010-05-01

    Full Text Available We have investigated cell growth dynamics and cyclins B1 and E expression in cell lines derived from mycosis fungoides (MyLa, Sézary syndrome (SeAx, and CD30+ lympho-proliferative diseases (Mac1, Mac2a, JK. Mac1 and Mac2a had the highest growth rate (doubling time 18-28 h, >90% cycling cells whereas SeAx was proliferating slowly (doub-ling time 55 h, approximately 35% cycling cells. Expression of cyclin B1 correlated positively with doubling time whereas expression of cyclin E was unscheduled and constant across the investigated cell lines. All cell lines exhibited high expression of PCNA. Thus, we concluded that cyclin B1 could be used for rapid screening of cell proliferation in malignant lymphocytes derived from cutaneous T-cell lymphoma.

  15. LOSS FACTOR AND DYNAMIC YOUNG MODULUS DETERMINATION FOR COMPOSITE SANDWICH BARS REINFORCED WITH STEEL FABRIC

    Directory of Open Access Journals (Sweden)

    Cosmin-Mihai MIRIŢOIU

    2015-05-01

    Full Text Available In this paper I have build some composite sandwich bars. For these bars I have determined the dynamic response by recording their free vibrations. These bars have the core made of polypropylene honeycomb with upper and lower layers reinforced with steel wire mesh. For these bars I have determined the the eigenfrequency of the first eigenmode in this way: the bar was embedded at one end and free at the other where there was placed an accelerometer at 10 mm distance from the edge and I applied an initial force at the free end. I have determined the eigenfrequency because I will use its values for the loss factor and dynamic Young modulus determination.

  16. A Unified Approach to Nonlinear Dynamic Inversion Control with Parameter Determination by Eigenvalue Assignment

    Directory of Open Access Journals (Sweden)

    Yu-Chi Wang

    2015-01-01

    Full Text Available This paper presents a unified approach to nonlinear dynamic inversion control algorithm with the parameters for desired dynamics determined by using an eigenvalue assignment method, which may be applied in a very straightforward and convenient way. By using this method, it is not necessary to transform the nonlinear equations into linear equations by feedback linearization before beginning control designs. The applications of this method are not limited to affine nonlinear control systems or limited to minimum phase problems if the eigenvalues of error dynamics are carefully assigned so that the desired dynamics is stable. The control design by using this method is shown to be robust to modeling uncertainties. To validate the theory, the design of a UAV control system is presented as an example. Numerical simulations show the performance of the design to be quite remarkable.

  17. Principles of Bacterial Cell-Size Determination Revealed by Cell-Wall Synthesis Perturbations

    Directory of Open Access Journals (Sweden)

    Carolina Tropini

    2014-11-01

    Full Text Available Although bacterial cell morphology is tightly controlled, the principles of size regulation remain elusive. In Escherichia coli, perturbation of cell-wall synthesis often results in similar morphologies, making it difficult to deconvolve the complex genotype-phenotype relationships underlying morphogenesis. Here we modulated cell width through heterologous expression of sequences encoding the essential enzyme PBP2 and through sublethal treatments with drugs that inhibit PBP2 and the MreB cytoskeleton. We quantified the biochemical and biophysical properties of the cell wall across a wide range of cell sizes. We find that, although cell-wall chemical composition is unaltered, MreB dynamics, cell twisting, and cellular mechanics exhibit systematic large-scale changes consistent with altered chirality and a more isotropic cell wall. This multiscale analysis enabled identification of distinct roles for MreB and PBP2, despite having similar morphological effects when depleted. Altogether, our results highlight the robustness of cell-wall synthesis and physical principles dictating cell-size control.

  18. Catalysis of protein folding by chaperones accelerates evolutionary dynamics in adapting cell populations.

    Science.gov (United States)

    Cetinbaş, Murat; Shakhnovich, Eugene I

    2013-01-01

    Although molecular chaperones are essential components of protein homeostatic machinery, their mechanism of action and impact on adaptation and evolutionary dynamics remain controversial. Here we developed a physics-based ab initio multi-scale model of a living cell for population dynamics simulations to elucidate the effect of chaperones on adaptive evolution. The 6-loci genomes of model cells encode model proteins, whose folding and interactions in cellular milieu can be evaluated exactly from their genome sequences. A genotype-phenotype relationship that is based on a simple yet non-trivially postulated protein-protein interaction (PPI) network determines the cell division rate. Model proteins can exist in native and molten globule states and participate in functional and all possible promiscuous non-functional PPIs. We find that an active chaperone mechanism, whereby chaperones directly catalyze protein folding, has a significant impact on the cellular fitness and the rate of evolutionary dynamics, while passive chaperones, which just maintain misfolded proteins in soluble complexes have a negligible effect on the fitness. We find that by partially releasing the constraint on protein stability, active chaperones promote a deeper exploration of sequence space to strengthen functional PPIs, and diminish the non-functional PPIs. A key experimentally testable prediction emerging from our analysis is that down-regulation of chaperones that catalyze protein folding significantly slows down the adaptation dynamics.

  19. Catalysis of protein folding by chaperones accelerates evolutionary dynamics in adapting cell populations.

    Directory of Open Access Journals (Sweden)

    Murat Cetinbaş

    Full Text Available Although molecular chaperones are essential components of protein homeostatic machinery, their mechanism of action and impact on adaptation and evolutionary dynamics remain controversial. Here we developed a physics-based ab initio multi-scale model of a living cell for population dynamics simulations to elucidate the effect of chaperones on adaptive evolution. The 6-loci genomes of model cells encode model proteins, whose folding and interactions in cellular milieu can be evaluated exactly from their genome sequences. A genotype-phenotype relationship that is based on a simple yet non-trivially postulated protein-protein interaction (PPI network determines the cell division rate. Model proteins can exist in native and molten globule states and participate in functional and all possible promiscuous non-functional PPIs. We find that an active chaperone mechanism, whereby chaperones directly catalyze protein folding, has a significant impact on the cellular fitness and the rate of evolutionary dynamics, while passive chaperones, which just maintain misfolded proteins in soluble complexes have a negligible effect on the fitness. We find that by partially releasing the constraint on protein stability, active chaperones promote a deeper exploration of sequence space to strengthen functional PPIs, and diminish the non-functional PPIs. A key experimentally testable prediction emerging from our analysis is that down-regulation of chaperones that catalyze protein folding significantly slows down the adaptation dynamics.

  20. Cdc42/N-WASP signaling links actin dynamics to pancreatic β cell delamination and differentiation

    Science.gov (United States)

    Kesavan, Gokul; Lieven, Oliver; Mamidi, Anant; Öhlin, Zarah Löf; Johansson, Jenny Kristina; Li, Wan-Chun; Lommel, Silvia; Greiner, Thomas Uwe; Semb, Henrik

    2014-01-01

    Delamination plays a pivotal role during normal development and cancer. Previous work has demonstrated that delamination and epithelial cell movement within the plane of an epithelium are associated with a change in cellular phenotype. However, how this positional change is linked to differentiation remains unknown. Using the developing mouse pancreas as a model system, we show that β cell delamination and differentiation are two independent events, which are controlled by Cdc42/N-WASP signaling. Specifically, we show that expression of constitutively active Cdc42 in β cells inhibits β cell delamination and differentiation. These processes are normally associated with junctional actin and cell-cell junction disassembly and the expression of fate-determining transcription factors, such as Isl1 and MafA. Mechanistically, we demonstrate that genetic ablation of N-WASP in β cells expressing constitutively active Cdc42 partially restores both delamination and β cell differentiation. These findings elucidate how junctional actin dynamics via Cdc42/N-WASP signaling cell-autonomously control not only epithelial delamination but also cell differentiation during mammalian organogenesis. PMID:24449844

  1. DETERMINANTS OF RED-BLOOD-CELL DEFORMABILITY IN RELATION TO CELL AGE

    NARCIS (Netherlands)

    BOSCH, FH; WERRE, JM; ROERDINKHOLDERSTOELWINDER, B; HULS, T; WILLEKENS, FLA; WICHERS, G; HALIE, MR

    1994-01-01

    Red blood cell (RBC) deformability was determined with an ektacytometer in fractions separated on the basis of differences in cell volume or density. Deformability was measured with ektacytometry (rpm-scan and osmo-scan). We studied three groups of RBC fractions:l. By counterflow centrifugation we o

  2. Sex ratio selection and multi-factorial sex determination in the housefly : A dynamic model

    NARCIS (Netherlands)

    Kozielska, M.A.; Pen, I.R.; Beukeboom, L.W.; Weissing, F.J.

    Sex determining (SD) mechanisms are highly variable between different taxonomic groups and appear to change relatively quickly during evolution. Sex ratio selection could be a dominant force causing such changes. We investigate theoretically the effect of sex ratio selection on the dynamics of a

  3. Determination of thermal inactivation kinetics of Listeria monocytogenes in chicken meat by isothermal and dynamic methods

    Science.gov (United States)

    The objective of this research is to determine the thermal inactivation kinetics of Listeria monocytogenes in chicken breast meat using both isothermal and dynamic conditions. A four-strain cocktail of L. monocytogenes was inoculated to chicken breast meat. Isothermal studies were performed by sub...

  4. Error compensation of single-antenna attitude determination using GNSS for Low-dynamic applications

    Science.gov (United States)

    Chen, Wen; Yu, Chao; Cai, Miaomiao

    2017-04-01

    GNSS-based single-antenna pseudo-attitude determination method has attracted more and more attention from the field of high-dynamic navigation due to its low cost, low system complexity, and no temporal accumulated errors. Related researches indicate that this method can be an important complement or even an alternative to the traditional sensors for general accuracy requirement (such as small UAV navigation). The application of single-antenna attitude determining method to low-dynamic carrier has just started. Different from the traditional multi-antenna attitude measurement technique, the pseudo-attitude attitude determination method calculates the rotation angle of the carrier trajectory relative to the earth. Thus it inevitably contains some deviations comparing with the real attitude angle. In low-dynamic application, these deviations are particularly noticeable, which may not be ignored. The causes of the deviations can be roughly classified into three categories, including the measurement error, the offset error, and the lateral error. Empirical correction strategies for the formal two errors have been promoted in previous study, but lack of theoretical support. In this paper, we will provide quantitative description of the three type of errors and discuss the related error compensation methods. Vehicle and shipborne experiments were carried out to verify the feasibility of the proposed correction methods. Keywords: Error compensation; Single-antenna; GNSS; Attitude determination; Low-dynamic

  5. Pulsatile microfluidics as an analytical tool for determining the dynamic characteristics of microfluidic systems

    DEFF Research Database (Denmark)

    Vedel, Søren; Olesen, Laurits Højgaard; Bruus, Henrik

    2010-01-01

    -filled interconnected elastic microfluidic tubes containing a large, trapped air bubble and driven by a pulsatile pressure difference. We demonstrate good agreement between the system-level model and the experimental results, allowing us to determine the dynamic time scales of the system. However, the generic analysis...

  6. Sex ratio selection and multi-factorial sex determination in the housefly : A dynamic model

    NARCIS (Netherlands)

    Kozielska, M.A.; Pen, I.R.; Beukeboom, L.W.; Weissing, F.J.

    2006-01-01

    Sex determining (SD) mechanisms are highly variable between different taxonomic groups and appear to change relatively quickly during evolution. Sex ratio selection could be a dominant force causing such changes. We investigate theoretically the effect of sex ratio selection on the dynamics of a mul

  7. Determination of the smoke-plume heights and their dynamics with ground-based scanning LIDAR

    Science.gov (United States)

    V. Kovalev; A. Petkov; C. Wold; S. Urbanski; W. M. Hao

    2015-01-01

    Lidar-data processing techniques are analyzed, which allow determining smoke-plume heights and their dynamics and can be helpful for the improvement of smoke dispersion and air quality models. The data processing algorithms considered in the paper are based on the analysis of two alternative characteristics related to the smoke dispersion process: the regularized...

  8. Upper Limb Asymmetries in the Perception of Proprioceptively Determined Dynamic Position Sense

    Science.gov (United States)

    Goble, Daniel J.; Brown, Susan H.

    2010-01-01

    Recent studies of position-related proprioceptive sense have provided evidence of a nonpreferred left arm advantage in right-handed individuals. The present study sought to determine whether similar asymmetries might exist in "dynamic position" sense. Thirteen healthy, right-handed adults were blindfolded and seated with arms placed on…

  9. The Dynamics and Turnover of Tau Aggregates in Cultured Cells

    Science.gov (United States)

    Guo, Jing L.; Buist, Arjan; Soares, Alberto; Callaerts, Kathleen; Calafate, Sara; Stevenaert, Frederik; Daniels, Joshua P.; Zoll, Bryan E.; Crowe, Alex; Brunden, Kurt R.; Moechars, Diederik; Lee, Virginia M. Y.

    2016-01-01

    Filamentous tau aggregates, the hallmark lesions of Alzheimer disease (AD), play key roles in neurodegeneration. Activation of protein degradation systems has been proposed to be a potential strategy for removing pathological tau, but it remains unclear how effectively tau aggregates can be degraded by these systems. By applying our previously established cellular model system of AD-like tau aggregate induction using preformed tau fibrils, we demonstrate that tau aggregates induced in cells with regulated expression of full-length mutant tau can be gradually cleared when soluble tau expression is suppressed. This clearance is at least partially mediated by the autophagy-lysosome pathway, although both the ubiquitin-proteasome system and the autophagy-lysosome pathway are deficient in handling large tau aggregates. Importantly, residual tau aggregates left after the clearance phase leads to a rapid reinstatement of robust tau pathology once soluble tau expression is turned on again. Moreover, we succeeded in generating monoclonal cells persistently carrying tau aggregates without obvious cytotoxicity. Live imaging of GFP-tagged tau aggregates showed that tau inclusions are dynamic structures constantly undergoing “fission” and “fusion,” which facilitate stable propagation of tau pathology in dividing cells. These findings provide a greater understanding of cell-to-cell transmission of tau aggregates in dividing cells and possibly neurons. PMID:27129267

  10. Determinants of intrinsic radiosensitivity of mammalian cell lines

    Energy Technology Data Exchange (ETDEWEB)

    Radford, I.R. [Peter MacCallum Cancer Institute, East Melbourne, VIC (Australia). Research Division

    1998-12-31

    Differences in the radiosensitivity of normal and cancerous cells could arise in various ways. Although there is no compelling data to support the view, the currently prevailing opinion is that differences in radiosensitivity are related to differences in some aspect of enzymatic DNA repair. A test of the importance of possible differences in enzymatic DNA repair in determining relative radiosensitivity would be to compare lethality in cells containing equivalent numbers of DNA lesions. Six cell lines were used in these studies: two Chinese hamster (CHO and V79) and a monkey (Vero) fibroblast-like line, a mouse melanoma line (B16-F1), and a rat (RUC-2) and a human (SQ-20B) carcinoma line. This group of cell lines displays a wide range of sensitivities to external beam low-LET radiation, ranging from the relatively radiosensitive B16-F1 and Vero lines through to the highly radioresistant RUC-2 line. However, it is important to note that none of the lines has a demonstrated defect in enzymatic DNA repair and that all appear to die by necrosis following a lethal radiation insult. Despite having significantly different radiosensitivities, CHO and V79 cells showed comparable responses to DNA-associated {sup 125}I-decays with D{sub o} values of around 65. More surprisingly, the radiosensitive B16-F1 line and the radioresistant RUC-2 line both had responses with D{sub o} values of around 133 {sup 125}I-decays. The factor of two difference between the D{sub o} values for these two pairs of cell lines is probably attributable to CHO and V79 cells being pseudo-diploid whereas B 16-F1 and RUC2 appear to have derived from tetraploid cells. The generality of the above result, for DNA lesions of different quality, was tested by comparing the sensitivities of CHO and V79 cells to DNA-associated {sup 3}H-decays. Again, consistent with the {sup 125}I-decay data, there was no significant difference in the D{sub o} values for these lines. Our {sup 3}H- and {sup 125}I-decay data are

  11. Dynamic Scaling of Lipofuscin Deposition in Aging Cells

    Science.gov (United States)

    Family, Fereydoon; Mazzitello, K. I.; Arizmendi, C. M.; Grossniklaus, H. E.

    2011-07-01

    Lipofuscin is a membrane-bound cellular waste that can be neither degraded nor ejected from the cell but can only be diluted through cell division and subsequent growth. The fate of postmitotic (non-dividing) cells such as neurons, cardiac myocytes, skeletal muscle fibers, and retinal pigment epithelial cells (RPE) is to accumulate lipofuscin, which as an "aging pigment" has been considered a reliable biomarker for the age of cells. Environmental stress can accelerate the accumulation of lipofuscin. For example, accumulation in brain cells appears to be an important issue connected with heavy consumption of alcohol. Lipofuscin is made of free-radical-damaged protein and fat, whose abnormal accumulation is related to a range of disorders including Type IV mucolipidosis (ML4), Amyotrophic Lateral Sclerosis (ALS), Alzheimer's disease, Parkinson disease, and age-related macular degeneration (AMD) which is the leading cause of blindness beyond the age of 50 years. The study of lipofuscin formation and growth is important, because of their association with cellular aging. We introduce a model of non-equilibrium cluster growth and aggregation that we have developed for studying the formation and growth of lipofuscin. As an example of lipofuscin deposit in a given kind of postmitotic cell, we study the kinetics of lipofuscin growth in a RPE cell. Our results agree with a linear growth of the number of lipofuscin granules with age. We apply the dynamic scaling approach to our model and find excellent data collapse for the cluster size distribution. An unusual feature of our model is that while small particles are removed from the cell the larger ones become fixed and grow by aggregation.

  12. Androgen action via testicular arteriole smooth muscle cells is important for Leydig cell function, vasomotion and testicular fluid dynamics.

    Directory of Open Access Journals (Sweden)

    Michelle Welsh

    Full Text Available Regulation of blood flow through the testicular microvasculature by vasomotion is thought to be important for normal testis function as it regulates interstitial fluid (IF dynamics which is an important intra-testicular transport medium. Androgens control vasomotion, but how they exert these effects remains unclear. One possibility is by signalling via androgen receptors (AR expressed in testicular arteriole smooth muscle cells. To investigate this and determine the overall importance of this mechanism in testis function, we generated a blood vessel smooth muscle cell-specific AR knockout mouse (SMARKO. Gross reproductive development was normal in SMARKO mice but testis weight was reduced in adulthood compared to control littermates; this reduction was not due to any changes in germ cell volume or to deficits in testosterone, LH or FSH concentrations and did not cause infertility. However, seminiferous tubule lumen volume was reduced in adult SMARKO males while interstitial volume was increased, perhaps indicating altered fluid dynamics; this was associated with compensated Leydig cell failure. Vasomotion was impaired in adult SMARKO males, though overall testis blood flow was normal and there was an increase in the overall blood vessel volume per testis in adult SMARKOs. In conclusion, these results indicate that ablating arteriole smooth muscle AR does not grossly alter spermatogenesis or affect male fertility but does subtly impair Leydig cell function and testicular fluid exchange, possibly by locally regulating microvascular blood flow within the testis.

  13. Dynamics of Cell Ensembles on Adhesive Micropatterns: Bridging the Gap between Single Cell Spreading and Collective Cell Migration.

    Directory of Open Access Journals (Sweden)

    Philipp J Albert

    2016-04-01

    Full Text Available The collective dynamics of multicellular systems arise from the interplay of a few fundamental elements: growth, division and apoptosis of single cells; their mechanical and adhesive interactions with neighboring cells and the extracellular matrix; and the tendency of polarized cells to move. Micropatterned substrates are increasingly used to dissect the relative roles of these fundamental processes and to control the resulting dynamics. Here we show that a unifying computational framework based on the cellular Potts model can describe the experimentally observed cell dynamics over all relevant length scales. For single cells, the model correctly predicts the statistical distribution of the orientation of the cell division axis as well as the final organisation of the two daughters on a large range of micropatterns, including those situations in which a stable configuration is not achieved and rotation ensues. Large ensembles migrating in heterogeneous environments form non-adhesive regions of inward-curved arcs like in epithelial bridge formation. Collective migration leads to swirl formation with variations in cell area as observed experimentally. In each case, we also use our model to predict cell dynamics on patterns that have not been studied before.

  14. Stem cell fate determination during development and regeneration of ectodermal organs

    Directory of Open Access Journals (Sweden)

    Lucia eJimenez-Rojo

    2012-04-01

    Full Text Available The development of ectoderm-derived appendages results in a large variety of highly specialized organs such as hair follicles, mammary glands, salivary glands and teeth. Despite varying in number, shape and function, all these ectodermal organs develop through continuous and reciprocal epithelial-mesenchymal interactions, sharing common morphological and molecular features especially during their embryonic development. Diseases such as ectodermal dysplasias can affect simultaneously these organs, suggesting that they may arise from common multipotent precursors residing in the embryonic ectoderm. During embryogenesis, these putative ectodermal stem cells may adopt different fates and consequently be able to generate a variety of tissue-specific stem cells, which are the sources for the various cell lineages that form the diverse organs. The specification of those common epithelial precursors, as well as their further lineage commitment to tissue-specific stem cells, might be controlled by specific signals. It has been well documented that Notch, Wnt, bone morphogenetic protein (BMP and fibroblast growth factor (FGF signaling pathways regulate cell fate decisions during the various stages of ectodermal organ development. However, the in vivo spatial and temporal dynamics of these signaling pathways are not yet well understood. Improving the current knowledge on the mechanisms involved in stem cell fate determination during organogenesis and homeostasis of ectodermal organs is crucial to develop effective stem cell-based therapies in order to regenerate or replace pathological and damaged tissues.

  15. Stem Cell Fate Determination during Development and Regeneration of Ectodermal Organs

    Science.gov (United States)

    Jiménez-Rojo, Lucía; Granchi, Zoraide; Graf, Daniel; Mitsiadis, Thimios A.

    2012-01-01

    The development of ectoderm-derived appendages results in a large variety of highly specialized organs such as hair follicles, mammary glands, salivary glands, and teeth. Despite varying in number, shape, and function, all these ectodermal organs develop through continuous and reciprocal epithelial–mesenchymal interactions, sharing common morphological and molecular features especially during their embryonic development. Diseases such as ectodermal dysplasias can affect simultaneously these organs, suggesting that they may arise from common multipotent precursors residing in the embryonic ectoderm. During embryogenesis, these putative ectodermal stem cells may adopt different fates and consequently be able to generate a variety of tissue-specific stem cells, which are the sources for the various cell lineages that form the diverse organs. The specification of those common epithelial precursors, as well as their further lineage commitment to tissue-specific stem cells, might be controlled by specific signals. It has been well documented that Notch, Wnt, bone morphogenetic protein, and fibroblast growth factor signaling pathways regulate cell fate decisions during the various stages of ectodermal organ development. However, the in vivo spatial and temporal dynamics of these signaling pathways are not yet well understood. Improving the current knowledge on the mechanisms involved in stem cell fate determination during organogenesis and homeostasis of ectodermal organs is crucial to develop effective stem cell-based therapies in order to regenerate or replace pathological and damaged tissues. PMID:22539926

  16. Determination of telomerase activity in stem cells and non-stem cells of breast cancer

    Institute of Scientific and Technical Information of China (English)

    LI Zhi; HE Yanli; ZHANG Jiahua; ZHANG Jinghui; HUANG Tao

    2007-01-01

    Although all normal tissue cells,including stem cells,are genetically homologous,variation in gene expression patterns has already determined the distinct roles for individual cells in the physiological process due to the occurrence of epigenetic modification.This is of special importance for the existenee of tissue stem cells because they are exclusively immortal within the body,capable of selfreplicating and differentiating by which tissues renew and repair itself and the total tissue cell population maintains a steady-state.Impairment of tissue stem cells is usually accompanied by a reduction in cell number,slows down the repair process and causes hypofunction.For instance,chemotherapy usually leads to depression of bone marrow and hair loss.Cellular aging is closely associated with the continuous erosion of the telomere while activation of telomerase repairs and maintains telomeres,thus slowing the aging process and prolonging cell life.In normal adults,telomerase activation mainly presents in tissue stem cells and progenitor cells giving them unlimited growth potential.Despite the extensive demonstration of telomerase activation in malignancy(>80%),scientists found that heterogeneity also exists among the tumor cells and only minorities of cells,designated as cancer stem cells,andergo processes analogous to the self-renewal and differentiation of normal stem ceils while the rest have limited lifespans.In this study,telomerase activity was measured and compared in breast cancer stem cells and non-stem cells that were phenotypically sorted by examining surface marker expression.The results indicated that cancer stem cells show a higher level of enzyme activity than non-stem cells.In addition,associated with the repair of cancer tissue(or relapse)after chemotherapy,telomerase activity in stem cells was markedly increased.

  17. Cellular adhesome screen identifies critical modulators of focal adhesion dynamics, cellular traction forces and cell migration behaviour.

    Science.gov (United States)

    Fokkelman, Michiel; Balcıoğlu, Hayri E; Klip, Janna E; Yan, Kuan; Verbeek, Fons J; Danen, Erik H J; van de Water, Bob

    2016-08-17

    Cancer cells migrate from the primary tumour into surrounding tissue in order to form metastasis. Cell migration is a highly complex process, which requires continuous remodelling and re-organization of the cytoskeleton and cell-matrix adhesions. Here, we aimed to identify genes controlling aspects of tumour cell migration, including the dynamic organization of cell-matrix adhesions and cellular traction forces. In a siRNA screen targeting most cell adhesion-related genes we identified 200+ genes that regulate size and/or dynamics of cell-matrix adhesions in MCF7 breast cancer cells. In a subsequent secondary screen, the 64 most effective genes were evaluated for growth factor-induced cell migration and validated by tertiary RNAi pool deconvolution experiments. Four validated hits showed significantly enlarged adhesions accompanied by reduced cell migration upon siRNA-mediated knockdown. Furthermore, loss of PPP1R12B, HIPK3 or RAC2 caused cells to exert higher traction forces, as determined by traction force microscopy with elastomeric micropillar post arrays, and led to considerably reduced force turnover. Altogether, we identified genes that co-regulate cell-matrix adhesion dynamics and traction force turnover, thereby modulating overall motility behaviour.

  18. Determining the benefits of Vorticella cell body motion

    Science.gov (United States)

    Specht, Matty C.; Pepper, Rachel E.

    2016-11-01

    Microscopic sessile suspension feeders are single-celled organisms found in aquatic ecosystems. They live attached to underwater surfaces and create a fluid flow in order to feed on bacteria and debris. They participate in the natural degradation of contaminants in water. Understanding the fluid flow they create enhances our knowledge of their environmental impact. One type of suspension feeder, Vorticella, have been observed to vary their cell body orientation with respect to their surface, but the benefits of this motion are still unknown. We use simulations to investigate the effect of Vorticella body motion on the feeding current and the nutrient flux to the cell body to determine whether or not the motion increases nutrient consumption. We determine the nutrient flux using COMSOL Multiphysics software to solve the advection-diffusion equation with the flow given by a stokeslet model. We use a range of motions similar and dissimilar to that of live Vorticella. We find that most patterns of motion do not increase the nutrient flux, since the Vorticella feed from regions where they already have depleted the water of nutrients. However, it is possible that their motion could help the Vorticella find nutrients that are inhomogenously distributed in water.

  19. Dynamic metabolic flux analysis using a convex analysis approach: Application to hybridoma cell cultures in perfusion.

    Science.gov (United States)

    Fernandes de Sousa, Sofia; Bastin, Georges; Jolicoeur, Mario; Vande Wouwer, Alain

    2016-05-01

    In recent years, dynamic metabolic flux analysis (DMFA) has been developed in order to evaluate the dynamic evolution of the metabolic fluxes. Most of the proposed approaches are dedicated to exactly determined or overdetermined systems. When an underdetermined system is considered, the literature suggests the use of dynamic flux balance analysis (DFBA). However the main challenge of this approach is to determine an appropriate objective function, which remains valid over the whole culture. In this work, we propose an alternative dynamic metabolic flux analysis based on convex analysis, DMFCA, which allows the determination of bounded intervals for the fluxes using the available knowledge of the metabolic network and information provided by the time evolution of extracellular component concentrations. Smoothing splines and mass balance differential equations are used to estimate the time evolution of the uptake and excretion rates from this experimental data. The main advantage of the proposed procedure is that it does not require additional constraints or objective functions, and provides relatively narrow intervals for the intracellular metabolic fluxes. DMFCA is applied to experimental data from hybridoma HB58 cell perfusion cultures, in order to investigate the influence of the operating mode (batch and perfusion) on the metabolic flux distribution.

  20. Cell mass and cell cycle dynamics of an asynchronous budding yeast population

    DEFF Research Database (Denmark)

    Lencastre Fernandes, Rita; Carlquist, Magnus; Lundin, Luisa

    2013-01-01

    consumption observed during batch cultivation. The good agreement between the proposed multi-scale model (a population balance model [PBM] coupled to an unstructured model) and experimental data (both the overall physiology and cell size and cell cycle distributions) indicates that a mechanistic model...... of model predictions for cell property distributions against experimental data is scarce. This study focuses on the experimental and mathematical description of the dynamics of cell size and cell cycle position distributions, of a population of Saccharomyces cerevisiae, in response to the substrate......Despite traditionally regarded as identical, cells in a microbial cultivation present a distribution of phenotypic traits, forming a heterogeneous cell population. Moreover, the degree of heterogeneity is notably enhanced by changes in micro-environmental conditions. A major development...

  1. Dynamic modulation of thymidylate synthase gene expression and fluorouracil sensitivity in human colorectal cancer cells.

    Directory of Open Access Journals (Sweden)

    Kentaro Wakasa

    Full Text Available Biomarkers have revolutionized cancer chemotherapy. However, many biomarker candidates are still in debate. In addition to clinical studies, a priori experimental approaches are needed. Thymidylate synthase (TS expression is a long-standing candidate as a biomarker for 5-fluorouracil (5-FU treatment of cancer patients. Using the Tet-OFF system and a human colorectal cancer cell line, DLD-1, we first constructed an in vitro system in which TS expression is dynamically controllable. Quantitative assays have elucidated that TS expression in the transformant was widely modulated, and that the dynamic range covered 15-fold of the basal level. 5-FU sensitivity of the transformant cells significantly increased in response to downregulated TS expression, although being not examined in the full dynamic range because of the doxycycline toxicity. Intriguingly, our in vitro data suggest that there is a linear relationship between TS expression and the 5-FU sensitivity in cells. Data obtained in a mouse model using transformant xenografts were highly parallel to those obtained in vitro. Thus, our in vitro and in vivo observations suggest that TS expression is a determinant of 5-FU sensitivity in cells, at least in this specific genetic background, and, therefore, support the possibility of TS expression as a biomarker for 5-FU-based cancer chemotherapy.

  2. A new method for decreasing cell-load variation in dynamic cellular manufacturing systems

    Directory of Open Access Journals (Sweden)

    Aidin Delgoshaei

    2016-01-01

    Full Text Available Cell load variation is considered a significant shortcoming in scheduling of cellular manufacturing systems. In this article, a new method is proposed for scheduling dynamic cellular manufacturing systems in the presence of bottleneck and parallel machines. The aim of this method is to control cell load variation during the process of determining the best trading off values between in-house manufacturing and outsourcing. A genetic algorithm (GA is developed because of the high potential of trapping in the local optima, and results are compared with the results of LINGO® 12.0 software. The Taguchi method (an L_9 orthogonal optimization is used to estimate parameters of GA in order to solve experiments derived from literature. An in-depth analysis is conducted on the results in consideration of various factors, and control charts are used on machine-load variation. Our findings indicate that the dynamic condition of product demands affects the routing of product parts and may induce machine-load variations that yield to cell-load diversity. An increase in product uncertainty level causes the loading level of each cell to vary, which in turn results in the development of “complex dummy sub-cells”. The effect of the complex sub-cells is measured using another mathematical index. The results showed that the proposed GA can provide solutions with limited cell-load variations.

  3. Glucose Levels in Culture Medium Determine Cell Death Mode in MPP(+)-treated Dopaminergic Neuronal Cells.

    Science.gov (United States)

    Yoon, So-Young; Oh, Young J

    2015-09-01

    We previously demonstrated that 1-methyl-4-phenylpyridinium (MPP(+)) causes caspase-independent, non-apoptotic death of dopaminergic (DA) neuronal cells. Here, we specifically examined whether change of glucose concentration in culture medium may play a role for determining cell death modes of DA neurons following MPP(+) treatment. By incubating MN9D cells in medium containing varying concentrations of glucose (5~35 mM), we found that cells underwent a distinct cell death as determined by morphological and biochemical criteria. At 5~10 mM glucose concentration (low glucose levels), MPP(+) induced typical of the apoptotic dell death accompanied with caspase activation and DNA fragmentation as well as cell shrinkage. In contrast, MN9D cells cultivated in medium containing more than 17.5 mM (high glucose levels) did not demonstrate any of these changes. Subsequently, we observed that MPP(+) at low glucose levels but not high glucose levels led to ROS generation and subsequent JNK activation. Therefore, MPP(+)-induced cell death only at low glucose levels was significantly ameliorated following co-treatment with ROS scavenger, caspase inhibitor or JNK inhibitor. We basically confirmed the quite similar pattern of cell death in primary cultures of DA neurons. Taken together, our results suggest that a biochemically distinct cell death mode is recruited by MPP(+) depending on extracellular glucose levels.

  4. Ureaplasma parvum infection alters filamin a dynamics in host cells

    Directory of Open Access Journals (Sweden)

    Brown Mary B

    2011-04-01

    Full Text Available Abstract Background Ureaplasmas are among the most common bacteria isolated from the human urogenital tract. Ureaplasmas can produce asymptomatic infections or disease characterized by an exaggerated inflammatory response. Most investigations have focused on elucidating the pathogenic potential of Ureaplasma species, but little attention has been paid to understanding the mechanisms by which these organisms are capable of establishing asymptomatic infection. Methods We employed differential proteome profiling of bladder tissues from rats experimentally infected with U. parvum in order to identify host cell processes perturbed by colonization with the microbe. Tissues were grouped into four categories: sham inoculated controls, animals that spontaneously cleared infection, asymptomatic urinary tract infection (UTI, and complicated UTI. One protein that was perturbed by infection (filamin A was used to further elucidate the mechanism of U. parvum-induced disruption in human benign prostate cells (BPH-1. BPH-1 cells were evaluated by confocal microscopy, immunoblotting and ELISA. Results Bladder tissue from animals actively colonized with U. parvum displayed significant alterations in actin binding proteins (profilin 1, vinculin, α actinin, and filamin A that regulate both actin polymerization and cell cytoskeletal function pertaining to focal adhesion formation and signal transduction (Fisher's exact test, P U. parvum perturbed the regulation of filamin A. Specifically, infected BPH-1 cells exhibited a significant increase in filamin A phosphorylated at serine2152 (P ≤ 0.01, which correlated with impaired proteolysis of the protein and its normal intracellular distribution. Conclusion Filamin A dynamics were perturbed in both models of infection. Phosphorylation of filamin A occurs in response to various cell signaling cascades that regulate cell motility, differentiation, apoptosis and inflammation. Thus, this phenomenon may be a useful

  5. Thickness determination in textile material design: dynamic modeling and numerical algorithms

    Science.gov (United States)

    Xu, Dinghua; Ge, Meibao

    2012-03-01

    Textile material design is of paramount importance in the study of functional clothing design. It is therefore important to determine the dynamic heat and moisture transfer characteristics in the human body-clothing-environment system, which directly determine the heat-moisture comfort level of the human body. Based on a model of dynamic heat and moisture transfer with condensation in porous fabric at low temperature, this paper presents a new inverse problem of textile thickness determination (IPTTD). Adopting the idea of the least-squares method, we formulate the IPTTD into a function minimization problem. By means of the finite-difference method, quasi-solution method and direct search method for one-dimensional minimization problems, we construct iterative algorithms of the approximated solution for the IPTTD. Numerical simulation results validate the formulation of the IPTTD and demonstrate the effectiveness of the proposed numerical algorithms.

  6. The cell-cycle state of stem cells determines cell fate propensity.

    Science.gov (United States)

    Pauklin, Siim; Vallier, Ludovic

    2013-09-26

    Self-renewal and differentiation of stem cells are fundamentally associated with cell-cycle progression to enable tissue specification, organ homeostasis, and potentially tumorigenesis. However, technical challenges have impaired the study of the molecular interactions coordinating cell fate choice and cell-cycle progression. Here, we bypass these limitations by using the FUCCI reporter system in human pluripotent stem cells and show that their capacity of differentiation varies during the progression of their cell cycle. These mechanisms are governed by the cell-cycle regulators cyclin D1-3 that control differentiation signals such as the TGF-β-Smad2/3 pathway. Conversely, cell-cycle manipulation using a small molecule directs differentiation of hPSCs and provides an approach to generate cell types with a clinical interest. Our results demonstrate that cell fate decisions are tightly associated with the cell-cycle machinery and reveal insights in the mechanisms synchronizing differentiation and proliferation in developing tissues.

  7. The roles and regulation of Sertoli cells in fate determinations of spermatogonial stem cells and spermatogenesis.

    Science.gov (United States)

    Hai, Yanan; Hou, Jingmei; Liu, Yun; Liu, Yang; Yang, Hao; Li, Zheng; He, Zuping

    2014-05-01

    Spermatogenesis is a complex process by which spermatogonial stem cells (SSCs) self-renew and differentiate into spermatozoa under the elaborate coordination of testicular microenvironment, namely, niche. Sertoli cells, which locate around male germ cells, are the most critical component of the niche. Significant progress has recently been made by peers and us on uncovering the effects of Sertoli cells on regulating fate determinations of SSCs. Here we addressed the roles and regulation of Sertoli cells in normal and abnormal spermatogenesis. Specifically, we summarized the biological characteristics of Sertoli cells, and we emphasized the roles of Sertoli cells in mediating the self-renewal, differentiation, apoptosis, de-differentiation, and trans-differentiation of SSCs. The association between abnormal function of Sertoli cells and impaired spermatogenesis was discussed. Finally, we highlighted several issues to be addressed for further investigation on the effects and mechanisms of Sertoli cells in spermatogenesis. Since Sertoli cells are the key supportive cells for SSCs and they are very receptive to modification, a better understanding of the roles and regulation of Sertoli cells in SSC biology and spermatogenesis would make it feasible to identify novel targets for gene therapy of male infertility as well as seek more efficient and safer strategies for male contraception.

  8. Phase resetting reveals network dynamics underlying a bacterial cell cycle.

    Directory of Open Access Journals (Sweden)

    Yihan Lin

    Full Text Available Genomic and proteomic methods yield networks of biological regulatory interactions but do not provide direct insight into how those interactions are organized into functional modules, or how information flows from one module to another. In this work we introduce an approach that provides this complementary information and apply it to the bacterium Caulobacter crescentus, a paradigm for cell-cycle control. Operationally, we use an inducible promoter to express the essential transcriptional regulatory gene ctrA in a periodic, pulsed fashion. This chemical perturbation causes the population of cells to divide synchronously, and we use the resulting advance or delay of the division times of single cells to construct a phase resetting curve. We find that delay is strongly favored over advance. This finding is surprising since it does not follow from the temporal expression profile of CtrA and, in turn, simulations of existing network models. We propose a phenomenological model that suggests that the cell-cycle network comprises two distinct functional modules that oscillate autonomously and couple in a highly asymmetric fashion. These features collectively provide a new mechanism for tight temporal control of the cell cycle in C. crescentus. We discuss how the procedure can serve as the basis for a general approach for probing network dynamics, which we term chemical perturbation spectroscopy (CPS.

  9. Dynamics of Tetrahymena macronuclear lamina during cell division

    Institute of Scientific and Technical Information of China (English)

    CHENBIN; ZHONGHEZHAI

    1994-01-01

    During mitosis,the nuclear lamina in higher eukaryotic cells undergoes a distinctly morphological change.It breaks down into lamin polymers or monomers at prophase.At telophase,the lamins reassemble around the condensed chromatin to form the layer of lamina.Using antiserum to mammalian lamins,we studied the dynamics of lamina during cell division in the macronuleus of Tetrahymena shanghaiensis,which divided in the way of amitosis.In contrast to those in higher animal cells,the typical perinuclear lamin distribution in the macronucleus persisted throughout the whole cell cycle.It was further found that in some synchronized cells,the lamin distribution bisplayed an unusual pattern consisting of a series of spots within the macronucleus.Using South-western hybridization,we found that the purified 66 KD lamin in Tetrahymena showed specific affinity with the telomere DNA sequence in the same species.Therefore,we propose that pattern of immunofluorescence may be due to the interaction of lamin protein with the nucleoli and the condensed chromatins in the macronucleus.

  10. Imaging the ageing dynamics of polymer solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Seeland, Marco; Roland, Roesch; Harald, Hoppe [Institute of Physics, Ilmenau University of Technology (Germany)

    2010-07-01

    Nowadays, many attempts are existing on the route towards higher power conversion efficiencies in polymer solar cells. In addition, the lifetimes of such devices play a key role for the market entry as commercial products. To investigate the timescale of degradation processes, we applied long-time stability measurements with devices stored in the dark and under illumination and compare the results with luminescence images. The application of those techniques allows us to investigate the ageing dynamics in our devices consisting of an interpenetrating network of P3HT and PCBM, sandwiched between the ITO/PEDOT:PSS and aluminium electrode.

  11. Dynamics and Synchrony of Pancreatic beta-cells and Islets

    DEFF Research Database (Denmark)

    Pedersen, Morten Gram

    2006-01-01

    biological hypotheses. The subjects addressed are: Quasi-steady-state approximations of enzyme reactions, the effect of noise on bursting electrical behavior, exciation wave propagation in pancreatic islets, intra- and inter-islet synchronization and pulsatile insulin secretion, and mitochondrial dynamics.......Pancreatic beta-cells secrete insulin in response to raised glucose levels. Malfunctioning of this system plays an important role in the metabolic disease diabetes. The biological steps from glucose stimulus to the final release of insulin are incompletely understood, and a more complete...

  12. Dynamic Cell Formation based on Multi-objective Optimization Model

    Directory of Open Access Journals (Sweden)

    Guozhu Jia

    2013-08-01

    Full Text Available In this paper, a multi-objective model is proposed to address the dynamic cellular manufacturing (DCM formation problem. This model considers four conflicting objectives: relocation cost, machine utilization, material handling cost and maintenance cost. The model also considers the situation that some machines could be shared by more than one cell at the same period. A genetic algorithm is applied to get the solution of this mathematical model. Three numerical examples are simulated to evaluate the validity of this model.  

  13. Testing Object-Oriented Programs using Dynamic Aspects and Non-Determinism

    DEFF Research Database (Denmark)

    Achenbach, Michael; Ostermann, Klaus

    2010-01-01

    without parameterization or generation of tests. It also eases modelling naturally non-deterministic program features like IO or multi-threading in integration tests. Dynamic AOP facilitates powerful design adaptations without exposing test features, keeping the scope of these adaptations local to each...... test. We also combine non-determinism and dynamic aspects in a new approach to testing multi-threaded programs using co-routines.......The implementation of unit tests with mock objects and stubs often involves substantial manual work. Stubbed methods return simple default values, therefore variations of these values require separate test cases. The integration of mock objects often requires more infrastructure code and design...

  14. Determination of Mean Inner Potential by Electron Holography Along with Electron Dynamic Simulation

    Institute of Scientific and Technical Information of China (English)

    王岩国; 刘红荣; 杨奇斌; 张泽

    2003-01-01

    Off-axis electron holography in a field-emission-gun transmission electron microscope and electron dynamic simulation is used to determine the mean inner potential of copper. The phase shift of object wave versus specimen thickness is calculated up to 30 nm using electron dynamic formula, and the sample thickness is decided by match of the experimental and calculated phase shift. Based on the measured phase shift, the calculated mean inner potential of Cu is 21.2 V, which agrees with the reported values within the experimental error.

  15. Experimental determination of dynamic characteristics of the VentrAssist implantable rotary blood pump.

    Science.gov (United States)

    Chung, Michael K H; Zhang, Nong; Tansley, Geoff D; Qian, Yi

    2004-12-01

    The VentrAssist implantable rotary blood pump, intended for long-term ventricular assist, is under development and is currently being tested for its rotor-dynamic stability. The pump consists of a shaftless impeller, which also acts as the rotor of the brushless DC motor. The impeller remains passively suspended in the pump cavity by hydrodynamic forces, which result from the small clearances between the outside surfaces of the impeller and the pump cavity. These small clearances range from approximately 50 microm to 230 microm in size in the version of pump reported here. This article presents experimental investigation into the dynamic characteristics of the impeller-bearing-pump housing system of the rotary blood pump for increasing pump speeds at different flow rates. The pump was mounted on a suspension system consisting of a platform and springs, where the natural frequency and damping ratio for the suspension system were determined. Real-time measurements of the impeller's displacement were performed using Hall effect sensors. A vertical disturbance force was exerted onto the pump housing, causing the impeller to be displaced in vertical direction from its dynamic equilibrium position within the pump cavity. The impeller displacement was represented by a decaying sine wave, which indicated the impeller restoring to its equilibrium position. From the decaying sine wave the natural frequency and stiffness coefficient of the system were determined. Furthermore, the logarithmic decrement method was used to determine the damping ratio and eventually the damping coefficient of the system. Results indicate that stiffness and damping coefficients increased as flow rate and pump speed increased, representing an increase in stability with these changing conditions. However, pump speed had a greater influence on the stiffness and damping coefficients than flow rate did, which was evident through dynamic analysis. Overall the experimental method presented in this

  16. MEMS-based dynamic cell-to-cell culture platforms using electrochemical surface modifications

    Science.gov (United States)

    Chang, Jiyoung; Yoon, Sang-Hee; Mofrad, Mohammad R. K.; Lin, Liwei

    2011-05-01

    MEMS-based biological platforms with the capability of both spatial placements and time releases of living cells for cell-to-cell culture experiments have been designed and demonstrated utilizing electrochemical surface modification effects. The spatial placement is accomplished by electrochemical surface modification of substrate surfaces to be either adhesive or non-adhesive for living cells. The time control is achieved by the electrical activation of the selective indium tin oxide co-culture electrode to allow the migration of living cells onto the electrode to start the cell-to-cell culture studies. Prototype devices have a three-electrode design with an electrode size of 50 × 50 µm2 and the separation gaps of 2 µm between them. An electrical voltage of -1.5 V has been used to activate the electrodes independently and sequentially to demonstrate the dynamic cell-to-cell culture experiments of NIH 3T3 fibroblast and Madin Darby canine kidney cells. As such, this MEMS platform could be a basic yet versatile tool to characterize transient cell-to-cell interactions.

  17. Charge carrier recombination dynamics in perovskite and polymer solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Paulke, Andreas; Kniepert, Juliane; Kurpiers, Jona; Wolff, Christian M.; Schön, Natalie; Brenner, Thomas J. K.; Neher, Dieter [Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476, Potsdam (Germany); Stranks, Samuel D. [Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU (United Kingdom); Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); Cavendish Laboratory, JJ Thomson Avenue, Cambridge CB3 0HE (United Kingdom); Snaith, Henry J. [Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU (United Kingdom)

    2016-03-14

    Time-delayed collection field experiments are applied to planar organometal halide perovskite (CH{sub 3}NH{sub 3}PbI{sub 3}) based solar cells to investigate charge carrier recombination in a fully working solar cell at the nanosecond to microsecond time scale. Recombination of mobile (extractable) charges is shown to follow second-order recombination dynamics for all fluences and time scales tested. Most importantly, the bimolecular recombination coefficient is found to be time-dependent, with an initial value of ca. 10{sup −9} cm{sup 3}/s and a progressive reduction within the first tens of nanoseconds. Comparison to the prototypical organic bulk heterojunction device PTB7:PC{sub 71}BM yields important differences with regard to the mechanism and time scale of free carrier recombination.

  18. Dynamic capabilities for cooperation in Brazilian multinational and factors determining its management

    Directory of Open Access Journals (Sweden)

    Priscila Rezende da Costa

    2015-05-01

    Full Text Available In the context of emerging companies’ growth, current challenges depend on the local generation of product and process innovations, as well as dynamic capability to generate innovative solutions cooperatively and new globe business models. The objective of this study is to analyse the determining managerial factors for the dynamic capability of cooperation in Brazilian multinationals (BMNs. A survey was conducted with a sample of 60 BMNs, and a structured questionnaire and statistical tests with factorial analysis and Cronbach's alpha were used. The aggregate analysis of the results indicates that BMNs are going through a transitional process between the operational capability of cooperation and the capability for dynamic cooperation, which are relevant to the continuous adaptation of already-established cooperative management routines and the evaluation and incorporation of the relational capability of management practices that consider systemic flows, open innovation and integrate strategic intentionality into cooperative processes.

  19. The growth of stem cells within {beta}-TCP scaffolds in a fluid-dynamic environment

    Energy Technology Data Exchange (ETDEWEB)

    Xu Shanglong [School of Mechatronics Engineering, University of Electronic Science and Technology, Chengdu (China); State Key Laboratory of Mechanical Manufacture System Engineering, Xi' an Jiaotong University, Xi' an (China); Li Dichen [State Key Laboratory of Mechanical Manufacture System Engineering, Xi' an Jiaotong University, Xi' an (China)], E-mail: dcli@mail.xjtu.edu.cn; Xie Youzhuan; Lu Jianxi; Dai Kerong [Department of Orthopaedic Surgery, Ninth People' s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai (China)

    2008-01-10

    A three-dimensional dynamic perfusion system was developed to provide mass transport and nutrient supply to permit the cell proliferation during the long-term culture inside a {beta}-tricalcium phosphate ({beta}-TCP) scaffold. Also the flow field throughout the scaffold was studied. The porous cylindrical scaffold with a central channel was seeded with the sheep mesenchymal stem cells (MSCs). Then the cell-seeded scaffolds were continuously perfused with the complete {alpha}-MEM medium by a peristaltic pump for 7, 14 and 28 days, respectively. Histological study showed that the cell proliferation rates were different throughout the whole scaffolds and the different cell coverage was shown in different positions of the scaffold. Unoccupied spaces were found in many macropores. A computational fluid dynamics (CFD) modeling was used to simulate the flow conditions within perfused cell-seeded scaffolds to give an insight into the mechanisms of these cell growth phenomena. Relating the simulation results to perfusion experiments, the even fluid velocity (approximately 0.52 mm/s) and shear stress (approximately 0.0055 Pa) were found to correspond to increased cell proliferation within the cell-scaffold constructs. Flow speeds were between 0.25 and 0.75 mm/s and shear stresses were between 0.003 and 0.008 Pa in approximately 75% of the regions. This method exhibits novel capabilities to compare the results obtained for different perfusion rates or different scaffold microarchitectures. It may allow specific fluid velocities and shear stresses to be determined to optimize the perfusion flow rate, porous scaffold architecture and distribution of in vitro tissue growth.

  20. Determination of dynamic performance of freight cars taking into account technical condition of side bearers

    Directory of Open Access Journals (Sweden)

    S.Myamlin

    2013-02-01

    Full Text Available Purpose. The railway transport plays an important role in social and economic life of the country and carries out the large containment of transportation activities. The transport industry should migrate towards innovation changes and increase its significance as an important transit subsystem on the way of renovation of both the infrastructure and the strategy of all transportation process components including the interaction with other transport modes. At present the life sets strategic challenges for the railway branch, and the basic goals among them are as follows: high-speed train traffic development, increase of the weight of freight trains, new rolling stock development etc. Due to the urgency of this subject, the researchers should cope with the task devoted to one of aspects of improving the freight transportation efficiency, namely to the study of effects of various factors and characteristics of technical conditions of the freight cars running gears (which are unavoidable to arise during operation on their basic dynamic indices. The deviations of technical conditions of running gears from the normal state of the wedge system of bogie swing suspension also play an important role among them. The purpose of the paper is to investigate the influence of different factors of the technical conditions of freight car running gears (size deviation in both the bearers and the wedge system during operation on their basic indices – coefficients of horizontal and vertical dynamics, vehicle body acceleration, frame strength, and derailment stability coefficient. Methodology. The study was conducted by numerical integration and mathematical modeling of the freight car dynamic loading using the software package “Dynamics of Rail Vehicles” (“DYNRAIL”. Findings. As a result of the research for freight car dynamic coefficients determination taking into account technical conditions of the side bearers, the dependencies of the basic freight cars

  1. Quantum molecular dynamics simulations of hydrogen production and solar cells

    Science.gov (United States)

    Mou, Weiwei

    The global energy crisis presents two major challenges for scientists around the world: Producing cleaner energy which is sustainable for the environment; And improving the efficiency of energy production as well as consumption. It is crucial and yet elusive to understand the atomistic mechanisms and electronic properties, which are needed in order to tackle those challenges. Quantum molecular dynamics simulations and nonadiabatic quantum molecular dynamics are two of the dominant methods used to address the atomistic and electronic properties in various energy studies. This dissertation is an ensemble of three studies in energy research: (1) Hydrogen production from the reaction of aluminum clusters with water to provide a renewable energy cycle; (2) The photo-excited charge transfer and recombination at a quaterthiophene/zinc oxide interface to improve the power conversion efficiency of hybrid poly(3-hexylthiophene) (P3HT) /ZnO solar cells; and (3) the charge transfer at a rubrene/C60 interface to understand why phenyl groups in rubrene improve the performance of rubrene/C60 solar cells.

  2. Revealing the Dynamics of Thylakoid Membranes in Living Cyanobacterial Cells

    Science.gov (United States)

    Stingaciu, Laura-Roxana; O'Neill, Hugh; Liberton, Michelle; Urban, Volker S.; Pakrasi, Himadri B.; Ohl, Michael

    2016-01-01

    Cyanobacteria are photosynthetic prokaryotes that make major contributions to the production of the oxygen in the Earth atmosphere. The photosynthetic machinery in cyanobacterial cells is housed in flattened membrane structures called thylakoids. The structural organization of cyanobacterial cells and the arrangement of the thylakoid membranes in response to environmental conditions have been widely investigated. However, there is limited knowledge about the internal dynamics of these membranes in terms of their flexibility and motion during the photosynthetic process. We present a direct observation of thylakoid membrane undulatory motion in vivo and show a connection between membrane mobility and photosynthetic activity. High-resolution inelastic neutron scattering experiments on the cyanobacterium Synechocystis sp. PCC 6803 assessed the flexibility of cyanobacterial thylakoid membrane sheets and the dependence of the membranes on illumination conditions. We observed softer thylakoid membranes in the dark that have three-to four fold excess mobility compared to membranes under high light conditions. Our analysis indicates that electron transfer between photosynthetic reaction centers and the associated electrochemical proton gradient across the thylakoid membrane result in a significant driving force for excess membrane dynamics. These observations provide a deeper understanding of the relationship between photosynthesis and cellular architecture.

  3. Dynamics of lipid transfer by phosphatidylinositol transfer proteins in cells.

    Science.gov (United States)

    Shadan, Sadaf; Holic, Roman; Carvou, Nicolas; Ee, Patrick; Li, Michelle; Murray-Rust, Judith; Cockcroft, Shamshad

    2008-09-01

    Of many lipid transfer proteins identified, all have been implicated in essential cellular processes, but the activity of none has been demonstrated in intact cells. Among these, phosphatidylinositol transfer proteins (PITP) are of particular interest as they can bind to and transfer phosphatidylinositol (PtdIns)--the precursor of important signalling molecules, phosphoinositides--and because they have essential functions in neuronal development (PITPalpha) and cytokinesis (PITPbeta). Structural analysis indicates that, in the cytosol, PITPs are in a 'closed' conformation completely shielding the lipid within them. But during lipid exchange at the membrane, they must transiently 'open'. To study PITP dynamics in intact cells, we chemically targeted their C95 residue that, although non-essential for lipid transfer, is buried within the phospholipid-binding cavity, and so, its chemical modification prevents PtdIns binding because of steric hindrance. This treatment resulted in entrapment of open conformation PITPs at the membrane and inactivation of the cytosolic pool of PITPs within few minutes. PITP isoforms were differentially inactivated with the dynamics of PITPbeta faster than PITPalpha. We identify two tryptophan residues essential for membrane docking of PITPs.

  4. The Cell Probe Complexity of Dynamic Range Counting

    DEFF Research Database (Denmark)

    Larsen, Kasper Green

    2012-01-01

    In this paper we develop a new technique for proving lower bounds on the update time and query time of dynamic data structures in the cell probe model. With this technique, we prove the highest lower bound to date for any explicit problem, namely a lower bound of tq = ((lg n/ lg(wtu))2). Here n...... is the number of update operations, w the cell size, tq the query time and tu the update time. In the most natural setting of cell size w = (lg n), this gives a lower bound of tq = ((lg n/ lg lg n)2) for any polylogarithmic update time. This bound is almost a quadratic improvement over the highest previous...... is specified by a point q = (x, y), and the goal is to report the sum of the weights assigned to the points dominated by q, where a point (x0, y0) is dominated by q if x0 x and y0 y. In addition to being the highest cell probe lower bound to date, our lower bound is also tight for data struc- tures with update...

  5. Dynamics of Red Cells in Spleen: How Does Vesiculation Happen?

    Science.gov (United States)

    Zhu, Qiang; Salehyar, Sara; Cabrales, Pedro; Asaro, Robert

    2016-11-01

    Vesiculation of red blood cells as a result of local separation between lipid bilayer and cytoskeleton is known to happen in vivo, most likely inside spleen where they sustain large mechanical loads during the passage through venus slits. There is, however, little knowledge about the detailed scenario and condition. We address this question via a fluid-cell interaction model by coupling a multiscale model of the cell membrane (including molecular details) with a fluid dynamics model based on boundary-integral equations. A numerical flow channel is created where the cell is driven through a narrow slit by pressure (imitating the transit through venus slits in spleen). The concentration is the occurrence of large dissociation (negative) pressure between the skeleton/membrane connection that promotes separation, a precursor of vesicle formation. Critical levels for the negative pressure are estimated using published data. By following the maximum range of pressure, we conclude that for vesiculation to happen there must be biochemical influences (e.g. binding of degraded haemoglobin) that significantly reduce effective attachment density. This is consistent with reported trends in vesiculation that are believed to occur in cases of various hereditary anemias and during blood storage. Our findings also suggest the criticality of understanding the biochemical phenomena involved with cytoskeleton/membrane attachment.

  6. Lipid signalling dynamics at the β-cell plasma membrane.

    Science.gov (United States)

    Wuttke, Anne

    2015-04-01

    Pancreatic β-cells are clustered in islets of Langerhans and secrete insulin in response to increased concentrations of circulating glucose. Insulin in turn acts on liver, muscle and fat tissue to store energy and normalize the blood glucose level. Inappropriate insulin release may lead to impaired glucose tolerance and diabetes. In addition to glucose, other nutrients, neural stimuli and hormonal stimuli control insulin secretion. Many of these signals are perceived at the plasma membrane, which is also the site where insulin granules undergo exocytosis. Therefore, it is not surprising that membrane lipids play an important role in the regulation of insulin secretion. β-cells release insulin in a pulsatile fashion. Signalling lipids integrate the nutrient and neurohormonal inputs to fine-tune, shape and co-ordinate the pulsatility. An important group of signalling lipids are phosphoinositides and their downstream messengers. This MiniReview will discuss new insights into lipid signalling dynamics in β-cells obtained from live-cell imaging experiments with fluorescent translocation biosensors. The plasma membrane concentration of several phosphoinositides and of their downstream messengers changes rapidly upon nutrient or neurohormonal stimulation. Glucose induces the most complex spatio-temporal patterns, typically involving oscillations of messenger concentrations, which sometimes are locally restricted. The tightly controlled levels of lipid messengers can mediate specific binding of downstream effectors to the plasma membrane, contributing to the appropriate regulation of insulin secretion.

  7. The Cell Probe Complexity of Dynamic Range Counting

    DEFF Research Database (Denmark)

    Larsen, Kasper Green

    2012-01-01

    In this paper we develop a new technique for proving lower bounds on the update time and query time of dynamic data structures in the cell probe model. With this technique, we prove the highest lower bound to date for any explicit problem, namely a lower bound of tq = ((lg n/ lg(wtu))2). Here n...... is the number of update operations, w the cell size, tq the query time and tu the update time. In the most natural setting of cell size w = (lg n), this gives a lower bound of tq = ((lg n/ lg lg n)2) for any polylogarithmic update time. This bound is almost a quadratic improvement over the highest previous...... is specified by a point q = (x, y), and the goal is to report the sum of the weights assigned to the points dominated by q, where a point (x0, y0) is dominated by q if x0 x and y0 y. In addition to being the highest cell probe lower bound to date, our lower bound is also tight for data struc- tures with update...

  8. Quantitative single cell analysis of cell population dynamics during submandibular salivary gland development and differentiation

    Directory of Open Access Journals (Sweden)

    Deirdre A. Nelson

    2013-04-01

    Epithelial organ morphogenesis involves reciprocal interactions between epithelial and mesenchymal cell types to balance progenitor cell retention and expansion with cell differentiation for evolution of tissue architecture. Underlying submandibular salivary gland branching morphogenesis is the regulated proliferation and differentiation of perhaps several progenitor cell populations, which have not been characterized throughout development, and yet are critical for understanding organ development, regeneration, and disease. Here we applied a serial multiplexed fluorescent immunohistochemistry technology to map the progressive refinement of the epithelial and mesenchymal cell populations throughout development from embryonic day 14 through postnatal day 20. Using computational single cell analysis methods, we simultaneously mapped the evolving temporal and spatial location of epithelial cells expressing subsets of differentiation and progenitor markers throughout salivary gland development. We mapped epithelial cell differentiation markers, including aquaporin 5, PSP, SABPA, and mucin 10 (acinar cells; cytokeratin 7 (ductal cells; and smooth muscle α-actin (myoepithelial cells and epithelial progenitor cell markers, cytokeratin 5 and c-kit. We used pairwise correlation and visual mapping of the cells in multiplexed images to quantify the number of single- and double-positive cells expressing these differentiation and progenitor markers at each developmental stage. We identified smooth muscle α-actin as a putative early myoepithelial progenitor marker that is expressed in cytokeratin 5-negative cells. Additionally, our results reveal dynamic expansion and redistributions of c-kit- and K5-positive progenitor cell populations throughout development and in postnatal glands. The data suggest that there are temporally and spatially discreet progenitor populations that contribute to salivary gland development and homeostasis.

  9. Simple and effective lumped mass models for determining kinetics and dynamics of car-to-car crashes

    NARCIS (Netherlands)

    Mooi, H.G.; Huibers, J.H.A.M.

    1998-01-01

    A simple two-mass-spring model was developed to describe the dynamics of car-to-car collisions. The characteristics of the spring in this model can be chosen as a piecewise linear function. The model was applied to determine the dynamics of a range of crashes and to compare the dynamics of a

  10. Fuel cell-based instrumentation for ethanol determination in alcoholic beverages, fermentations, and biofluids

    Energy Technology Data Exchange (ETDEWEB)

    Parry, K.W.

    1988-01-01

    The main aim of this project was to devise an alternative method for ethanol assay, employing an electrochemical fuel cell sensor. Thus, the early part of this thesis describes the work carried out in the development of a new analytical technique for this purpose. This work resulted in the production of a successful prototype unit which has led to the development of a commercial instrument, vis., the Lion Drinks Alcolmeter (DA-1) available from Lion Laboratories Ltd. The problem of determining the ethanol content of a fermenting liquor at any point during a fermentation process was also broached and a novel technique combining a flow dilution system, dynamic headspace analysis and a fuel cell sensor was developed. This procedure, suitably automated, will enable the ethanolic content of a fermenting beverage to be determined at any stage during a fermentation, the results obtained in this manner being in excellent agreement with those obtained gas chromatographically. Methods of extending the linear working range of a fuel cell-based sampling system are reported in the hope that the encouraging results obtained may initiate further progress in this field. Finally, the sensing system used in this work has also been utilized with an alternative sampling procedure for the determination of ethanol in biological fluids, mainly for clinical and forensic applications. This work has also led to the production of a commercial instrument, viz. the Lion AE-D3 Alcolmeter.

  11. Nanoscale live cell optical imaging of the dynamics of intracellular microvesicles in neural cells.

    Science.gov (United States)

    Lee, Sohee; Heo, Chaejeong; Suh, Minah; Lee, Young Hee

    2013-11-01

    Recent advances in biotechnology and imaging technology have provided great opportunities to investigate cellular dynamics. Conventional imaging methods such as transmission electron microscopy, scanning electron microscopy, and atomic force microscopy are powerful techniques for cellular imaging, even at the nanoscale level. However, these techniques have limitations applications in live cell imaging because of the experimental preparation required, namely cell fixation, and the innately small field of view. In this study, we developed a nanoscale optical imaging (NOI) system that combines a conventional optical microscope with a high resolution dark-field condenser (Cytoviva, Inc.) and halogen illuminator. The NOI system's maximum resolution for live cell imaging is around 100 nm. We utilized NOI to investigate the dynamics of intracellular microvesicles of neural cells without immunocytological analysis. In particular, we studied direct, active random, and moderate random dynamic motions of intracellular microvesicles and visualized lysosomal vesicle changes after treatment of cells with a lysosomal inhibitor (NH4Cl). Our results indicate that the NOI system is a feasible, high-resolution optical imaging system for live small organelles that does not require complicated optics or immunocytological staining processes.

  12. Climate Effects and Feedback Structure Determining Weed Population Dynamics in a Long-Term Experiment

    Science.gov (United States)

    Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis

    2012-01-01

    Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements. PMID:22272362

  13. Climate effects and feedback structure determining weed population dynamics in a long-term experiment.

    Science.gov (United States)

    Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis

    2012-01-01

    Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements.

  14. Climate effects and feedback structure determining weed population dynamics in a long-term experiment.

    Directory of Open Access Journals (Sweden)

    Mauricio Lima

    Full Text Available Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors. Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements.

  15. Towards wafer scale inductive determination of magnetostatic and dynamic parameters of magnetic thin films and multilayers

    CERN Document Server

    Sievers, Sibylle; Nass, Paul; Serrano-Guisan, Santiago; Pasquale, Massimo; Schumacher, Hans Werner

    2013-01-01

    We investigate an inductive probe head suitable for non-invasive characterization of the magnetostatic and dynamic parameters of magnetic thin films and multilayers on the wafer scale. The probe is based on a planar waveguide with rearward high frequency connectors that can be brought in close contact to the wafer surface. Inductive characterization of the magnetic material is carried out by vector network analyzer ferromagnetic resonance. Analysis of the field dispersion of the resonance allows the determination of key material parameters such as the saturation magnetization MS or the effective damping parameter Meff. Three waveguide designs are tested. The broadband frequency response is characterized and the suitability for inductive determination of MS and Meff is compared. Integration of such probes in a wafer prober could in the future allow wafer scale in-line testing of magnetostatic and dynamic key material parameters of magnetic thin films and multilayers.

  16. Determination of Inelastic Mean Free Path by Electron Holography Along with Electron Dynamic Calculation

    Institute of Scientific and Technical Information of China (English)

    王岩国; 刘红荣; 杨奇斌; 张泽

    2003-01-01

    Off-axis electron holography in a field emission gun transmission-electron microscope and electron dynamic calculation are used to determine the absorption coefficient and inelastic mean free path (IMFP) of copper.Dependence of the phase shift of the exit electron wave on the specimen thickness is established by electron dynamic simulation. The established relationship makes it possible to determine the specimen thickness with the calculated phase shift by match of the phase shift measured in the reconstructed phase image. Based on the measured amplitudes in reconstructed exit electron wave and reference wave in the vacuum, the examined IMFP of electron with energy of 200kV in Cu is obtained to be 96nm.

  17. Stable morphology, but dynamic internal reorganisation, of interphase human chromosomes in living cells.

    Directory of Open Access Journals (Sweden)

    Iris Müller

    Full Text Available Despite the distinctive structure of mitotic chromosomes, it has not been possible to visualise individual chromosomes in living interphase cells, where chromosomes spend over 90% of their time. Studies of interphase chromosome structure and dynamics use fluorescence in-situ hybridisation (FISH on fixed cells, which potentially damages structure and loses dynamic information. We have developed a new methodology, involving photoactivation of labelled histone H3 at mitosis, to visualise individual and specific human chromosomes in living interphase cells. Our data revealed bulk chromosome volume and morphology are established rapidly after mitosis, changing only incrementally after the first hour of G1. This contrasted with the behaviour of specific loci on labelled chromosomes, which showed more progressive reorganisation, and revealed that "looping out" of chromatin from chromosome territories is a dynamic state. We measured considerable heterogeneity in chromosome decondensation, even between sister chromatids, which may reflect local structural impediments to decondensation and could potentially amplify transcriptional noise. Chromosome structure showed tremendous resistance to inhibitors of transcription, histone deacetylation and chromatin remodelling. Together, these data indicate steric constraints determine structure, rather than innate chromosome architecture or function-driven anchoring, with interphase chromatin organisation governed primarily by opposition between needs for decondensation and the space available for this to happen.

  18. A model of calcium signaling and degranulation dynamics induced by laser irradiation in mast cells

    Institute of Scientific and Technical Information of China (English)

    SHI XiaoMin; ZHENG YuFan; LIU ZengRong; YANG WenZhong

    2008-01-01

    Recent experiments show that calcium signaling and degranulation dynamics induced by low power laser irradiation in mast cells must rely on extracellular Ca2+ influx. An analytical expression of Ca2+ flux through TRPV4 cation channel in response to interaction of laser photon energy and extracellular Ca2+ is deduced, and a model characterizing dynamics of calcium signaling and degranulation activated by laser irradiation in mast cells is established. The model indicates that the characteristics of calcium signaling and degranulation dynamics are determined by interaction between laser photon energy and Ca2+ influx. Extracellular Ca2+ concentration is so high that even small photon energy can activate mast cells, thus avoiding the possible injury caused by laser irradiation with shorter wavelengths. The model predicts that there exists a narrow parameter domain of photon energy and extracellular Ca2+ concentration of which results in cytosolic Ca2+ limit cycle oscillations, and shows that PKC activity is in direct proportion to the frequency of Ca2+ oscillations. With the model it is found that sustained and stable maximum plateau of cytosolic Ca2+ concentration can get optimal degranulation rate. Furthermore, the idea of introducing the realistic physical energy into model is applicable to modeling other physical signal transduction systems.

  19. Hoxb1b controls oriented cell division, cell shape and microtubule dynamics in neural tube morphogenesis.

    Science.gov (United States)

    Zigman, Mihaela; Laumann-Lipp, Nico; Titus, Tom; Postlethwait, John; Moens, Cecilia B

    2014-02-01

    Hox genes are classically ascribed to function in patterning the anterior-posterior axis of bilaterian animals; however, their role in directing molecular mechanisms underlying morphogenesis at the cellular level remains largely unstudied. We unveil a non-classical role for the zebrafish hoxb1b gene, which shares ancestral functions with mammalian Hoxa1, in controlling progenitor cell shape and oriented cell division during zebrafish anterior hindbrain neural tube morphogenesis. This is likely distinct from its role in cell fate acquisition and segment boundary formation. We show that, without affecting major components of apico-basal or planar cell polarity, Hoxb1b regulates mitotic spindle rotation during the oriented neural keel symmetric mitoses that are required for normal neural tube lumen formation in the zebrafish. This function correlates with a non-cell-autonomous requirement for Hoxb1b in regulating microtubule plus-end dynamics in progenitor cells in interphase. We propose that Hox genes can influence global tissue morphogenesis by control of microtubule dynamics in individual cells in vivo.

  20. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.

    Science.gov (United States)

    Trapnell, Cole; Cacchiarelli, Davide; Grimsby, Jonna; Pokharel, Prapti; Li, Shuqiang; Morse, Michael; Lennon, Niall J; Livak, Kenneth J; Mikkelsen, Tarjei S; Rinn, John L

    2014-04-01

    Defining the transcriptional dynamics of a temporal process such as cell differentiation is challenging owing to the high variability in gene expression between individual cells. Time-series gene expression analyses of bulk cells have difficulty distinguishing early and late phases of a transcriptional cascade or identifying rare subpopulations of cells, and single-cell proteomic methods rely on a priori knowledge of key distinguishing markers. Here we describe Monocle, an unsupervised algorithm that increases the temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points. Applied to the differentiation of primary human myoblasts, Monocle revealed switch-like changes in expression of key regulatory factors, sequential waves of gene regulation, and expression of regulators that were not known to act in differentiation. We validated some of these predicted regulators in a loss-of function screen. Monocle can in principle be used to recover single-cell gene expression kinetics from a wide array of cellular processes, including differentiation, proliferation and oncogenic transformation.

  1. Cell receptor and surface ligand density effects on dynamic states of adhering circulating tumor cells.

    Science.gov (United States)

    Zheng, Xiangjun; Cheung, Luthur Siu-Lun; Schroeder, Joyce A; Jiang, Linan; Zohar, Yitshak

    2011-10-21

    Dynamic states of cancer cells moving under shear flow in an antibody-functionalized microchannel are investigated experimentally and theoretically. The cell motion is analyzed with the aid of a simplified physical model featuring a receptor-coated rigid sphere moving above a solid surface with immobilized ligands. The motion of the sphere is described by the Langevin equation accounting for the hydrodynamic loadings, gravitational force, receptor-ligand bindings, and thermal fluctuations; the receptor-ligand bonds are modeled as linear springs. Depending on the applied shear flow rate, three dynamic states of cell motion have been identified: (i) free motion, (ii) rolling adhesion, and (iii) firm adhesion. Of particular interest is the fraction of captured circulating tumor cells, defined as the capture ratio, via specific receptor-ligand bonds. The cell capture ratio decreases with increasing shear flow rate with a characteristic rate. Based on both experimental and theoretical results, the characteristic flow rate increases monotonically with increasing either cell-receptor or surface-ligand density within certain ranges. Utilizing it as a scaling parameter, flow-rate dependent capture ratios for various cell-surface combinations collapse onto a single curve described by an exponential formula.

  2. ULTRASTRUCTURAL CHANGES OF THYROTROPIC CELLS IN THE DYNAMICS OF EXPERIMENTAL IMMUNOSTIMULATION

    Directory of Open Access Journals (Sweden)

    Inessa Bobrysheva

    2013-06-01

    Full Text Available The endocrine and immune systems are interrelated via a bidirectional network.Thyroid-stimulating hormone plays a critical role as an endogenous mediator of immune activity. Purpose of study was to determine the dynamics of changes of thyrotropic cells ultrastructure in modeling immunostimulation in mature male rats by subcutaneous injection of imunofan in a dosage 0,7 mg/kg of body weight.The pituitary samples were taken on 1st, 7th, 15th, 30th and 60th, day after treatment and thenfixed in glutaraldehyde for electron microscope. The study showed theincrease of functional activity of the thyrotropic cells. The significant increase of areas of the cells and their nuclei, area of mitochondria and secretory granules was established since 7th day after imunofan treatment.

  3. Dynamics of red blood cells and vesicles in microchannels of oscillating width.

    Science.gov (United States)

    Braunmüller, S; Schmid, L; Franke, T

    2011-05-11

    We have studied the dynamics of red blood cells and fluid lipid vesicles in hydrodynamic flow fields created by microchannels with periodically varying channel width. For red blood cells we find a transition from a regime with oscillating tilt angle and fixed shape to a regime with oscillating shape with increasing flow velocity. We have determined the crossover to occur at a critical ratio L(y)/v(m) ≈ 2.2 × 10⁻³ s with channel width L(y) and red blood cell velocity v(m). These oscillations are superposed by shape transitions from a discocyte to a slipper shape at low velocities and a slipper to parachute transition at high flow velocities.

  4. Cell differentiation versus cell death: extracellular glucose is a key determinant of cell fate following oxidative stress exposure

    OpenAIRE

    Poulsen, R C; Knowles, H.J.; Carr, A. J.; HULLEY, P. A.

    2014-01-01

    Cells, particularly mechano-sensitive musculoskeletal cells such as tenocytes, routinely encounter oxidative stress. Oxidative stress can not only stimulate tissue repair, but also cause damage leading to tissue degeneration. As diabetes is associated with increased oxidative damage as well as increased risk of tendon degeneration, the aim of this study was to determine if extracellular glucose levels alter the response of tendon cells to oxidative stress. Primary human tenocytes were culture...

  5. Specific determination of benzene in urine using dynamic headspace and mass-selective detection.

    Science.gov (United States)

    Ljungkvist, G; Lärstad, M; Mathiasson, L

    1999-01-08

    A method for the determination of benzene in urine was developed, based on dynamic headspace and preconcentration of the analyte on a solid sorbent. The subsequent analysis by thermal desorption of the sorbent, capillary gas chromatography and mass-selective detection ascertained a low limit of detection (6.5 ng/l) and a highly specific determination. The limit of detection is an order of magnitude lower than that reported earlier and allows reliable quantitation of occupational exposure and of most environmental exposures. Samples could be stored frozen for at least a month without significant loss.

  6. Factors determining the diurnal dynamics of blooming of chosen plant species

    Directory of Open Access Journals (Sweden)

    Bożena Denisow

    2012-12-01

    Full Text Available The paper attempts to synthesize the determinants which may influence the diurnal rhythm of blooming. Additionally, I tried to explore and bring together topics that concern blooming and have always been considered separately because of their origin in different disciplines. The following species were included: Hydrangea arborescens L. subsp. discolor (Raf., H. paniculata Sieb., Viburnum opulus L., Chaenomeles japonica Lindl., Knautia arvensis L., Adonis vernalis L., Aster saggitifolius Willd., Taraxacum officinale L. Chelidonium majus L. The taxons were observed in Lublin (51008' - 51018' N and 21027' - 21041' E in the years 2001-2007. The blooming of species was determined at least for two vegetation seasons. During observations all flowers developed in one-hour intervals were counted. The diurnal dynamics of blooming differs among species and is modified by different endogenous and exogenous factors. The endogenous determinants of diurnal dynamics of blooming are morphological diversity of flowers (fertility or sterility within species or heterostyly. The different pattern of blooming succour different mechanisms which prevent self-pollination (Chaenomeles japonica Lindl., Knautia arvensis L.. The abiotic factors, such as day length and temperature during the vegetation season, influence the change in the process of diurnal dynamics of blooming (e. g. Taraxacum officinale, Chelidonium majus.

  7. Determination of Water Diffusion Coefficients and Dynamics in Adhesive/ Carbon Fiber Reinforced Epoxy Resin Composite Joints

    Institute of Scientific and Technical Information of China (English)

    WANG Chao; WANG Zhi; WANG Jing; SU Tao

    2007-01-01

    To determinate the water diffusion coefficients and dynamics in adhesive/carbon fiber reinforced epoxy resin composite joints, energy dispersive X-ray spectroscopy analysis(EDX) is used to establish the content change of oxygen in the adhesive in adhesive/carbon fiber reinforced epoxy resin composite joints. As water is made up of oxygen and hydrogen, the water diffusion coefficients and dynamics in adhesive/carbon fiber reinforced epoxy resin composite joints can be obtained from the change in the content of oxygen in the adhesive during humidity aging, via EDX analysis. The authors have calculated the water diffusion coefficients and dynamics in the adhesive/carbon fiber reinforced epoxy resin composite joints with the aid of both energy dispersive X-ray spectroscopy and elemental analysis. The determined results with EDX analysis are almost the same as those determined with elemental analysis and the results also show that the durability of the adhesive/carbon fiber reinforced epoxy resin composite joints subjected to silane coupling agent treatment is better than those subjected to sand paper burnishing treatment and chemical oxidation treatment.

  8. Determining dynamical parameters of the Milky Way Galaxy based on high-accuracy radio astrometry

    Science.gov (United States)

    Honma, Mareki; Nagayama, Takumi; Sakai, Nobuyuki

    2015-08-01

    In this paper we evaluate how the dynamical structure of the Galaxy can be constrained by high-accuracy VLBI (Very Long Baseline Interferometry) astrometry such as VERA (VLBI Exploration of Radio Astrometry). We generate simulated samples of maser sources which follow the gas motion caused by a spiral or bar potential, with their distribution similar to those currently observed with VERA and VLBA (Very Long Baseline Array). We apply the Markov chain Monte Carlo analyses to the simulated sample sources to determine the dynamical parameter of the models. We show that one can successfully determine the initial model parameters if astrometric results are obtained for a few hundred sources with currently achieved astrometric accuracy. If astrometric data are available from 500 sources, the expected accuracy of R0 and Θ0 is ˜ 1% or higher, and parameters related to the spiral structure can be constrained by an error of 10% or with higher accuracy. We also show that the parameter determination accuracy is basically independent of the locations of resonances such as corotation and/or inner/outer Lindblad resonances. We also discuss the possibility of model selection based on the Bayesian information criterion (BIC), and demonstrate that BIC can be used to discriminate different dynamical models of the Galaxy.

  9. Use of Direct Dynamics Simulations to Determine Unimolecular Reaction Paths and Arrhenius Parameters for Large Molecules.

    Science.gov (United States)

    Yang, Li; Sun, Rui; Hase, William L

    2011-11-08

    In a previous study (J. Chem. Phys.2008, 129, 094701) it was shown that for a large molecule, with a total energy much greater than its barrier for decomposition and whose vibrational modes are harmonic oscillators, the expressions for the classical Rice-Ramsperger-Kassel-Marcus (RRKM) (i.e., RRK) and classical transition-state theory (TST) rate constants become equivalent. Using this relationship, a molecule's unimolecular rate constants versus temperature may be determined from chemical dynamics simulations of microcanonical ensembles for the molecule at different total energies. The simulation identifies the molecule's unimolecular pathways and their Arrhenius parameters. In the work presented here, this approach is used to study the thermal decomposition of CH3-NH-CH═CH-CH3, an important constituent in the polymer of cross-linked epoxy resins. Direct dynamics simulations, at the MP2/6-31+G* level of theory, were used to investigate the decomposition of microcanonical ensembles for this molecule. The Arrhenius A and Ea parameters determined from the direct dynamics simulation are in very good agreement with the TST Arrhenius parameters for the MP2/6-31+G* potential energy surface. The simulation method applied here may be particularly useful for large molecules with a multitude of decomposition pathways and whose transition states may be difficult to determine and have structures that are not readily obvious.

  10. Cell wall dynamics modulate acetic acid-induced apoptotic cell death of Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    António Rego

    2014-08-01

    Full Text Available Acetic acid triggers apoptotic cell death in Saccharomyces cerevisiae, similar to mammalian apoptosis. To uncover novel regulators of this process, we analyzed whether impairing MAPK signaling affected acetic acid-induced apoptosis and found the mating-pheromone response and, especially, the cell wall integrity pathways were the major mediators, especially the latter, which we characterized further. Screening downstream effectors of this pathway, namely targets of the transcription factor Rlm1p, highlighted decreased cell wall remodeling as particularly important for acetic acid resistance. Modulation of cell surface dynamics therefore emerges as a powerful strategy to increase acetic acid resistance, with potential application in industrial fermentations using yeast, and in biomedicine to exploit the higher sensitivity of colorectal carcinoma cells to apoptosis induced by acetate produced by intestinal propionibacteria.

  11. Cell wall dynamics modulate acetic acid-induced apoptotic cell death of Saccharomyces cerevisiae

    Science.gov (United States)

    Rego, António; Duarte, Ana M.; Azevedo, Flávio; Sousa, Maria J.; Côrte-Real, Manuela; Chaves, Susana R.

    2014-01-01

    Acetic acid triggers apoptotic cell death in Saccharomyces cerevisiae, similar to mammalian apoptosis. To uncover novel regulators of this process, we analyzed whether impairing MAPK signaling affected acetic acid-induced apoptosis and found the mating-pheromone response and, especially, the cell wall integrity pathways were the major mediators, especially the latter, which we characterized further. Screening downstream effectors of this pathway, namely targets of the transcription factor Rlm1p, highlighted decreased cell wall remodeling as particularly important for acetic acid resistance. Modulation of cell surface dynamics therefore emerges as a powerful strategy to increase acetic acid resistance, with potential application in industrial fermentations using yeast, and in biomedicine to exploit the higher sensitivity of colorectal carcinoma cells to apoptosis induced by acetate produced by intestinal propionibacteria. PMID:28357256

  12. Sox17-Mediated XEN Cell Conversion Identifies Dynamic Networks Controlling Cell-Fate Decisions in Embryo-Derived Stem Cells

    Directory of Open Access Journals (Sweden)

    Angela C.H. McDonald

    2014-10-01

    Full Text Available Little is known about the gene regulatory networks (GRNs distinguishing extraembryonic endoderm (ExEn stem (XEN cells from those that maintain the extensively characterized embryonic stem cell (ESC. An intriguing network candidate is Sox17, an essential transcription factor for XEN derivation and self-renewal. Here, we show that forced Sox17 expression drives ESCs toward ExEn, generating XEN cells that contribute to ExEn when placed back into early mouse embryos. Transient Sox17 expression is sufficient to drive this fate change during which time cells transit through distinct intermediate states prior to the generation of functional XEN-like cells. To orchestrate this conversion process, Sox17 acts in autoregulatory and feedforward network motifs, regulating dynamic GRNs directing cell fate. Sox17-mediated XEN conversion helps to explain the regulation of cell-fate changes and reveals GRNs regulating lineage decisions in the mouse embryo.

  13. Prevention of cytotoxic T cell escape using a heteroclitic subdominant viral T cell determinant.

    Directory of Open Access Journals (Sweden)

    Noah S Butler

    2008-10-01

    Full Text Available High affinity antigen-specific T cells play a critical role during protective immune responses. Epitope enhancement can elicit more potent T cell responses and can subsequently lead to a stronger memory pool; however, the molecular basis of such enhancement is unclear. We used the consensus peptide-binding motif for the Major Histocompatibility Complex molecule H-2K(b to design a heteroclitic version of the mouse hepatitis virus-specific subdominant S598 determinant. We demonstrate that a single amino acid substitution at a secondary anchor residue (Q to Y at position 3 increased the stability of the engineered determinant in complex with H-2K(b. The structural basis for this enhanced stability was associated with local alterations in the pMHC conformation as a result of the Q to Y substitution. Recombinant viruses encoding this engineered determinant primed CTL responses that also reacted to the wildtype epitope with significantly higher functional avidity, and protected against selection of virus mutated at a second CTL determinant and consequent disease progression in persistently infected mice. Collectively, our findings provide a basis for the enhanced immunogenicity of an engineered determinant that will serve as a template for guiding the development of heteroclitic T cell determinants with applications in prevention of CTL escape in chronic viral infections as well as in tumor immunity.

  14. Natural biased coin encoded in the genome determines cell strategy.

    Science.gov (United States)

    Dorri, Faezeh; Mahini, Hamid; Sharifi-Zarchi, Ali; Totonchi, Mehdi; Tusserkani, Ruzbeh; Pezeshk, Hamid; Sadeghi, Mehdi

    2014-01-01

    Decision making at a cellular level determines different fates for isogenic cells. However, it is not yet clear how rational decisions are encoded in the genome, how they are transmitted to their offspring, and whether they evolve and become optimized throughout generations. In this paper, we use a game theoretic approach to explain how rational decisions are made in the presence of cooperators and competitors. Our results suggest the existence of an internal switch that operates as a biased coin. The biased coin is, in fact, a biochemical bistable network of interacting genes that can flip to one of its stable states in response to different environmental stimuli. We present a framework to describe how the positions of attractors in such a gene regulatory network correspond to the behavior of a rational player in a competing environment. We evaluate our model by considering lysis/lysogeny decision making of bacteriophage lambda in E. coli.

  15. Natural biased coin encoded in the genome determines cell strategy.

    Directory of Open Access Journals (Sweden)

    Faezeh Dorri

    Full Text Available Decision making at a cellular level determines different fates for isogenic cells. However, it is not yet clear how rational decisions are encoded in the genome, how they are transmitted to their offspring, and whether they evolve and become optimized throughout generations. In this paper, we use a game theoretic approach to explain how rational decisions are made in the presence of cooperators and competitors. Our results suggest the existence of an internal switch that operates as a biased coin. The biased coin is, in fact, a biochemical bistable network of interacting genes that can flip to one of its stable states in response to different environmental stimuli. We present a framework to describe how the positions of attractors in such a gene regulatory network correspond to the behavior of a rational player in a competing environment. We evaluate our model by considering lysis/lysogeny decision making of bacteriophage lambda in E. coli.

  16. Using weigh-in-motion data to determine bridge dynamic amplification factor

    Directory of Open Access Journals (Sweden)

    Kalin Jan

    2015-01-01

    Full Text Available The dynamic component of bridge traffic loading is commonly taken into account with a Dynamic Amplification Factor (DAF – the ratio between the maximum dynamic and static load effects on a bridge. In the design codes, this factor is generally higher than in reality. While this is fine for new bridges that must account for various risks during their life-time, it imposes unnecessary conservativism into assessment of the existing well defined bridges. Therefore, analysis of existing bridges should apply more realistic DAF values. One way of obtaining them experimentally is by bridge weigh-in-motion (B-WIM measurements, which use an existing instrumented bridge or culvert to weigh all crossing vehicles at highway speeds. The B-WIM system had been equipped with two methods of obtaining an approximation to the static response of the. The first method uses the sum of influence lines. This method relies on accurate axle identification, the failure of which can have a large influence on the DAF value. The other method uses a pre-determined low-pass filter to remove the dynamic component of the measured signal; however an expert is needed to set the filter parameters. A new approach that tries to eliminate these two drawbacks has been developed. In this approach the parameters for the filter are determined automatically by fitting the filtered response to the sum of the influence lines. The measurement of DAF on a typical bridge site agrees with experiments performed in the ARCHES [1] project: dynamic amplification decreases as static loading increases.

  17. Intermediate regime and a phase diagram of red blood cell dynamics in a linear flow

    Science.gov (United States)

    Levant, Michael; Steinberg, Victor

    2016-12-01

    In this paper we investigate the in vitro dynamics of a single rabbit red blood cell (RBC) in a planar linear flow as a function of a shear stress σ and the dynamic viscosity of outer fluid ηo. A linear flow is a generalization of previous studies dynamics of soft objects including RBC in shear flow and is realized in the experiment in a microfluidic four-roll mill device. We verify that the RBC stable orientation dynamics is found in the experiment being the in-shear-plane orientation and the RBC dynamics is characterized by observed three RBC dynamical states, namely tumbling (TU), intermediate (INT), and swinging (SW) [or tank-treading (TT)] on a single RBC. The main results of these studies are the following. (i) We completely characterize the RBC dynamical states and reconstruct their phase diagram in the case of the RBC in-shear-plane orientation in a planar linear flow and find it in a good agreement with that obtained in early experiments in a shear flow for human RBCs. (ii) The value of the critical shear stress σc of the TU-TT(SW) transition surprisingly coincides with that found in early experiments in spite of a significant difference in the degree of RBC shape deformations in both the SW and INT states. (iii) We describe the INT regime, which is stationary, characterized by strong RBC shape deformations and observed in a wide range of the shear stresses. We argue that our observations cast doubts on the main claim of the recent numerical simulations that the only RBC spheroidal stress-free shape is capable to explain the early experimental data. Finally, we suggest that the amplitude dependence of both θ and the shape deformation parameter D on σ can be used as the quantitative criterion to determine the RBC stress-free shape.

  18. Calcium dynamics in the secretory granules of neuroendocrine cells.

    Science.gov (United States)

    Alvarez, Javier

    2012-01-01

    Cellular Ca(2+)signaling results from a complex interplay among a variety of Ca(2+) fluxes going across the plasma membrane and across the membranes of several organelles, together with the buffering effect of large numbers of Ca(2+)-binding sites distributed along the cell architecture. Endoplasmic and sarcoplasmic reticulum, mitochondria and even nucleus have all been involved in cellular Ca(2+) signaling, and the mechanisms for Ca(2+) uptake and release from these organelles are well known. In neuroendocrine cells, the secretory granules also constitute a very important Ca(2+)-storing organelle, and the possible role of the stored Ca(2+) as a trigger for secretion has attracted considerable attention. However, this possibility is frequently overlooked, and the main reason for that is that there is still considerable uncertainty on the main questions related with granular Ca(2+) dynamics, e.g., the free granular [Ca(2+)], the physical state of the stored Ca(2+) or the mechanisms for Ca(2+) accumulation and release from the granules. This review will give a critical overview of the present state of knowledge and the main conflicting points on secretory granule Ca(2+) homeostasis in neuroendocrine cells.

  19. The Cell Probe Complexity of Dynamic Range Counting

    CERN Document Server

    Larsen, Kasper Green

    2011-01-01

    In this paper we develop a new technique for proving dynamic cell probe lower bounds. With this technique, we achieve the highest lower bound to date for any explicit problem, namely a lower bound of $t_q=\\Omega((\\lg n/\\lg(wt_u))^2)$. Here $n$ is the number of update operations, $w$ the cell size, $t_q$ the query time and $t_u$ the update time. In the most natural setting of cell size $w=\\Theta(\\lg n)$, this gives a lower bound of $t_q=\\Omega((\\lg n/\\lg \\lg n)^2)$ for any polylogarithmic update time. This bound is almost a quadratic improvement over the highest previous lower bound of $\\Omega(\\lg n)$, due to P\\v{a}tra\\c{s}cu and Demaine [SICOMP'06]. We prove our lower bound for the fundamental problem of weighted orthogonal range counting. In this problem, we are to support insertions of two-dimensional points, each assigned a $\\Theta(\\lg n)$-bit integer weight. A query to this problem is specified by a point $q=(x,y)$, and the goal is to report the sum of the weights assigned to the points dominated by $q$, ...

  20. Dynamic modeling, experimental evaluation, optimal design and control of integrated fuel cell system and hybrid energy systems for building demands

    Science.gov (United States)

    Nguyen, Gia Luong Huu

    obtained experimental data, the research studied the control of airflow to regulate the temperature of reactors within the fuel processor. The dynamic model provided a platform to test the dynamic response for different control gains. With sufficient sensing and appropriate control, a rapid response to maintain the temperature of the reactor despite an increase in power was possible. The third part of the research studied the use of a fuel cell in conjunction with photovoltaic panels, and energy storage to provide electricity for buildings. This research developed an optimization framework to determine the size of each device in the hybrid energy system to satisfy the electrical demands of buildings and yield the lowest cost. The advantage of having the fuel cell with photovoltaic and energy storage was the ability to operate the fuel cell at baseload at night, thus reducing the need for large battery systems to shift the solar power produced in the day to the night. In addition, the dispatchability of the fuel cell provided an extra degree of freedom necessary for unforeseen disturbances. An operation framework based on model predictive control showed that the method is suitable for optimizing the dispatch of the hybrid energy system.

  1. Dynamical modeling of the cell cycle and cell fate emergence in Caulobacter crescentus.

    Directory of Open Access Journals (Sweden)

    César Quiñones-Valles

    Full Text Available The division of Caulobacter crescentus, a model organism for studying cell cycle and differentiation in bacteria, generates two cell types: swarmer and stalked. To complete its cycle, C. crescentus must first differentiate from the swarmer to the stalked phenotype. An important regulator involved in this process is CtrA, which operates in a gene regulatory network and coordinates many of the interactions associated to the generation of cellular asymmetry. Gaining insight into how such a differentiation phenomenon arises and how network components interact to bring about cellular behavior and function demands mathematical models and simulations. In this work, we present a dynamical model based on a generalization of the Boolean abstraction of gene expression for a minimal network controlling the cell cycle and asymmetric cell division in C. crescentus. This network was constructed from data obtained from an exhaustive search in the literature. The results of the simulations based on our model show a cyclic attractor whose configurations can be made to correspond with the current knowledge of the activity of the regulators participating in the gene network during the cell cycle. Additionally, we found two point attractors that can be interpreted in terms of the network configurations directing the two cell types. The entire network is shown to be operating close to the critical regime, which means that it is robust enough to perturbations on dynamics of the network, but adaptable to environmental changes.

  2. Dynamical modeling of the cell cycle and cell fate emergence in Caulobacter crescentus.

    Science.gov (United States)

    Quiñones-Valles, César; Sánchez-Osorio, Ismael; Martínez-Antonio, Agustino

    2014-01-01

    The division of Caulobacter crescentus, a model organism for studying cell cycle and differentiation in bacteria, generates two cell types: swarmer and stalked. To complete its cycle, C. crescentus must first differentiate from the swarmer to the stalked phenotype. An important regulator involved in this process is CtrA, which operates in a gene regulatory network and coordinates many of the interactions associated to the generation of cellular asymmetry. Gaining insight into how such a differentiation phenomenon arises and how network components interact to bring about cellular behavior and function demands mathematical models and simulations. In this work, we present a dynamical model based on a generalization of the Boolean abstraction of gene expression for a minimal network controlling the cell cycle and asymmetric cell division in C. crescentus. This network was constructed from data obtained from an exhaustive search in the literature. The results of the simulations based on our model show a cyclic attractor whose configurations can be made to correspond with the current knowledge of the activity of the regulators participating in the gene network during the cell cycle. Additionally, we found two point attractors that can be interpreted in terms of the network configurations directing the two cell types. The entire network is shown to be operating close to the critical regime, which means that it is robust enough to perturbations on dynamics of the network, but adaptable to environmental changes.

  3. Cell proliferation dynamics and morphological differentiation during regeneration in Dorvillea bermudensis (Polychaeta, Dorvilleidae).

    Science.gov (United States)

    Paulus, Tanja; Müller, Monika C M

    2006-04-01

    Although some species of Annelida have an enormous capacity to regenerate, it is not yet known whether reestablishment of lost body parts is performed by stem cells, depends on preceding dedifferentiation of somatic cells, or is a combination of both. In order to clarify how, in the case of epimorphic regeneration, the blastemas are formed, we applied the thymidine analog 5'-bromo-2'-deoxyuridine (BrdU) in the dorvilleid polychaete Dorvillea bermudensis to identify cells in the S-phase of the cell cycle. Regeneration pulse-chase experiments were carried out to determine onset and dynamics of the proliferation process, and BrdU pulse-chase experiments were undertaken to follow cell fate. We found irregularly distributed S-phase cells throughout the body of adult specimens. Subsequent to amputation, these cells do not migrate from the amputee towards the wound site, where proliferation activity was documented no earlier than 16 h after fragmentation. In the initial phase, the proliferation rate at the anterior end exceeds the rate at the posterior end. Observance of identity could be demonstrated for the ectoderm and can be assumed for the two other germ layers. The anterior blastema transforms into the head, while the posterior forms the pygidium and persists as a proliferation zone; four or numerous segments are formed by intercalation between the former anterior or posterior blastema and the amputee.

  4. Btbd7 is essential for region-specific epithelial cell dynamics and branching morphogenesis in vivo

    DEFF Research Database (Denmark)

    Daley, William P; Matsumoto, Kazue; Doyle, Andrew D

    2017-01-01

    Branching morphogenesis of developing organs requires coordinated but poorly understood changes in epithelial cell-cell adhesion and cell motility. We report that Btbd7 is a crucial regulator of branching morphogenesis in vivo. Btbd7 levels are elevated in peripheral cells of branching epithelial...... end buds, where it enhances cell motility and cell-cell adhesion dynamics. Genetic ablation of Btbd7 in mice disrupts branching morphogenesis of salivary gland, lung, and kidney. Btbd7 knockout results in more tightly packed outer bud cells, which display stronger E-cadherin localization, reduced cell...... motility, and decreased dynamics of transient cell separations associated with cleft formation; inner bud cells remain unaffected. Mechanistic analyses using in vitro MDCK cells to mimic outer bud cell behavior establish that Btbd7 promotes loss of E-cadherin from cell-cell adhesions with enhanced...

  5. Dynamics of Human Telomerase Holoenzyme Assembly and Subunit Exchange across the Cell Cycle.

    Science.gov (United States)

    Vogan, Jacob M; Collins, Kathleen

    2015-08-28

    Human telomerase acts on telomeres during the genome synthesis phase of the cell cycle, accompanied by its concentration in Cajal bodies and transient colocalization with telomeres. Whether the regulation of human telomerase holoenzyme assembly contributes to the cell cycle restriction of telomerase function is unknown. We investigated the steady-state levels, assembly, and exchange dynamics of human telomerase subunits with quantitative in vivo cross-linking and other methods. We determined the physical association of telomerase subunits in cells blocked or progressing through the cell cycle as synchronized by multiple protocols. The total level of human telomerase RNA (hTR) was invariant across the cell cycle. In vivo snapshots of telomerase holoenzyme composition established that hTR remains bound to human telomerase reverse transcriptase (hTERT) throughout all phases of the cell cycle, and subunit competition assays suggested that hTERT-hTR interaction is not readily exchangeable. In contrast, the telomerase holoenzyme Cajal body-associated protein, TCAB1, was released from hTR in mitotic cells coincident with TCAB1 delocalization from Cajal bodies. This telomerase holoenzyme disassembly was reversible with cell cycle progression without any change in total TCAB1 protein level. Consistent with differential cell cycle regulation of hTERT-hTR and TCAB1-hTR protein-RNA interactions, overexpression of hTERT or TCAB1 had limited if any influence on hTR assembly of the other subunit. Overall, these findings revealed a cell cycle regulation that disables human telomerase association with telomeres while preserving the co-folded hTERT-hTR ribonucleoprotein catalytic core. Studies here, integrated with previous work, led to a unifying model for telomerase subunit assembly and trafficking in human cells.

  6. Factors influencing the determination of cell traction forces.

    Science.gov (United States)

    Zündel, Manuel; Ehret, Alexander E; Mazza, Edoardo

    2017-01-01

    Methods summarized by the term Traction Force Microscopy are widely used to quantify cellular forces in mechanobiological studies. These methods are inverse, in the sense that forces must be determined such that they comply with a measured displacement field. This study investigates how several experimental and analytical factors, originating in the realization of the experiments and the procedures for the analysis, affect the determined traction forces. The present results demonstrate that even for very high resolution measurements free of noise, traction forces can be significantly underestimated, while traction peaks are typically overestimated by 50% or more, even in the noise free case. Compared to this errors, which are inherent to the nature of the mechanical problem and its discretization, the effect of ignoring the out-of-plane displacement component, the interpolation scheme used between the discrete measurement points and the disregard of the geometrical non-linearities when using a nearly linear substrate material are less consequential. Nevertheless, a nonlinear elastic substrate, with strain-stiffening response and some degree of compressibility, can substantially improve the robustness of the reconstruction of traction forces over a wide range of magnitudes. This poses the need for a correct mechanical representation of these non-linearities during the traction reconstruction and a correct mechanical characterization of the substrate itself, especially for the large strain shear domain which is shown to plays a major role in the deformations induced by cells.

  7. Determination of thermal/dynamic characteristics of lava flow from surface thermal measurements

    Science.gov (United States)

    Ismail-Zadeh, Alik; Melnik, Oleg; Korotkii, Alexander; Tsepelev, Igor; Kovtunov, Dmitry

    2016-04-01

    Rapid development of ground based thermal cameras, drones and satellite data allows getting repeated thermal images of the surface of the lava flow. Available instrumentation allows getting a large amount of data during a single lava flow eruption. These data require development of appropriate quantitative techniques to link subsurface dynamics with observations. We present a new approach to assimilation of thermal measurements at lava's surface to the bottom of the lava flow to determine lava's thermal and dynamic characteristics. Mathematically this problem is reduced to solving an inverse boundary problem. Namely, using known conditions at one part of the model boundary we determine the missing condition at the remaining part of the boundary. Using an adjoint method we develop a numerical approach to the mathematical problem based on the determination of the missing boundary condition and lava flow characteristics. Numerical results show that in the case of smooth input data lava temperature and velocity can be determined with a high accuracy. A noise imposed on the smooth input data results in a less accurate solution, but still acceptable below some noise level. The proposed approach to assimilate measured data brings an opportunity to estimate thermal budget of the lava flow.

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

    Indian Academy of Sciences (India)

    SEBASTIAN JOHN; RASHMI MISHRA

    2016-09-01

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

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

    Science.gov (United States)

    John, Sebastian; Mishra, Rashmi

    2016-09-01

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

  10. Direct Adaptive Aircraft Control Using Dynamic Cell Structure Neural Networks

    Science.gov (United States)

    Jorgensen, Charles C.

    1997-01-01

    A Dynamic Cell Structure (DCS) Neural Network was developed which learns topology representing networks (TRNS) of F-15 aircraft aerodynamic stability and control derivatives. The network is integrated into a direct adaptive tracking controller. The combination produces a robust adaptive architecture capable of handling multiple accident and off- nominal flight scenarios. This paper describes the DCS network and modifications to the parameter estimation procedure. The work represents one step towards an integrated real-time reconfiguration control architecture for rapid prototyping of new aircraft designs. Performance was evaluated using three off-line benchmarks and on-line nonlinear Virtual Reality simulation. Flight control was evaluated under scenarios including differential stabilator lock, soft sensor failure, control and stability derivative variations, and air turbulence.

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

    Science.gov (United States)

    Kummer, A.; Ocone, R.

    2003-04-01

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

  12. Bloodstain Pattern Analysis: implementation of a fluid dynamic model for position determination of victims

    Science.gov (United States)

    Laan, Nick; de Bruin, Karla G.; Slenter, Denise; Wilhelm, Julie; Jermy, Mark; Bonn, Daniel

    2015-06-01

    Bloodstain Pattern Analysis is a forensic discipline in which, among others, the position of victims can be determined at crime scenes on which blood has been shed. To determine where the blood source was investigators use a straight-line approximation for the trajectory, ignoring effects of gravity and drag and thus overestimating the height of the source. We determined how accurately the location of the origin can be estimated when including gravity and drag into the trajectory reconstruction. We created eight bloodstain patterns at one meter distance from the wall. The origin’s location was determined for each pattern with: the straight-line approximation, our method including gravity, and our method including both gravity and drag. The latter two methods require the volume and impact velocity of each bloodstain, which we are able to determine with a 3D scanner and advanced fluid dynamics, respectively. We conclude that by including gravity and drag in the trajectory calculation, the origin’s location can be determined roughly four times more accurately than with the straight-line approximation. Our study enables investigators to determine if the victim was sitting or standing, or it might be possible to connect wounds on the body to specific patterns, which is important for crime scene reconstruction.

  13. Dynamic windowing algorithm for the fast and accurate determination of luminescence lifetimes.

    Science.gov (United States)

    Collier, Bradley B; McShane, Michael J

    2012-06-05

    An algorithm for the accurate calculation of luminescence lifetimes in near-real-time is described. The dynamic rapid lifetime determination (DRLD) method uses a window-summing technique and dynamically selects the appropriate window width for each lifetime decay such that a large range of lifetimes can be accurately calculated. The selection of window width is based on an optimal range of window-sum ratios. The algorithm was compared to alternative approaches for rapid lifetime determination as well as nonlinear least-squares (NLLS) fitting in both simulated and real experimental conditions. A palladium porphyrin was used as a model luminophore to quantitatively evaluate the algorithm in a dynamic situation, where oxygen concentration was modulated to induce a change in lifetime. Unlike other window-summing techniques, the new algorithm calculates lifetimes that are not significantly different than the slower, traditional NLLS. In addition, the computation time required to calculate the lifetime is 4 orders of magnitude less than NLLS and 2 orders less than other iterative methods. This advance will improve the accuracy of real-time measurements that must be made on samples that are expected to exhibit widely varying lifetimes, such as sensors and biosensors.

  14. Tracheomalacia in adults with cystic fibrosis: determination of prevalence and severity with dynamic cine CT.

    LENUS (Irish Health Repository)

    McDermott, Shaunagh

    2012-02-01

    PURPOSE: To determine the prevalence and severity of tracheomalacia in adults with cystic fibrosis (CF) by using dynamic cine multidetector computed tomography (CT) and to correlate these findings with pulmonary function test (PFT) results and the severity of parenchymal lung disease. MATERIALS AND METHODS: In this institutional review board-approved HIPAA-compliant study, 40 patients with CF (22 men, 18 women; mean age, 28 years +\\/- 8 [standard deviation]; age range, 18-54 years) prospectively underwent PFTs, standard thin-section CT, and two dynamic cine multidetector CT acquisitions. Ten control subjects underwent dynamic cine multidetector CT. After standard thin-section CT was completed, dynamic cine multidetector CT was performed during a forced expiratory maneuver and during coughing. Dynamic cine multidetector CT images in nine patients were excluded. Maximal inspiratory, dynamic expiratory, and end-expiratory tracheal luminal areas were compared (Student t test) and correlated (Spearman rank) with PFT results and severity of parenchymal lung disease. RESULTS: Mean predicted forced expiratory volume in 1 second (FEV(1)) was 70.6% +\\/- 20.7, and mean Bhalla CT score was 41.8% +\\/- 13.6. In patients with CF, dynamic cine mean tracheal cross-sectional area reduction was 51.7% +\\/- 18.4 (range, 9%-89%) for forced expiratory maneuvers and 68.8% +\\/- 11.7 (range, 18%-88%) for coughing (P = .001). Tracheomalacia was demonstrated in 24 (69%) patients and no control subjects during forced expiratory maneuvers (P = .001) and in 10 (29%) patients and one (10%) control subject during coughing. For end-expiration images, mean tracheal luminal reduction was 16.1% +\\/- 14.0% (range, 0.0%-53.0%), with one patient demonstrating tracheal luminal reduction of more than 50%. There was no correlation between tracheal cross-sectional luminal reduction and either predicted FEV(1) or CT Bhalla score. CONCLUSION: Tracheomalacia depicted at dynamic cine multidetector CT is a

  15. Imaging regulatory T cell dynamics and CTLA4-mediated suppression of T cell priming.

    Science.gov (United States)

    Matheu, Melanie P; Othy, Shivashankar; Greenberg, Milton L; Dong, Tobias X; Schuijs, Martijn; Deswarte, Kim; Hammad, Hamida; Lambrecht, Bart N; Parker, Ian; Cahalan, Michael D

    2015-02-05

    Foxp3(+) regulatory T cells (Tregs) maintain immune homoeostasis through mechanisms that remain incompletely defined. Here by two-photon (2P) imaging, we examine the cellular dynamics of endogenous Tregs. Tregs are identified as two non-overlapping populations in the T-zone and follicular regions of the lymph node (LN). In the T-zone, Tregs migrate more rapidly than conventional T cells (Tconv), extend longer processes and interact with resident dendritic cells (DC) and Tconv. Tregs intercept immigrant DCs and interact with antigen-induced DC:Tconv clusters, while continuing to form contacts with activated Tconv. During antigen-specific responses, blocking CTLA4-B7 interactions reduces Treg-Tconv interaction times, increases the volume of DC:Tconv clusters and enhances subsequent Tconv proliferation in vivo. Our results demonstrate a role for altered cellular choreography of Tregs through CTLA4-based interactions to limit T-cell priming.

  16. GPS Based Reduced-Dynamic Orbit Determination for Low Earth Orbiters with Ambiguity Fixing

    Directory of Open Access Journals (Sweden)

    Yang Yang

    2015-01-01

    Full Text Available With the ever-increasing number of satellites in Low Earth Orbit (LEO for scientific missions, the precise determination of the position and velocity of the satellite is a necessity. GPS (Global Positioning System based reduced-dynamic orbit determination (RPOD method is commonly used in the post processing with high precision. This paper presents a sequential RPOD strategy for LEO satellite in the framework of Extended Kalman Filter (EKF. Precise Point Positioning (PPP technique is used to process the GPS observations, with carrier phase ambiguity resolution using Integer Phase Clocks (IPCs products. A set of GRACE (Gravity Recovery And Climate Experiment mission data is used to test and validate the RPOD performance. Results indicate that orbit determination accuracy could be improved by 15% in terms of 3D RMS error in comparison with traditional RPOD method with float ambiguity solutions.

  17. Determination of the experimental equilibrium structure of solid nitromethane using path-integral molecular dynamics simulations

    Science.gov (United States)

    Reilly, Anthony M.; Habershon, Scott; Morrison, Carole A.; Rankin, David W. H.

    2010-03-01

    Path-integral molecular dynamics (PIMD) simulations with an empirical interaction potential have been used to determine the experimental equilibrium structure of solid nitromethane at 4.2 and 15 K. By comparing the time-averaged molecular structure determined in a PIMD simulation to the calculated minimum-energy (zero-temperature) molecular structure, we have derived structural corrections that describe the effects of thermal motion. These corrections were subsequently used to determine the equilibrium structure of nitromethane from the experimental time-averaged structure. We find that the corrections to the intramolecular and intermolecular bond distances, as well as to the torsion angles, are quite significant, particularly for those atoms participating in the anharmonic motion of the methyl group. Our results demonstrate that simple harmonic models of thermal motion may not be sufficiently accurate, even at low temperatures, while molecular simulations employing more realistic potential-energy surfaces can provide important insight into the role and magnitude of anharmonic atomic motions.

  18. Local positive feedback regulation determines cell shape in root hair cells.

    Science.gov (United States)

    Takeda, Seiji; Gapper, Catherine; Kaya, Hidetaka; Bell, Elizabeth; Kuchitsu, Kazuyuki; Dolan, Liam

    2008-02-29

    The specification and maintenance of growth sites are tightly regulated during cell morphogenesis in all organisms. ROOT HAIR DEFECTIVE 2 reduced nicotinamide adenine dinucleotide phosphate (RHD2 NADPH) oxidase-derived reactive oxygen species (ROS) stimulate a Ca2+ influx into the cytoplasm that is required for root hair growth in Arabidopsis thaliana. We found that Ca2+, in turn, activated the RHD2 NADPH oxidase to produce ROS at the growing point in the root hair. Together, these components could establish a means of positive feedback regulation that maintains an active growth site in expanding root hair cells. Because the location and stability of growth sites predict the ultimate form of a plant cell, our findings demonstrate how a positive feedback mechanism involving RHD2, ROS, and Ca2+ can determine cell shape.

  19. Age related differences in dynamics of specific memory B cell populations after clinical pertussis infection.

    Directory of Open Access Journals (Sweden)

    Inonge van Twillert

    Full Text Available For a better understanding of the maintenance of immune mechanisms to Bordetella pertussis (Bp in relation to age, we investigated the dynamic range of specific B cell responses in various age-groups at different time points after a laboratory confirmed pertussis infection. Blood samples were obtained in a Dutch cross sectional observational study from symptomatic pertussis cases. Lymphocyte subpopulations were phenotyped by flowcytometry before and after culture. Memory B (Bmem cells were differentiated into IgG antibody secreting cells (ASC by polyclonal stimulation and detected by an ELISPOT assay specific for pertussis antigens pertussis toxin (Ptx, filamentous haemagglutinin (FHA and pertactin (Prn. Bp antigen specific IgG concentrations in plasma were determined using multiplex technology. The majority of subjects having experienced a clinical pertussis episode demonstrated high levels of both Bp specific IgG and Bmem cell levels within the first 6 weeks after diagnosis. Significantly lower levels were observed thereafter. Waning of cellular and humoral immunity to maintenance levels occurred within 9 months after antigen encounter. Age was found to determine the maximum but not base-line frequencies of Bmem cell populations; higher levels of Bmem cells specific for Ptx and FHA were reached in adults and (pre- elderly compared to under-fours and schoolchildren in the first 6 weeks after Bp exposure, whereas not in later phases. This age effect was less obvious for specific IgG levels. Nonetheless, subjects' levels of specific Bmem cells and specific IgG were weakly correlated. This is the first study to show that both age and closeness to last Bp encounter impacts the size of Bp specific Bmem cell and plasma IgG levels.

  20. Dynamic interplay between adhesion surfaces in carcinomas:Cell-cell and cell-matrix crosstalk

    Institute of Scientific and Technical Information of China (English)

    Yvonne E Smith; Sri HariKrishna Vellanki; Ann M Hopkins

    2016-01-01

    Cell-cell and cell-matrix signaling and communication between adhesion sites involve mechanisms which are required for cellular functions during normal development and homeostasis; however these cellular functions and mechanisms are often deregulated in cancer. Aberrant signaling at cell-cell and cell-matrix adhesion sites often involves downstream mediators including Rho GTPases and tyrosine kinases. This review discusses these molecules as putative mediators of cellular crosstalk between cell-cell and cell-matrix adhesion sites, in addition to their attractiveness as therapeutic targets in cancer. Interestingly, inter-junctional crosstalk mechanisms are frequently typified by the way in which bacterial and viral pathogens opportunistically infect or intoxicate mammalian cells. This review therefore also discusses the concept of learning from pathogen-host interaction studies to better understand coordinated communication between cell-cell and cell-matrix adhesion sites, in addition to highlighting the potential therapeutic usefulness of exploiting pathogens or their products to tap into inter-junctional crosstalk. Taken together, we feel that increased knowledge around mechanisms of cell-cell and cell-matrix adhesion site crosstalk and consequently a greater understanding of their therapeutic targeting offers a unique opportunity to contribute to the emerging molecular revolution in cancer biology.

  1. Dynamics of genomic clones in breast cancer patient xenografts at single cell resolution

    Science.gov (United States)

    Eirew, Peter; Steif, Adi; Khattra, Jaswinder; Ha, Gavin; Yap, Damian; Farahani, Hossein; Gelmon, Karen; Chia, Stephen; Mar, Colin; Wan, Adrian; Laks, Emma; Biele, Justina; Shumansky, Karey; Rosner, Jamie; McPherson, Andrew; Nielsen, Cydney; Roth, Andrew J. L.; Lefebvre, Calvin; Bashashati, Ali; de Souza, Camila; Siu, Celia; Aniba, Radhouane; Brimhall, Jazmine; Oloumi, Arusha; Osako, Tomo; Bruna, Alejandra; Sandoval, Jose; Algara, Teresa; Greenwood, Wendy; Leung, Kaston; Cheng, Hongwei; Xue, Hui; Wang, Yuzhuo; Lin, Dong; Mungall, Andrew J.; Moore, Richard; Zhao, Yongjun; Lorette, Julie; Nguyen, Long; Huntsman, David; Eaves, Connie J.; Hansen, Carl; Marra, Marco A.; Caldas, Carlos; Shah, Sohrab P.; Aparicio, Samuel

    2016-01-01

    Human cancers, including breast cancers, are comprised of clones differing in mutation content. Clones evolve dynamically in space and time following principles of Darwinian evolution1,2, underpinning important emergent features such as drug resistance and metastasis3–7. Human breast cancer xenoengraftment is used as a means of capturing and studying tumour biology, and breast tumour xenografts are generally assumed to be reasonable models of the originating tumours8–10. However the consequences and reproducibility of engraftment and propagation on the genomic clonal architecture of tumours has not been systematically examined at single cell resolution. Here we show by both deep genome and single cell sequencing methods, the clonal dynamics of initial engraftment and subsequent serial propagation of primary and metastatic human breast cancers in immunodeficient mice. In all 15 cases examined, clonal selection on engraftment was observed in both primary and metastatic breast tumours, varying in degree from extreme selective engraftment of minor (<5% of starting population) clones to moderate, polyclonal engraftment. Furthermore, ongoing clonal dynamics during serial passaging is a feature of tumours experiencing modest initial selection. Through single cell sequencing, we show that major mutation clusters estimated from tumour population sequencing relate predictably to the most abundant clonal genotypes, even in clonally complex and rapidly evolving cases. Finally, we show that similar clonal expansion patterns can emerge in independent grafts of the same starting tumour population, indicating that genomic aberrations can be reproducible determinants of evolutionary trajectories. Our results show that measurement of genomically defined clonal population dynamics will be highly informative for functional studies utilizing patient-derived breast cancer xenoengraftment. PMID:25470049

  2. Determination of a dynamic feeding strategy for recombinant Pichia pastoris strains.

    Science.gov (United States)

    Spadiut, Oliver; Dietzsch, Christian; Herwig, Christoph

    2014-01-01

    The knowledge of certain strain specific parameters of recombinant P. pastoris strains is required to be able to set up a feeding regime for fed-batch cultivations. To date, these parameters are commonly determined either by time-consuming and labor-intensive continuous cultivations or by several, consecutive fed-batch cultivations. Here, we describe a fast method based on batch experiments with methanol pulses to extract certain strain characteristic parameters, which are required to set up a dynamic feeding strategy for P. pastoris strains based on specific substrate uptake rate (q(s)). We further describe in detail the course of actions which have to be taken to obtain the desired dynamics during feeding.

  3. Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

    Science.gov (United States)

    Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

  4. Aggregate size and structure determination of nanomaterials in physiological media: importance of dynamic evolution

    Science.gov (United States)

    Afrooz, A. R. M. Nabiul; Hussain, Saber M.; Saleh, Navid B.

    2014-12-01

    Most in vitro nanotoxicological assays are performed after 24 h exposure. However, in determining size and shape effect of nanoparticles in toxicity assays, initial characterization data are generally used to describe experimental outcome. The dynamic size and structure of aggregates are typically ignored in these studies. This brief communication reports dynamic evolution of aggregation characteristics of gold nanoparticles. The study finds that gradual increase in aggregate size of gold nanospheres (AuNS) occurs up to 6 h duration; beyond this time period, the aggregation process deviates from gradual to a more abrupt behavior as large networks are formed. Results of the study also show that aggregated clusters possess unique structural conformation depending on nominal diameter of the nanoparticles. The differences in fractal dimensions of the AuNS samples likely occurred due to geometric differences, causing larger packing propensities for smaller sized particles. Both such observations can have profound influence on dosimetry for in vitro nanotoxicity analyses.

  5. Differentiation state determines neural effects on microvascular endothelial cells

    Energy Technology Data Exchange (ETDEWEB)

    Muffley, Lara A., E-mail: muffley@u.washington.edu [University of Washington, Campus Box 359796, 300 9th Avenue, Seattle, WA 98104 (United States); Pan, Shin-Chen, E-mail: pansc@mail.ncku.edu.tw [University of Washington, Campus Box 359796, 300 9th Avenue, Seattle, WA 98104 (United States); Smith, Andria N., E-mail: gnaunderwater@gmail.com [University of Washington, Campus Box 359796, 300 9th Avenue, Seattle, WA 98104 (United States); Ga, Maricar, E-mail: marga16@uw.edu [University of Washington, Campus Box 359796, 300 9th Avenue, Seattle, WA 98104 (United States); Hocking, Anne M., E-mail: ahocking@u.washington.edu [University of Washington, Campus Box 359796, 300 9th Avenue, Seattle, WA 98104 (United States); Gibran, Nicole S., E-mail: nicoleg@u.washington.edu [University of Washington, Campus Box 359796, 300 9th Avenue, Seattle, WA 98104 (United States)

    2012-10-01

    Growing evidence indicates that nerves and capillaries interact paracrinely in uninjured skin and cutaneous wounds. Although mature neurons are the predominant neural cell in the skin, neural progenitor cells have also been detected in uninjured adult skin. The aim of this study was to characterize differential paracrine effects of neural progenitor cells and mature sensory neurons on dermal microvascular endothelial cells. Our results suggest that neural progenitor cells and mature sensory neurons have unique secretory profiles and distinct effects on dermal microvascular endothelial cell proliferation, migration, and nitric oxide production. Neural progenitor cells and dorsal root ganglion neurons secrete different proteins related to angiogenesis. Specific to neural progenitor cells were dipeptidyl peptidase-4, IGFBP-2, pentraxin-3, serpin f1, TIMP-1, TIMP-4 and VEGF. In contrast, endostatin, FGF-1, MCP-1 and thrombospondin-2 were specific to dorsal root ganglion neurons. Microvascular endothelial cell proliferation was inhibited by dorsal root ganglion neurons but unaffected by neural progenitor cells. In contrast, microvascular endothelial cell migration in a scratch wound assay was inhibited by neural progenitor cells and unaffected by dorsal root ganglion neurons. In addition, nitric oxide production by microvascular endothelial cells was increased by dorsal root ganglion neurons but unaffected by neural progenitor cells. -- Highlights: Black-Right-Pointing-Pointer Dorsal root ganglion neurons, not neural progenitor cells, regulate microvascular endothelial cell proliferation. Black-Right-Pointing-Pointer Neural progenitor cells, not dorsal root ganglion neurons, regulate microvascular endothelial cell migration. Black-Right-Pointing-Pointer Neural progenitor cells and dorsal root ganglion neurons do not effect microvascular endothelial tube formation. Black-Right-Pointing-Pointer Dorsal root ganglion neurons, not neural progenitor cells, regulate

  6. Comparative in situ analyses of cell wall matrix polysaccharide dynamics in developing rice and wheat grain.

    Science.gov (United States)

    Palmer, Richard; Cornuault, Valérie; Marcus, Susan E; Knox, J Paul; Shewry, Peter R; Tosi, Paola

    2015-03-01

    Cell wall polysaccharides of wheat and rice endosperm are an important source of dietary fibre. Monoclonal antibodies specific to cell wall polysaccharides were used to determine polysaccharide dynamics during the development of both wheat and rice grain. Wheat and rice grain present near synchronous developmental processes and significantly different endosperm cell wall compositions, allowing the localisation of these polysaccharides to be related to developmental changes. Arabinoxylan (AX) and mixed-linkage glucan (MLG) have analogous cellular locations in both species, with deposition of AX and MLG coinciding with the start of grain filling. A glucuronoxylan (GUX) epitope was detected in rice, but not wheat endosperm cell walls. Callose has been reported to be associated with the formation of cell wall outgrowths during endosperm cellularisation and xyloglucan is here shown to be a component of these anticlinal extensions, occurring transiently in both species. Pectic homogalacturonan (HG) was abundant in cell walls of maternal tissues of wheat and rice grain, but only detected in endosperm cell walls of rice in an unesterified HG form. A rhamnogalacturonan-I (RG-I) backbone epitope was observed to be temporally regulated in both species, detected in endosperm cell walls from 12 DAA in rice and 20 DAA in wheat grain. Detection of the LM5 galactan epitope showed a clear distinction between wheat and rice, being detected at the earliest stages of development in rice endosperm cell walls, but not detected in wheat endosperm cell walls, only in maternal tissues. In contrast, the LM6 arabinan epitope was detected in both species around 8 DAA and was transient in wheat grain, but persisted in rice until maturity.

  7. Correlation between Dynamic Spiral-CT Enhancement Parameters and Tumor Angiogenesis in Renal Cell Carcinomas

    Institute of Scientific and Technical Information of China (English)

    Jinhong Wang; Weixia Chen; Xiuhui Zhang; Pengqiu Min; Rongbo Liu; Hengxuan Yang

    2005-01-01

    OBJECTIVE To prospectively investigate the correlation between the enhancement parameters of a dynamic-CT (D-CT) scan for renal cell carcinomas (RCC) and the carcinoma tissue microvessel density (MVD) in renal cell carcinomas (RCC).METHODS Twenty-four cases of renal cell carcinoma verifyied by histopathology were scanned via dynamic-CT, followed by a whole kidney scan. Enhancement parameters were derived as follows .The slope of the contrast media uptake curve (S), area under the curve(AR), the density difference before and after tissue enhancement (△HU) and tissue blood ratio (TBR) were calculated for all lesions. Time-density curve types were ranked from the lowest to the highest of the slope of the contrast media uptake curve (S) as type A, B and C. Pathologic slides corresponding to the CT imagings were subjected to CD34 monoclonal antibodies, then were evaluated with an image analyzer to count hot spots of MVD. By using the Spearman rank correlation tests, statistical analysis was performed to determine the strength of the relationship between enhancement parameters and MVD determinations.RESULTS The carcinoma tissue MVD showed a direct correlation with the enhancement parameters of D-CT (r=0.54, r=0.62, r=0.55, r=0.64, r=0.44,P< 0.05). Moreover the S, △HU, TBR and type curves all demonstrated a strong correlation with the MVD. By analyzing the various enhancement parameters of the time-density curves, the relationship between the enhancement CT parameters corresponding to the tumor's MVD was identified.CONCLUSION A dynamic spiral-CT scan may be a helpful method as a measurement of tumor angiogenesis in vivo in RCC.

  8. Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology.

    Directory of Open Access Journals (Sweden)

    Timothy R Lezon

    2010-06-01

    Full Text Available Comparison of elastic network model predictions with experimental data has provided important insights on the dominant role of the network of inter-residue contacts in defining the global dynamics of proteins. Most of these studies have focused on interpreting the mean-square fluctuations of residues, or deriving the most collective, or softest, modes of motions that are known to be insensitive to structural and energetic details. However, with increasing structural data, we are in a position to perform a more critical assessment of the structure-dynamics relations in proteins, and gain a deeper understanding of the major determinants of not only the mean-square fluctuations and lowest frequency modes, but the covariance or the cross-correlations between residue fluctuations and the shapes of higher modes. A systematic study of a large set of NMR-determined proteins is analyzed using a novel method based on entropy maximization to demonstrate that the next level of refinement in the elastic network model description of proteins ought to take into consideration properties such as contact order (or sequential separation between contacting residues and the secondary structure types of the interacting residues, whereas the types of amino acids do not play a critical role. Most importantly, an optimal description of observed cross-correlations requires the inclusion of destabilizing, as opposed to exclusively stabilizing, interactions, stipulating the functional significance of local frustration in imparting native-like dynamics. This study provides us with a deeper understanding of the structural basis of experimentally observed behavior, and opens the way to the development of more accurate models for exploring protein dynamics.

  9. Polarity, cell division, and out-of-equilibrium dynamics control the growth of epithelial structures

    Science.gov (United States)

    Cerruti, Benedetta; Puliafito, Alberto; Shewan, Annette M.; Yu, Wei; Combes, Alexander N.; Little, Melissa H.; Chianale, Federica; Primo, Luca; Serini, Guido; Mostov, Keith E.; Celani, Antonio

    2013-01-01

    The growth of a well-formed epithelial structure is governed by mechanical constraints, cellular apico-basal polarity, and spatially controlled cell division. Here we compared the predictions of a mathematical model of epithelial growth with the morphological analysis of 3D epithelial structures. In both in vitro cyst models and in developing epithelial structures in vivo, epithelial growth could take place close to or far from mechanical equilibrium, and was determined by the hierarchy of time-scales of cell division, cell–cell rearrangements, and lumen dynamics. Equilibrium properties could be inferred by the analysis of cell–cell contact topologies, and the nonequilibrium phenotype was altered by inhibiting ROCK activity. The occurrence of an aberrant multilumen phenotype was linked to fast nonequilibrium growth, even when geometric control of cell division was correctly enforced. We predicted and verified experimentally that slowing down cell division partially rescued a multilumen phenotype induced by altered polarity. These results improve our understanding of the development of epithelial organs and, ultimately, of carcinogenesis. PMID:24145168

  10. Genetic determinants and stroke in children with sickle cell disease.

    Science.gov (United States)

    Rodrigues, Daniela O W; Ribeiro, Luiz C; Sudário, Lysla C; Teixeira, Maria T B; Martins, Marina L; Pittella, Anuska M O L; Junior, Irtis de O Fernandes

    To verify genetic determinants associated with stroke in children with sickle cell disease (SCD). Prospective cohort with 110 children submitted to neonatal screening by the Neonatal Screening Program, between 1998 and 2007, with SCD diagnosis, followed at a regional reference public service for hemoglobinopathies. The analyzed variables were type of hemoglobinopathy, gender, coexistence with alpha thalassemia (α-thal), haplotypes of the beta globin chain cluster, and stroke. The final analysis was conducted with 66 children with sickle cell anemia (SCA), using the chi-squared test in the program SPSS(®) version 14.0. Among children with SCD, 60% had SCA. The prevalence of coexistence with α-thal was 30.3% and the Bantu haplotype (CAR) was identified in 89.2%. The incidence of stroke was significantly higher in those with SCA (27.3% vs. 2.3%; p=0.001) and males (24.1% vs. 9.6%; p=0.044). The presence of α-thal (p=0.196), the CAR haplotype (p=0.543), and socioeconomic factors were not statistically significant in association with the occurrence of stroke. There is a high incidence of stroke in male children and in children with SCA. Coexistence with α-thal and haplotypes of the beta globin chain cluster did not show any significant association with stroke. The heterogeneity between previously evaluated populations, the non-reproducibility between studies, and the need to identify factors associated with stroke in patients with SCA indicate the necessity of conducting further research to demonstrate the relevance of genetic factors in stroke related to SCD. Copyright © 2016 Sociedade Brasileira de Pediatria. Published by Elsevier Editora Ltda. All rights reserved.

  11. Genetic determinants and stroke in children with sickle cell disease,

    Directory of Open Access Journals (Sweden)

    Daniela O.W. Rodrigues

    Full Text Available Abstract Objective: To verify genetic determinants associated with stroke in children with sickle cell disease (SCD. Methods: Prospective cohort with 110 children submitted to neonatal screening by the Neonatal Screening Program, between 1998 and 2007, with SCD diagnosis, followed at a regional reference public service for hemoglobinopathies. The analyzed variables were type of hemoglobinopathy, gender, coexistence with alpha thalassemia (α-thal, haplotypes of the beta globin chain cluster, and stroke. The final analysis was conducted with 66 children with sickle cell anemia (SCA, using the chi-squared test in the program SPSS® version 14.0. Results: Among children with SCD, 60% had SCA. The prevalence of coexistence with α-thal was 30.3% and the Bantu haplotype (CAR was identified in 89.2%. The incidence of stroke was significantly higher in those with SCA (27.3% vs. 2.3%; p = 0.001 and males (24.1% vs. 9.6%; p = 0.044. The presence of α-thal (p = 0.196, the CAR haplotype (p = 0.543, and socioeconomic factors were not statistically significant in association with the occurrence of stroke. Conclusion: There is a high incidence of stroke in male children and in children with SCA. Coexistence with α-thal and haplotypes of the beta globin chain cluster did not show any significant association with stroke. The heterogeneity between previously evaluated populations, the non-reproducibility between studies, and the need to identify factors associated with stroke in patients with SCA indicate the necessity of conducting further research to demonstrate the relevance of genetic factors in stroke related to SCD.

  12. Dynamic equilibrium of reconstituting hematopoietic stem cell populations.

    Science.gov (United States)

    O'Quigley, John

    2010-12-01

    Clonal dominance in hematopoietic stem cell populations is an important question of interest but not one we can directly answer. Any estimates are based on indirect measurement. For marked populations, we can equate empirical and theoretical moments for binomial sampling, in particular we can use the well-known formula for the sampling variation of a binomial proportion. The empirical variance itself cannot always be reliably estimated and some caution is needed. We describe the difficulties here and identify ready solutions which only require appropriate use of variance-stabilizing transformations. From these we obtain estimators for the steady state, or dynamic equilibrium, of the number of hematopoietic stem cells involved in repopulating the marrow. The calculations themselves are not too involved. We give the distribution theory for the estimator as well as simple approximations for practical application. As an illustration, we rework on data recently gathered to address the question as to whether or not reconstitution of marrow grafts in the clinical setting might be considered to be oligoclonal.

  13. Order and stochastic dynamics in Drosophila planar cell polarity.

    Directory of Open Access Journals (Sweden)

    Yoram Burak

    2009-12-01

    Full Text Available Cells in the wing blade of Drosophila melanogaster exhibit an in-plane polarization causing distal orientation of hairs. Establishment of the Planar Cell Polarity (PCP involves intercellular interactions as well as a global orienting signal. Many of the genetic and molecular components underlying this process have been experimentally identified and a recently advanced system-level model has suggested that the observed mutant phenotypes can be understood in terms of intercellular interactions involving asymmetric localization of membrane bound proteins. Among key open questions in understanding the emergence of ordered polarization is the effect of stochasticity and the role of the global orienting signal. These issues relate closely to our understanding of ferromagnetism in physical systems. Here we pursue this analogy to understand the emergence of PCP order. To this end we develop a semi-phenomenological representation of the underlying molecular processes and define a "phase diagram" of the model which provides a global view of the dependence of the phenotype on parameters. We show that the dynamics of PCP has two regimes: rapid growth in the amplitude of local polarization followed by a slower process of alignment which progresses from small to large scales. We discuss the response of the tissue to various types of orienting signals and show that global PCP order can be achieved with a weak orienting signal provided that it acts during the early phase of the process. Finally we define and discuss some of the experimental predictions of the model.

  14. Dynamic Fluctuation of Circulating Tumor Cells during Cancer Progression

    Directory of Open Access Journals (Sweden)

    Mazen A. Juratli

    2014-01-01

    Full Text Available Circulating tumor cells (CTCs are a promising diagnostic and prognostic biomarker for metastatic tumors. We demonstrate that CTCs’ diagnostic value might be increased through real-time monitoring of CTC dynamics. Using preclinical animal models of breast cancer and melanoma and in vivo flow cytometry with photoacoustic and fluorescence detection schematics, we show that CTC count does not always correlate with the primary tumor size. Individual analysis elucidated many cases where the highest level of CTCs was detected before the primary tumor starts progressing. This phenomenon could be attributed to aggressive tumors developing from cancer stem cells. Furthermore, real-time continuous monitoring of CTCs reveals that they occur at highly variable rates in a detection point over a period of time (e.g., a range of 0–54 CTCs per 5 min. These same fluctuations in CTC numbers were observed in vivo in epithelial and non-epithelial metastatic tumors, in different stages of tumor progression, and in different vessels. These temporal CTC fluctuations can explain false negative results of a one-time snapshot test in humans. Indeed, we observed wide variations in the number of CTCs in subsequent blood samples taken from the same metastatic melanoma patient, with some samples being CTC-free. If these phenomena are confirmed in our ongoing in vivo clinical trials, this could support a personalized strategy of CTC monitoring for cancer patients.

  15. Dynamic Fluctuation of Circulating Tumor Cells during Cancer Progression

    Energy Technology Data Exchange (ETDEWEB)

    Juratli, Mazen A.; Sarimollaoglu, Mustafa; Nedosekin, Dmitry A. [Phillips Classic Laser and Nanomedicine Laboratories, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Melerzanov, Alexander V. [Moscow Institute of Physics and Technology (MIPT), Moscow Region, 141700 (Russian Federation); Zharov, Vladimir P. [Phillips Classic Laser and Nanomedicine Laboratories, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Arkansas Nanomedicine Center, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Moscow Institute of Physics and Technology (MIPT), Moscow Region, 141700 (Russian Federation); Galanzha, Ekaterina I., E-mail: egalanzha@uams.edu [Phillips Classic Laser and Nanomedicine Laboratories, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States)

    2014-01-15

    Circulating tumor cells (CTCs) are a promising diagnostic and prognostic biomarker for metastatic tumors. We demonstrate that CTCs’ diagnostic value might be increased through real-time monitoring of CTC dynamics. Using preclinical animal models of breast cancer and melanoma and in vivo flow cytometry with photoacoustic and fluorescence detection schematics, we show that CTC count does not always correlate with the primary tumor size. Individual analysis elucidated many cases where the highest level of CTCs was detected before the primary tumor starts progressing. This phenomenon could be attributed to aggressive tumors developing from cancer stem cells. Furthermore, real-time continuous monitoring of CTCs reveals that they occur at highly variable rates in a detection point over a period of time (e.g., a range of 0–54 CTCs per 5 min). These same fluctuations in CTC numbers were observed in vivo in epithelial and non-epithelial metastatic tumors, in different stages of tumor progression, and in different vessels. These temporal CTC fluctuations can explain false negative results of a one-time snapshot test in humans. Indeed, we observed wide variations in the number of CTCs in subsequent blood samples taken from the same metastatic melanoma patient, with some samples being CTC-free. If these phenomena are confirmed in our ongoing in vivo clinical trials, this could support a personalized strategy of CTC monitoring for cancer patients.

  16. Dynamics of Determining Motives in Choosing the Medical Profession by Medical Students

    Directory of Open Access Journals (Sweden)

    Kloktunova N.A.

    2013-06-01

    Full Text Available The purpose of the article is to study motivation of students of medical schools in choice of profession of the doctor and dynamics of defining motives in educational space of university. Material and methods: 497 students of the 1 st course took part in comparative research (356 students of medical faculty and 141 students of pediatric faculty and 382 students of the 6th course (270 students of medical faculty and 112 students of pediatric faculty of Saratov state medical university n.a. V. I. Razumovsky. In research methods of questioning and statistical data processing have been used. Results: The comparative analysis of the maximum and minimum values of the main types of motivation in professional field choice allowed to determine leading motives in medical students, and also to reveal their dynamics connected with various stages of professionalizing in the course of receiving medical education. Conclusion: Professional self-determination of the student of medical school has a multi-vector focus of structure of motivation. Determination by internal motives is supplemented with influence of external motivation, both positive, and negative value. In students of the 6th course indicators of motives included «Prestige», «Opportunity to help people», «Possibility of use of professional skills out of work».

  17. Adaptive SLICE method: an enhanced method to determine nonlinear dynamic respiratory system mechanics.

    Science.gov (United States)

    Zhao, Zhanqi; Guttmann, Josef; Möller, Knut

    2012-01-01

    The objective of this paper is to introduce and evaluate the adaptive SLICE method (ASM) for continuous determination of intratidal nonlinear dynamic compliance and resistance. The tidal volume is subdivided into a series of volume intervals called slices. For each slice, one compliance and one resistance are calculated by applying a least-squares-fit method. The volume window (width) covered by each slice is determined based on the confidence interval of the parameter estimation. The method was compared to the original SLICE method and evaluated using simulation and animal data. The ASM was also challenged with separate analysis of dynamic compliance during inspiration. If the signal-to-noise ratio (SNR) in the respiratory data decreased from +∞ to 10 dB, the relative errors of compliance increased from 0.1% to 22% for the ASM and from 0.2% to 227% for the SLICE method. Fewer differences were found in resistance. When the SNR was larger than 40 dB, the ASM delivered over 40 parameter estimates (42.2 ± 1.3). When analyzing the compliance during inspiration separately, the estimates calculated with the ASM were more stable. The adaptive determination of slice bounds results in consistent and reliable parameter values. Online analysis of nonlinear respiratory mechanics will profit from such an adaptive selection of interval size.

  18. Effect of Porosity and Cell Size on the Dynamic Compressive Properties of Aluminum Alloy Foams

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The dynamic mechanical properties of open-cell aluminum alloy foams with different relative densities and cell sizeshave been investigated by compressive tests. The strain rates varied from 700 s-1 to 2600 s-1. The experimentalresults showed that the dynamic compressive stress-strain curves exhibited a typical three-stage behavior: elastic,plateau and densification. The dynamic compressive strength of foams is affected not only by the relative densitybut also by the strain rate and cell size. Aluminum alloy foams with higher relative density or smaller cell size aremore sensitive to the strain rate than foams with lower relative density or larger cell size.

  19. Molecular Dynamics Simulation of Soft Grains: Malaria-Infected Red Blood Cells Motion within Obstructed 2-D Capillary Vessel

    CERN Document Server

    Haris, Luman; Haryanto, Freddy; Viridi, Sparisoma

    2013-01-01

    Molecular dynamics has been widely used to numerically solve equation of motion of classical many-particle system. It can be used to simulate many systems including biophysics, whose complexity level is determined by the involved elements. Based on this method, a numerical model had been constructed to mimic the behaviour of malaria-infected red blood cells within capillary vessel. The model was governed by three forces namely Coulomb force, normal force, and Stokes force. By utilizing two dimensional four-cells scheme, theoretical observation was carried out to test its capability. Although the parameters were chosen deliberately, all of the quantities were given arbitrary value. Despite this fact, the results were quite satisfactory. Combined with the previous results, it can be said that the proposed model were sufficient enough to mimic the malaria-infected red blood cells motion within obstructed capillary vessel. Keywords: molecular dynamics, two-dimensional model, red-blood cell motion, malaria

  20. Experimental analysis of microscale rain cells and their dynamic evolution

    Science.gov (United States)

    Enjamio, C.; Vilar, E.; RedañO, A.; FontáN, F. P.; Ndzi, D.

    2005-06-01

    This paper presents a detailed space-time analysis of rainfall rate using two dense networks of rain gauges covering two microscale areas of some 100 km2 each and located in two distinct climatic areas in the United Kingdom and Spain. The study has been carried out with the main objective of addressing dynamic fade mitigation techniques and scatter interference problems in terrestrial and satellite communication systems. The two databases, using a total of 49 and 23 rain gauges, respectively, are described, and the continuous interpolated field used for the subsequent analyses is explained in detail. The suitability of the networks in terms of density, correlation distance, and fractal dimension are briefly addressed. A to-scale comparison grid of the networks is also given. It has been found that when the maximum intensity reached during a rain event surpasses a certain threshold, different for each of the two areas, rainfall rates exhibit a spatial structure in the form of closed contours of thresholds referred to as cells. In statistical terms, the most probable diameter found is about 3.5 km, and distributions are presented. They are similar for the two sites but not so for the maxima reached inside the cells. Using cross-correlation techniques, displacement and velocities are analyzed in detail. Cells "zigzag" around a dominant trend because of the global cloud movements (driven by winds at heights of about 700 hPa). Local topography strongly affects local behavior. Analytical approximations to the experimental statistical distributions and selected histograms of the results are presented.

  1. Immediate postarousal sleep dynamics: an important determinant of sleep stability in obstructive sleep apnea.

    Science.gov (United States)

    Younes, Magdy; Hanly, Patrick J

    2016-04-01

    Arousability from sleep is increasingly recognized as an important determinant of the clinical spectrum of sleep disordered breathing (SDB). Patients with SDB display a wide range of arousability. The reason for these differences is not known. We hypothesized that differences in the speed with which sleep deepens following arousals/awakenings (postarousal sleep dynamics) is a major determinant of these differences in arousability in patients with SDB. We analyzed 40 preexisting clinical polysomnography records from patients with a range of SDB severity (apnea-hypopnea index 5-135/h). Sleep depth was determined every 3 s using the odds ratio product (ORP) method, a continuous index of sleep depth (0 = deep sleep, 2.5 = full wakefulness) that correlates strongly (r = 0.98) with arousability (Younes M, Ostrowski M, Soiferman M, Younes H, Younes M, Raneri J, and Hanly P. Sleep 38: 641-654, 2015). Time course of ORP was determined from end of arousal until the next arousal. All arousals were analyzed (142 ± 65/polysomnogram). ORP increased from 0.58 ± 0.32 during sleep to 1.67 ± 0.35 during arousals. ORP immediately (first 9 s) following arousals/awakenings (ORP-9) ranged from 0.21(very deep sleep) to 1.71 (highly arousable state) in different patients. In patients with high ORP-9, sleep deepened slowly (over minutes) beyond 9 s but only if no arousals/awakenings recurred. ORP-9 correlated strongly with average non-rapid eye movement sleep depth (r = 0.87, P sleep architecture. We conclude that postarousal sleep dynamics are highly variable among patients with sleep-disordered breathing and largely determine average sleep depth and continuity.

  2. Modelling and Simulation of the Dynamics of the Antigen-Specific T Cell Response Using Variable Structure Control Theory.

    Science.gov (United States)

    Anelone, Anet J N; Spurgeon, Sarah K

    2016-01-01

    Experimental and mathematical studies in immunology have revealed that the dynamics of the programmed T cell response to vigorous infection can be conveniently modelled using a sigmoidal or a discontinuous immune response function. This paper hypothesizes strong synergies between this existing work and the dynamical behaviour of engineering systems with a variable structure control (VSC) law. These findings motivate the interpretation of the immune system as a variable structure control system. It is shown that dynamical properties as well as conditions to analytically assess the transition from health to disease can be developed for the specific T cell response from the theory of variable structure control. In particular, it is shown that the robustness properties of the specific T cell response as observed in experiments can be explained analytically using a VSC perspective. Further, the predictive capacity of the VSC framework to determine the T cell help required to overcome chronic Lymphocytic Choriomeningitis Virus (LCMV) infection is demonstrated. The findings demonstrate that studying the immune system using variable structure control theory provides a new framework for evaluating immunological dynamics and experimental observations. A modelling and simulation tool results with predictive capacity to determine how to modify the immune response to achieve healthy outcomes which may have application in drug development and vaccine design.

  3. Role of the first coordination shell in determining the equilibrium structure and dynamics of simple liquids

    DEFF Research Database (Denmark)

    Toxværd, Søren; Dyre, J. C.

    2011-01-01

    . Lett. 103, 170601 (2009);10.1103/PhysRevLett.103.170601 J. Chem. Phys. 134, 214503 (2011)10.1063/1.3592709] . We present simulations of the standard Lennard-Jones liquid at several condensed-fluid state points, including a fairly low density state and a very high density state, as well as simulations......The traditional view that the physical properties of a simple liquid are determined primarily by its repulsive forces was recently challenged by Berthier and Tarjus, who showed that in some cases ignoring the attractions leads to large errors in the dynamics [L. Berthier and G. Tarjus, Phys. Rev...

  4. Dynamic Range of Vertebrate Retina Ganglion Cells: Importance of Active Dendrites and Coupling by Electrical Synapses

    Science.gov (United States)

    Publio, Rodrigo; Ceballos, Cesar Celis; Roque, Antonio C.

    2012-01-01

    The vertebrate retina has a very high dynamic range. This is due to the concerted action of its diverse cell types. Ganglion cells, which are the output cells of the retina, have to preserve this high dynamic range to convey it to higher brain areas. Experimental evidence shows that the firing response of ganglion cells is strongly correlated with their total dendritic area and only weakly correlated with their dendritic branching complexity. On the other hand, theoretical studies with simple neuron models claim that active and large dendritic trees enhance the dynamic range of single neurons. Theoretical models also claim that electrical coupling between ganglion cells via gap junctions enhances their collective dynamic range. In this work we use morphologically reconstructed multi-compartmental ganglion cell models to perform two studies. In the first study we investigate the relationship between single ganglion cell dynamic range and number of dendritic branches/total dendritic area for both active and passive dendrites. Our results support the claim that large and active dendrites enhance the dynamic range of a single ganglion cell and show that total dendritic area has stronger correlation with dynamic range than with number of dendritic branches. In the second study we investigate the dynamic range of a square array of ganglion cells with passive or active dendritic trees coupled with each other via dendrodendritic gap junctions. Our results suggest that electrical coupling between active dendritic trees enhances the dynamic range of the ganglion cell array in comparison with both the uncoupled case and the coupled case with cells with passive dendrites. The results from our detailed computational modeling studies suggest that the key properties of the ganglion cells that endow them with a large dynamic range are large and active dendritic trees and electrical coupling via gap junctions. PMID:23144767

  5. Dynamic range of vertebrate retina ganglion cells: importance of active dendrites and coupling by electrical synapses.

    Science.gov (United States)

    Publio, Rodrigo; Ceballos, Cesar Celis; Roque, Antonio C

    2012-01-01

    The vertebrate retina has a very high dynamic range. This is due to the concerted action of its diverse cell types. Ganglion cells, which are the output cells of the retina, have to preserve this high dynamic range to convey it to higher brain areas. Experimental evidence shows that the firing response of ganglion cells is strongly correlated with their total dendritic area and only weakly correlated with their dendritic branching complexity. On the other hand, theoretical studies with simple neuron models claim that active and large dendritic trees enhance the dynamic range of single neurons. Theoretical models also claim that electrical coupling between ganglion cells via gap junctions enhances their collective dynamic range. In this work we use morphologically reconstructed multi-compartmental ganglion cell models to perform two studies. In the first study we investigate the relationship between single ganglion cell dynamic range and number of dendritic branches/total dendritic area for both active and passive dendrites. Our results support the claim that large and active dendrites enhance the dynamic range of a single ganglion cell and show that total dendritic area has stronger correlation with dynamic range than with number of dendritic branches. In the second study we investigate the dynamic range of a square array of ganglion cells with passive or active dendritic trees coupled with each other via dendrodendritic gap junctions. Our results suggest that electrical coupling between active dendritic trees enhances the dynamic range of the ganglion cell array in comparison with both the uncoupled case and the coupled case with cells with passive dendrites. The results from our detailed computational modeling studies suggest that the key properties of the ganglion cells that endow them with a large dynamic range are large and active dendritic trees and electrical coupling via gap junctions.

  6. Chromatin Dynamics During DNA Replication and Uncharacterized Replication Factors determined by Nascent Chromatin Capture (NCC) Proteomics

    Science.gov (United States)

    Alabert, Constance; Bukowski-Wills, Jimi-Carlo; Lee, Sung-Bau; Kustatscher, Georg; Nakamura, Kyosuke; de Lima Alves, Flavia; Menard, Patrice; Mejlvang, Jakob; Rappsilber, Juri; Groth, Anja

    2014-01-01

    SUMMARY To maintain genome function and stability, DNA sequence and its organization into chromatin must be duplicated during cell division. Understanding how entire chromosomes are copied remains a major challenge. Here, we use Nascent Chromatin Capture (NCC) to profile chromatin proteome dynamics during replication in human cells. NCC relies on biotin-dUTP labelling of replicating DNA, affinity-purification and quantitative proteomics. Comparing nascent chromatin with mature post-replicative chromatin, we provide association dynamics for 3995 proteins. The replication machinery and 485 chromatin factors like CAF-1, DNMT1, SUV39h1 are enriched in nascent chromatin, whereas 170 factors including histone H1, DNMT3, MBD1-3 and PRC1 show delayed association. This correlates with H4K5K12diAc removal and H3K9me1 accumulation, while H3K27me3 and H3K9me3 remain unchanged. Finally, we combine NCC enrichment with experimentally derived chromatin probabilities to predict a function in nascent chromatin for 93 uncharacterized proteins and identify FAM111A as a replication factor required for PCNA loading. Together, this provides an extensive resource to understand genome and epigenome maintenance. PMID:24561620

  7. Neuropeptides control the dynamic behavior of airway mucosal dendritic cells.

    Science.gov (United States)

    Voedisch, Sabrina; Rochlitzer, Sabine; Veres, Tibor Z; Spies, Emma; Braun, Armin

    2012-01-01

    The airway mucosal epithelium is permanently exposed to airborne particles. A network of immune cells patrols at this interface to the environment. The interplay of immune cells is orchestrated by different mediators. In the current study we investigated the impact of neuronal signals on key functions of dendritic cells (DC). Using two-photon microscopic time-lapse analysis of living lung sections from CD11c-EYFP transgenic mice we studied the influence of neuropeptides on airway DC motility. Additionally, using a confocal microscopic approach, the phagocytotic capacity of CD11c(+) cells after neuropeptide stimulation was determined. Electrical field stimulation (EFS) leads to an unspecific release of neuropeptides from nerves. After EFS and treatment with the neuropeptides vasoactive intestinal peptide (VIP) or calcitonin gene-related peptide (CGRP), airway DC in living lung slices showed an altered motility. Furthermore, the EFS-mediated effect could partially be blocked by pre-treatment with the receptor antagonist CGRP(8-37). Additionally, the phagocytotic capacity of bone marrow-derived and whole lung CD11c(+) cells could be inhibited by neuropeptides CGRP, VIP, and Substance P. We then cross-linked these data with the in vivo situation by analyzing DC motility in two different OVA asthma models. Both in the acute and prolonged OVA asthma model altered neuropeptide amounts and DC motility in the airways could be measured. In summary, our data suggest that neuropeptides modulate key features motility and phagocytosis of mouse airway DC. Therefore altered neuropeptide levels in airways during allergic inflammation have impact on regulation of airway immune mechanisms and therefore might contribute to the pathophysiology of asthma.

  8. Live Cell Analysis and Mathematical Modeling Identify Determinants of Attenuation of Dengue Virus 2'-O-Methylation Mutant.

    Directory of Open Access Journals (Sweden)

    Bianca Schmid

    2015-12-01

    Full Text Available Dengue virus (DENV is the most common mosquito-transmitted virus infecting ~390 million people worldwide. In spite of this high medical relevance, neither a vaccine nor antiviral therapy is currently available. DENV elicits a strong interferon (IFN response in infected cells, but at the same time actively counteracts IFN production and signaling. Although the kinetics of activation of this innate antiviral defense and the timing of viral counteraction critically determine the magnitude of infection and thus disease, quantitative and kinetic analyses are lacking and it remains poorly understood how DENV spreads in IFN-competent cell systems. To dissect the dynamics of replication versus antiviral defense at the single cell level, we generated a fully viable reporter DENV and host cells with authentic reporters for IFN-stimulated antiviral genes. We find that IFN controls DENV infection in a kinetically determined manner that at the single cell level is highly heterogeneous and stochastic. Even at high-dose, IFN does not fully protect all cells in the culture and, therefore, viral spread occurs even in the face of antiviral protection of naïve cells by IFN. By contrast, a vaccine candidate DENV mutant, which lacks 2'-O-methylation of viral RNA is profoundly attenuated in IFN-competent cells. Through mathematical modeling of time-resolved data and validation experiments we show that the primary determinant for attenuation is the accelerated kinetics of IFN production. This rapid induction triggered by mutant DENV precedes establishment of IFN-resistance in infected cells, thus causing a massive reduction of virus production rate. In contrast, accelerated protection of naïve cells by paracrine IFN action has negligible impact. In conclusion, these results show that attenuation of the 2'-O-methylation DENV mutant is primarily determined by kinetics of autocrine IFN action on infected cells.

  9. Dynamic Thermal Model And Control Of A Pem Fuel Cell System

    DEFF Research Database (Denmark)

    Liso, Vincenzo; Nielsen, Mads Pagh

    2013-01-01

    A lumped parameter dynamic model is developed for predicting the stack performance, temperatures of the exit reactant gases and coolant liquid outlet in a proton-exchange membrane fuel cell (PEMFC) system. The air compressor, humidifier and cooling heat exchanger models are integrated to study...... the fuel cell system. A PID temperature control is implemented to study the effect of stack temperature on settling times of other variables such as stack voltage, air flow rate, oxygen excess ratio and net power of the stack. The model allows an assessment of the effect of operating parameters (stack...... power output, cooling water flow rate, air flow rate, and environmental temperature) and parameter interactions on the system thermal performance. The model represents a useful tool to determine the operating temperatures of the various components of the thermal system, and thus to fully assess...

  10. Sophisticated framework between cell cycle arrest and apoptosis induction based on p53 dynamics.

    Science.gov (United States)

    Hamada, Hiroyuki; Tashima, Yoshihiko; Kisaka, Yu; Iwamoto, Kazunari; Hanai, Taizo; Eguchi, Yukihiro; Okamoto, Masahiro

    2009-01-01

    The tumor suppressor, p53, regulates several gene expressions that are related to the DNA repair protein, cell cycle arrest and apoptosis induction, which activates the implementation of both cell cycle arrest and induction of apoptosis. However, it is not clear how p53 specifically regulates the implementation of these functions. By applying several well-known kinetic mathematical models, we constructed a novel model that described the influence that DNA damage has on the implementation of both the G2/M phase cell cycle arrest and the intrinsic apoptosis induction via its activation of the p53 synthesis process. The model, which consisted of 32 dependent variables and 115 kinetic parameters, was used to examine interference by DNA damage in the implementation of both G2/M phase cell cycle arrest and intrinsic apoptosis induction. A low DNA damage promoted slightly the synthesis of p53, which showed a sigmoidal behavior with time. In contrast, in the case of a high DNA damage, the p53 showed an oscillation behavior with time. Regardless of the DNA damage level, there were delays in the G2/M progression. The intrinsic apoptosis was only induced in situations where grave DNA damage produced an oscillation of p53. In addition, to wreck the equilibrium between Bcl-2 and Bax the induction of apoptosis required an extreme activation of p53 produced by the oscillation dynamics, and was only implemented after the release of the G2/M phase arrest. When the p53 oscillation is observed, there is possibility that the cell implements the apoptosis induction. Moreover, in contrast to the cell cycle arrest system, the apoptosis induction system is responsible for safeguarding the system that suppresses malignant transformations. The results of these experiments will be useful in the future for elucidating of the dominant factors that determine the cell fate such as normal cell cycles, cell cycle arrest and apoptosis.

  11. A Dynamic Analysis of the Determinants of the Greek Credit Default Swaps

    Directory of Open Access Journals (Sweden)

    Maria do Rosario CORREIA

    2016-06-01

    Full Text Available Abstract. There is a consensus in finance literature that credit default swap spreads can be used to calculate the default probability of a government bond. The question is therefore what determines the credit default swap spreads and also what is a good indicator that predicts the future behaviour of this security spreads. In this paper, we investigate several variables which have been used in the past to predict the CDS spreads. We do this by analysing the behaviour of credit swaps spreads of Greek sovereign debt over the recent financial crisis. We take into account the changes on the data generating process as the crisis evolves. Moreover, we also investigate which part of the dynamic process of CDS spreads is explained by each possible determinant. In order to do so, we use a time-frequency approach. As it turns out, some determinants are better in explaining the short term behaviour of the CDS spreads whilst others explain the long term behaviour. We can also say by how many months one factor determines the behaviour of the CDS spreads for Greek sovereign debt. With this information we are able to determine the probability of default and what it depends upon..Keywords. Eurozone crisis, Government default, Greek default, Credit default swap, Default probability.JEL. C22, C58, G14, G15, H63, H68.

  12. An Approach to Determining the Optimal Cell Number of Manufacturing Cell Formation

    Directory of Open Access Journals (Sweden)

    Jianwei Wang

    2013-04-01

    Full Text Available An approach to determining the optimal cell number of manufacturing cell formation is presented. Firstly, the difference of weighting exponent, cluster center and metrics how to have an impact upon the clustering results and membership function are studied. Secondly, a method to determine the optimal m value is given. Two-order partial derivative of the objective function for FCM is calculated, and the variational weighting exponent m is obtained that can prevent the parameter from being the unique value and play an important role in the process of fuzzy clustering. Moreover, in order to avoid a single validity index can not assess correctly, partition coefficient (PC, classification entropy (CE, Fukuyama and Sugeno (FS and Xie and Beni (XB are considered as multi-performance indexes to evaluate the cluster validity, and then an optimal number c is chosen based on these validity measures. Finally, test exampls are given to illustrate the validity of the proposed approach.

  13. Ammonia removal via microbial fuel cell (MFC) dynamic reactor

    Science.gov (United States)

    Alabiad, I.; Ali, U. F. M.; Zakarya, I. A.; Ibrahim, N.; Radzi, R. W.; Zulkurnai, N. Z.; Azmi, N. H.

    2017-06-01

    Landfill leachate is generally known as high-strength wastewater that is difficult to handle and contains dissolved extracts and suspended matter. Microbial fuel cells (MFCs) were designed to treat landfill leachate while continuously producing power (voltage output). Three different anodes were tested in MFC reactors: carbon black, activated carbon, and zinc electrodes. Movements in the MFC reactor during treatment were also a key factor for testing. Results showed a difference in ammonia levels in the three anodes used. The study compared the efficiency of static and dynamic modes of MFC in removing ammonia. Continual leachate movement in the reactor could increase the rate of removal of the ammonia components. The setup provided a viable condition for maximum removal because the reactor movement caused the sludge to disintegrate, which allowed ammonia to separate easily from the parent leachate. Ammonia removal also resulted from the transfer of ammonium through the membrane or from ammonia loss. Constant exchange of ionic content benefited the MFC performance by increasing power production and decreasing internal electrode material resistance. This paper presents the results of the analyses of leachate treatment from the solid waste landfill located in Padang Siding Landfill, Perlis. The performance of ammonia removal was enhanced using different types of electrodes. In both modes, activated carbon performed better than black carbon and zinc. The respective percentages of ammonia removal for activated carbon of dynamic over static were 96.6%, 66.6%, and 92.8% for activated carbon, zinc, and black carbon. The results provide further information on the possibility of using MFCs in landfill leachate treatment systems.

  14. Dynamics of regulatory networks in gastrin-treated adenocarcinoma cells.

    Directory of Open Access Journals (Sweden)

    Naresh Doni Jayavelu

    Full Text Available Understanding gene transcription regulatory networks is critical to deciphering the molecular mechanisms of different cellular states. Most studies focus on static transcriptional networks. In the current study, we used the gastrin-regulated system as a model to understand the dynamics of transcriptional networks composed of transcription factors (TFs and target genes (TGs. The hormone gastrin activates and stimulates signaling pathways leading to various cellular states through transcriptional programs. Dysregulation of gastrin can result in cancerous tumors, for example. However, the regulatory networks involving gastrin are highly complex, and the roles of most of the components of these networks are unknown. We used time series microarray data of AR42J adenocarcinoma cells treated with gastrin combined with static TF-TG relationships integrated from different sources, and we reconstructed the dynamic activities of TFs using network component analysis (NCA. Based on the peak expression of TGs and activity of TFs, we created active sub-networks at four time ranges after gastrin treatment, namely immediate-early (IE, mid-early (ME, mid-late (ML and very late (VL. Network analysis revealed that the active sub-networks were topologically different at the early and late time ranges. Gene ontology analysis unveiled that each active sub-network was highly enriched in a particular biological process. Interestingly, network motif patterns were also distinct between the sub-networks. This analysis can be applied to other time series microarray datasets, focusing on smaller sub-networks that are activated in a cascade, allowing better overview of the mechanisms involved at each time range.

  15. Habitat heterogeneity determines climate impact on zooplankton community structure and dynamics.

    Directory of Open Access Journals (Sweden)

    Saskia A Otto

    Full Text Available Understanding and predicting species distribution in space and time and consequently community structure and dynamics is an important issue in ecology, and particularly in climate change research. A crucial factor determining the composition and dynamics of animal populations is habitat heterogeneity, i.e., the number of structural elements in a given locality. In the marine pelagic environment habitat heterogeneity is represented by the distribution of physical oceanographic parameters such as temperature, salinity and oxygen that are closely linked to atmospheric conditions. Little attention has been given, however, to the role of habitat heterogeneity in modulating the response of animal communities to external climate forcing. Here we investigate the long-term dynamics of Acartia spp., Temora longicornis, and Pseudocalanus acuspes, three dominant zooplankton species inhabiting different pelagic habitats in the Central Baltic Sea (CBS. We use the three copepods as indicator species for changes in the CBS zooplankton community and apply non-linear statistical modeling techniques to compare spatial population trends and to identify their drivers. We demonstrate that effects of climate variability and change depend strongly on species-specific habitat utilization, being more direct and pronounced at the upper water layer. We propose that the differential functional response to climate-related drivers in relation to strong habitat segregation is due to alterations of the species' environmental niches. We stress the importance of understanding how anticipated climate change will affect ecological niches and habitats in order to project spatio-temporal changes in species abundance and distribution.

  16. Main Effect QTL with Dominance Determines Heterosis for Dynamic Plant Height in Upland Cotton.

    Science.gov (United States)

    Shang, Lianguang; Ma, Lingling; Wang, Yumei; Su, Ying; Wang, Xiaocui; Li, Yuhua; Abduweli, Abdugheni; Cai, Shihu; Liu, Fang; Wang, Kunbo; Hua, Jinping

    2016-10-13

    Plant height, which shows dynamic development and heterosis, is a major trait affecting plant architecture and has an indirect influence on economic yield related to biological yield in cotton. In the present study, we carried out dynamic analysis for plant height and its heterosis by quantitative trait loci (QTL) mapping at multiple developmental stages using two recombinant inbred lines (RILs) and their backcross progeny. At the single-locus level, 47 QTL were identified at five developmental stages in two hybrids. In backcross populations, QTL identified at an early stage mainly showed partial effects and QTL detected at a later stage mostly displayed overdominance effects. At the two-locus level, we found that main effect QTL played a more important role than epistatic QTL in the expression of heterosis in backcross populations. Therefore, this study implies that the genetic basis of plant height heterosis shows dynamic character and main effect QTL with dominance determines heterosis for plant height in Upland cotton. Copyright © 2016 Shang et al.

  17. Main Effect QTL with Dominance Determines Heterosis for Dynamic Plant Height in Upland Cotton

    Directory of Open Access Journals (Sweden)

    Lianguang Shang

    2016-10-01

    Full Text Available Plant height, which shows dynamic development and heterosis, is a major trait affecting plant architecture and has an indirect influence on economic yield related to biological yield in cotton. In the present study, we carried out dynamic analysis for plant height and its heterosis by quantitative trait loci (QTL mapping at multiple developmental stages using two recombinant inbred lines (RILs and their backcross progeny. At the single-locus level, 47 QTL were identified at five developmental stages in two hybrids. In backcross populations, QTL identified at an early stage mainly showed partial effects and QTL detected at a later stage mostly displayed overdominance effects. At the two-locus level, we found that main effect QTL played a more important role than epistatic QTL in the expression of heterosis in backcross populations. Therefore, this study implies that the genetic basis of plant height heterosis shows dynamic character and main effect QTL with dominance determines heterosis for plant height in Upland cotton.

  18. DETERMINATION OF PROMINENCE PLASMA {beta} FROM THE DYNAMICS OF RISING PLUMES

    Energy Technology Data Exchange (ETDEWEB)

    Hillier, Andrew [Kwasan and Hida Observatories, Kyoto University, Kyoto (Japan); Hillier, Richard [Department of Aeronautics, Imperial College, London (United Kingdom); Tripathi, Durgesh, E-mail: andrew@kwasan.kyoto-u.ac.jp [Inter-University Centre for Astronomy and Astrophysics, Post Bag 4, Ganeshkhind, Pune 411 007 (India)

    2012-12-20

    Observations by the Hinode satellite show in great detail the dynamics of rising plumes, dark in chromospheric lines, in quiescent prominences that propagate from large ({approx}10 Mm) bubbles that form at the base of the prominences. These plumes present a very interesting opportunity to study magnetohydrodynamic (MHD) phenomena in quiescent prominences, but obstacles still remain. One of the biggest issues is that of the magnetic field strength, which is not easily measurable in prominences. In this paper we present a method that may be used to determine a prominence's plasma {beta} when rising plumes are observed. Using the classic fluid dynamic solution for flow around a circular cylinder with an MHD correction, the compression of the prominence material can be estimated. This has been successfully confirmed through simulations; application to a prominence gave an estimate of the plasma {beta} as {beta} = 0.47 {+-} 0.079 to 1.13 {+-} 0.080 for the range {gamma} = 1.4-1.7. Using this method it may be possible to estimate the plasma {beta} of observed prominences, therefore helping our understanding of a prominence's dynamics in terms of MHD phenomena.

  19. Evolution of the global internal dynamics of a living cell nucleus during interphase.

    Science.gov (United States)

    Suissa, M; Place, C; Goillot, E; Freyssingeas, E

    2009-07-22

    Progress in cellular biology based on fluorescent microscopy techniques, shows that the spatial organization of the nucleus is dynamic. This dynamic is very complex and involves a multitude of phenomena that occur on very different time and size scales. Using an original light scattering experimental device, we investigated the global internal dynamics of the nucleus of a living cell according to the phases of the cell cycle. This dynamic presents two different and independent kinds of relaxation that are well separated in time and specific to the phase of the cell cycle.

  20. Single-cell protein dynamics reproduce universal fluctuations in cell populations

    CERN Document Server

    Brenner, Naama; Rotella, James S; Salman, Hanna

    2015-01-01

    Protein fluctuations in cell populations have recently been shown to exhibit a universal distribution shape under a broad range of biological realizations. Here, measuring protein content in individual bacteria continuously over ~70 generations, we show that single-cell trajectories fluctuate around their average with the same distribution shape as the population, i.e. their relative fluctuations are ergodic. Analysis of these temporal trajectories reveals that one effective random variable, sampled once each cell cycle, suffices to reconstruct the distribution from the trajectory. This in turn implies that cellular microscopic processes are strongly buffered and population-level protein distributions are insensitive to details of the intracellular dynamics. Probing them thus requires searching for novel universality-breaking experimental perturbations.

  1. THE DYNAMICS OF STUDENTS’ PROFESSIONAL SELF-DETERMINATION VALUE ORIENTATION (THE SOCIOLOGICAL ASPECT

    Directory of Open Access Journals (Sweden)

    Evgeniya Vladislavovna Yarina

    2014-10-01

    Full Text Available The article is devoted to the issues of students’ professional self-determination in the university community. It represents empirical analysis of the dynamics of professional value orientation of students in the period of  2005– 2013 as exemplified by the students of Moscow state university of railway engineering .The analysis revealed the motives for choice and the evaluation of the potential of the profession, the youngsters are studying for  in the university. The results of the research in certainty and expectations of the students in terms of employment are compared to the official statistic in the recruitment sphere.  The article also represented clearly defined conditions necessary for the provision of the successful formation of the professional self-determination in tertiary education.

  2. Dynamics of human respiratory virus-specific CD8+ T cell responses in blood and airways during episodes of common cold

    NARCIS (Netherlands)

    Heidema, Jojanneke; Rossen, John W A; Lukens, Michaël; Ketel, Marianne S; Scheltens, Eva; Kranendonk, Mariette E G; van Maren, Wendy W C; van Loon, Anton M; Otten, Henny G; Kimpen, Jan L L; van Bleek, Grada M

    2008-01-01

    We determined the dynamics of CD8(+) T cells specific for influenza virus and respiratory syncytial virus in blood and tracheostoma aspirates of children during the course of respiratory infections. We showed that during localized respiratory infections the ratio of activated effector CD8(+) T cells

  3. Repopulation dynamics of single haematopoietic stem cells in mouse transplantation experiments: Importance of stem cell composition in competitor cells.

    Science.gov (United States)

    Ema, Hideo; Uchinomiya, Kouki; Morita, Yohei; Suda, Toshio; Iwasa, Yoh

    2016-04-07

    The transplantation of blood tissues from bone marrow into a lethally irradiated animal is an experimental procedure that is used to study how the blood system is reconstituted by haematopoietic stem cells (HSC). In a competitive repopulation experiment, a lethally irradiated mouse was transplanted with a single HSC as a test cell together with a number of bone marrow cells as competitor cells, and the fraction of the test cell progeny (percentage of chimerism) was traced over time. In this paper, we studied the stem cell kinetics in this experimental procedure. The balance between symmetric self-renewal and differentiation divisions in HSC determined the number of cells which HSC produce and the length of time for which HSC live after transplantation. The percentage of chimerism depended on the type of test cell (long-, intermediate-, or short-term HSC), as well as the type and number of HSC included in competitor cells. We next examined two alternative HSC differentiation models, one-step and multi-step differentiation models. Although these models differed in blood cell production, the percentage of chimerism appeared very similar. We also estimated the numbers of different types of HSC in competitor cells. Based on these results, we concluded that the experimental results inevitably include stochasticity with regard to the number and the type of HSC in competitor cells, and that, in order to detect different types of HSC, an appropriate number of competitor cells needs to be used in transplantation experiments.

  4. Cancer Detection via Determination of Fractal Cell Dimension

    CERN Document Server

    Bauer, W; Bauer, Wolfgang; Mackenzie, Charles D.

    1995-01-01

    We utilize the fractal dimension of the perimeter surface of cell sections as a new observable to characterize cells of different types. We propose that it is possible to distinguish cancerous from healthy cells with the aid of this new approach. As a first application we show that it is possible to perform this distinction between patients with hairy-cell lymphocytic leukemia and those with normal blood lymphocytes.

  5. Triggering cell adhesion, migration or shape change with a dynamic surface coating.

    Science.gov (United States)

    van Dongen, Stijn F M; Maiuri, Paolo; Marie, Emmanuelle; Tribet, Christophe; Piel, Matthieu

    2013-03-25

    There's an APP for that: cell-repellent APP (azido-[polylysine-g-PEG]) is used to create substrates for spatially controlled dynamic cell adhesion. The simple addition of a functional peptide to the culture medium rapidly triggers cell adhesion. This highly accessible yet powerful technique allows diverse applications, demonstrated through tissue motility assays, patterned coculturing and triggered cell shape change.

  6. PREFACE: Structure and dynamics determined by neutron and x-ray scattering Structure and dynamics determined by neutron and x-ray scattering

    Science.gov (United States)

    Müller-Buschbaum, Peter

    2011-06-01

    Neutron and x-ray scattering have emerged as powerful methods for the determination of structure and dynamics. Driven by emerging new, powerful neutron and synchrotron radiation sources, the continuous development of new instrumentation and novel scattering techniques gives rise to exciting possibilities. For example, in situ observations become possible via a high neutron or x-ray flux at the sample and, as a consequence, morphological transitions with small time constants can be detected. This special issue covers a broad range of different materials from soft to hard condensed matter. Hence, different material classes such as colloids, polymers, alloys, oxides and metals are addressed. The issue is dedicated to the 60th birthday of Professor Winfried Petry, scientific director of the Research Neutron Source Heinz Maier-Leibnitz (FRM-II), Germany, advisor at the physics department for the Bayerische Elite-Akademie, chair person of the Arbeitsgemeinschaft Metall- und Materialphysik of the German Physical Society (DPG) and a member of the professional council of the German Science Foundation (Deutsche Forschungsgemeinschaft, DFG). We would like to acknowledge and thank all contributors for their submissions, which made this special issue possible in the first place. Moreover, we would like to thank the staff at IOP Publishing for helping us with the administrative aspects and for coordinating the refereeing process, and Valeria Lauter for the beautiful cover artwork. Finally, to the readers, we hope that you find this special issue a valuable resource that provides insights into the present possibilities of neutron and x-ray scattering as powerful tools for the investigation of structure and dynamics. Structure and dynamics determined by neutron and x-ray scattering contents In situ studies of mass transport in liquid alloys by means of neutron radiography F Kargl, M Engelhardt, F Yang, H Weis, P Schmakat, B Schillinger, A Griesche and A Meyer Magnetic spin

  7. Robust and Irreversible Development in Cell Society as a General Consequence of Intra-Inter Dynamics

    OpenAIRE

    Kaneko, Kunihiko; Furusawa, Chikara

    1999-01-01

    A dynamical systems scenario for developmental cell biology is proposed, based on numerical studies of a system with interacting units with internal dynamics and reproduction. Diversification, formation of discrete and recursive types, and rules for differentiation are found as a natural consequence of such a system. "Stem cells" that either proliferate or differentiate to different types stochastically are found to appear when intra-cellular dynamics are chaotic. Robustness of the developmen...

  8. The role of self-determined motivation in job search: A dynamic approach.

    Science.gov (United States)

    da Motta Veiga, Serge P; Gabriel, Allison S

    2016-03-01

    Job search is a dynamic self-regulated process during which job seekers need to stay motivated to secure a job. However, past research has taken a relatively static approach to examining motivation during the job search, in addition to ignoring how the quality of one's motivation--ranging from autonomous to controlled--can influence job search processes. Adopting a within-person perspective, the current study extends self-determination theory (SDT) to the job search context to investigate (a) when autonomous and controlled motivations are more or less prevalent and (b) whether they influence job search effort through metacognitive strategies in differing ways depending upon the amount of time elapsed in the search. In a weekly study of new labor market entrants (Level-2 n = 149; Level-1 n = 691), results indicated that autonomous motivation decreased until the midpoint of the job search and then plateaued, whereas controlled motivation remained stable. Results also showed that autonomous motivation had a consistent, positive relation with metacognitive strategies, whereas the relation between controlled motivation and such strategies was negative early in the job search, but became positive as the job search progressed. Finally, the effects of motivation on job search effort occurred via metacognitive strategies differentially depending upon the time elapsed in the search. Combined, we provide a first glimpse into the dynamics of self-determined motivation on job search processes. (c) 2016 APA, all rights reserved).

  9. Determining the number of kanbans for dynamic production systems: An integrated methodology

    Directory of Open Access Journals (Sweden)

    Özlem Uzun Araz

    2016-08-01

    Full Text Available Just-in-time (JIT is a management philosophy that reduces the inventory levels and eliminates manufacturing wastes by producing only the right quantity at the right time. A kanban system is one of the key elements of JIT philosophy. Kanbans are used to authorize production and to control movement of materials in JIT systems. In Kanban systems, the efficiency of the manufacturing system depends on several factors such as number of kanbans, container size etc. Hence, determining the number of kanbans is a critical decision in Kanban systems. The aim of this study is to develop a methodology that can be used in order to determine the number of kanbans in a dynamic production environment. In this methodology, the changes in system state is monitored in real time manner, and the number of the kanbans are dynamically re-arranged. The proposed methodology integrates simulation, neural networks and Mamdani type fuzzy inference system. The methodology is modelled in simulation environment and applied on a hypothetic production system. We also performed several comparisons for different control policies to show the effectiveness of the proposed methodology.

  10. Inverse Force Determination on a Small Scale Launch Vehicle Model Using a Dynamic Balance

    Science.gov (United States)

    Ngo, Christina L.; Powell, Jessica M.; Ross, James C.

    2017-01-01

    A launch vehicle can experience large unsteady aerodynamic forces in the transonic regime that, while usually only lasting for tens of seconds during launch, could be devastating if structural components and electronic hardware are not designed to account for them. These aerodynamic loads are difficult to experimentally measure and even harder to computationally estimate. The current method for estimating buffet loads is through the use of a few hundred unsteady pressure transducers and wind tunnel test. Even with a large number of point measurements, the computed integrated load is not an accurate enough representation of the total load caused by buffeting. This paper discusses an attempt at using a dynamic balance to experimentally determine buffet loads on a generic scale hammer head launch vehicle model tested at NASA Ames Research Center's 11' x 11' transonic wind tunnel. To use a dynamic balance, the structural characteristics of the model needed to be identified so that the natural modal response could be and removed from the aerodynamic forces. A finite element model was created on a simplified version of the model to evaluate the natural modes of the balance flexures, assist in model design, and to compare to experimental data. Several modal tests were conducted on the model in two different configurations to check for non-linearity, and to estimate the dynamic characteristics of the model. The experimental results were used in an inverse force determination technique with a psuedo inverse frequency response function. Due to the non linearity, the model not being axisymmetric, and inconsistent data between the two shake tests from different mounting configuration, it was difficult to create a frequency response matrix that satisfied all input and output conditions for wind tunnel configuration to accurately predict unsteady aerodynamic loads.

  11. Visualization and orchestration of the dynamic molecular society in cells

    Institute of Scientific and Technical Information of China (English)

    Xuebiao Yao; Guowei Fang

    2009-01-01

    @@ Visualization of specific molecules and their interactions in real space and time is essential to delineate how cellular plasticity and dynamics are achieved and orchestrated as perturbation of cellular plasticity and dynamics is detrimental to health. Elucidation of cellular dynamics requires molecular imaging at nanometer scale at millisecond resolution. The 1st International Conference on Cellular Dynamics and Chemical Biology held in Hefei, China (from 12 September to 15 September,2008) launched the quest by bringing synergism among photonics, chemistry and biology.

  12. A Dynamic Analysis on Determining of Housing Demand: A Comparison for Turkey, Hungary, and UK

    Institute of Scientific and Technical Information of China (English)

    Selahattin Bekmez; Ash Ozpolat

    2014-01-01

    Housing is both good and investment assets so that it plays an important role in the economy. Housing also can be characterized the most complex economic good because of its durability, heterogeneity, locational fixity, the possibility to raise loans against housing collateral, and the effect on well-developed secondary markets. On the other hand, income distribution, socio-economic justice, and regional disparities imply that housing market is an important concept for social and cultural transformation. In this study, the determinants of housing demand were compared for countries. These countries are selected according to economic situation: Turkey, Hungary, and United Kingdom. As a scope of this, the dynamic relationship between the housing demand and variables determining the housing demand in Turkey, Hungary, and UK has been analyzed. The model estimated uses quarterly data from January 2002 to January 2014. Building permits has been considered as housing demand. The other variables used for determining the housing demand are GDP, monetary aggregate, interest rate, and share prices. The long term relationship among variables has been analyzed with Vector Autoregressive Model (VAR) as impulse response and variance decomposition. The findings indicate that determining of housing demand changes according to economic and financial components such as government policies, mortgage system, consumer choice, tax, and subsidy in selected countries. All variables play an important role in housing demand, although the level of their impacts varies.

  13. DNA methylation dynamics in blood after hematopoietic cell transplant.

    Directory of Open Access Journals (Sweden)

    Ramon M Rodriguez

    Full Text Available Epigenetic deregulation is considered a common hallmark of cancer. Nevertheless, recent publications have demonstrated its association with a large array of human diseases. Here, we explore the DNA methylation dynamics in blood samples during hematopoietic cell transplant and how they are affected by pathophysiological events during transplant evolution. We analyzed global DNA methylation in a cohort of 47 patients with allogenic transplant up to 12 months post-transplant. Recipients stably maintained the donor's global methylation levels after transplant. Nonetheless, global methylation is affected by chimerism status. Methylation analysis of promoters revealed that methylation in more than 200 genes is altered 1 month post-transplant when compared with non-pathological methylation levels in the donor. This number decreased by 6 months post-transplant. Finally, we analyzed methylation in IFN-γ, FASL, IL-10, and PRF1 and found association with the severity of the acute graft-versus-host disease. Our results provide strong evidence that methylation changes in blood are linked to underlying physiological events and demonstrate that DNA methylation analysis is a viable strategy for the study of transplantation and for development of biomarkers.

  14. DNA Methylation Dynamics in Blood after Hematopoietic Cell Transplant

    Science.gov (United States)

    Rodriguez, Ramon M.; Suarez-Alvarez, Beatriz; Salvanés, Rubén; Muro, Manuel; Martínez-Camblor, Pablo; Colado, Enrique; Sánchez, Miguel Alcoceba; Díaz, Marcos González; Fernandez, Agustin F.; Fraga, Mario F.; Lopez-Larrea, Carlos

    2013-01-01

    Epigenetic deregulation is considered a common hallmark of cancer. Nevertheless, recent publications have demonstrated its association with a large array of human diseases. Here, we explore the DNA methylation dynamics in blood samples during hematopoietic cell transplant and how they are affected by pathophysiological events during transplant evolution. We analyzed global DNA methylation in a cohort of 47 patients with allogenic transplant up to 12 months post-transplant. Recipients stably maintained the donor’s global methylation levels after transplant. Nonetheless, global methylation is affected by chimerism status. Methylation analysis of promoters revealed that methylation in more than 200 genes is altered 1 month post-transplant when compared with non-pathological methylation levels in the donor. This number decreased by 6 months post-transplant. Finally, we analyzed methylation in IFN-γ, FASL, IL-10, and PRF1 and found association with the severity of the acute graft-versus-host disease. Our results provide strong evidence that methylation changes in blood are linked to underlying physiological events and demonstrate that DNA methylation analysis is a viable strategy for the study of transplantation and for development of biomarkers. PMID:23451113

  15. Measuring dynamic membrane fluctuations in cell membrane using quantitative phase imaging (Conference Presentation)

    Science.gov (United States)

    Lee, SangYun; Kim, Kyoohyun; Park, YongKeun

    2017-02-01

    There is a strong correlation between the dynamic membrane fluctuations and the biomechanical properties of living cells. The dynamic membrane fluctuation consists of submicron displacements, and can be altered by changing the cells' pathophysiological conditions. These results have significant relevance to the understanding of RBC biophysics and pathology, as follows. RBCs must withstand large mechanical deformations during repeated passages through the microvasculature and the fenestrated walls of the splenic sinusoids. This essential ability is diminished with senescence, resulting in physiological destruction of the aging RBCs. Pathological destruction of the red cells, however, occurs in cells affected by a host of diseases such as spherocytosis, malaria, and Sickle cell disease, as RBCs depart from their normal discoid shape and lose their deformability. Therefore, quantifying the RBC deformability insight into a variety of problems regarding the interplay of cell structure, dynamics, and function. Furthermore, the ability to monitor mechanical properties of RBCs is of vital interest in monitoring disease progression or response to treatment as molecular and pharmaceutical approaches for treatment of chronic diseases. Here, we present the measurements of dynamic membrane fluctuations in live cells using quantitative phase imaging techniques. Measuring both the 3-D refractive index maps and the dynamic phase images of live cells are simultaneously measured, from which dynamic membrane fluctuation and deformability of cells are precisely calculated. We also present its applications to various diseases ranging from sickle cell diseases, babesiosis, and to diabetes.

  16. A nanobiosensor for dynamic single cell analysis during microvascular self-organization.

    Science.gov (United States)

    Wang, S; Sun, J; Zhang, D D; Wong, P K

    2016-10-14

    The formation of microvascular networks plays essential roles in regenerative medicine and tissue engineering. Nevertheless, the self-organization mechanisms underlying the dynamic morphogenic process are poorly understood due to a paucity of effective tools for mapping the spatiotemporal dynamics of single cell behaviors. By establishing a single cell nanobiosensor along with live cell imaging, we perform dynamic single cell analysis of the morphology, displacement, and gene expression during microvascular self-organization. Dynamic single cell analysis reveals that endothelial cells self-organize into subpopulations with specialized phenotypes to form microvascular networks and identifies the involvement of Notch1-Dll4 signaling in regulating the cell subpopulations. The cell phenotype correlates with the initial Dll4 mRNA expression level and each subpopulation displays a unique dynamic Dll4 mRNA expression profile. Pharmacological perturbations and RNA interference of Notch1-Dll4 signaling modulate the cell subpopulations and modify the morphology of the microvascular network. Taken together, a nanobiosensor enables a dynamic single cell analysis approach underscoring the importance of Notch1-Dll4 signaling in microvascular self-organization.

  17. Sendai virus utilizes specific sialyloligosaccharides as host cell receptor determinants.

    OpenAIRE

    1980-01-01

    Purified sialyltransferases (CMP-N-acetyl-neuraminate:D-galactosyl-glycoprotein N-acetylneuraminyl-transferase, EC 2.4.99.1) in conjunction with neuraminidase (acylneuraminyl hydrolase, EC 3.2.1.18) were used to produce cell surface sialyloligosaccharides of defined sequence to investigate their role in paramyxovirus infection of host cells. Infection of Madin-Darby bovine kidney cells by Sendai virus was monitored by hemagglutination titer of the virus produced and by changes in morphologica...

  18. Dynamics and roles of phragmoplast microfilaments in cell plate formation during cytokinesis of tobacco BY-2 cells

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yan; ZHANG WenJie; BALUSKA Frantisek; MENZEL Diedrik; REN HaiYun

    2009-01-01

    The phragmoplast is a special apparatus that functions in establishing a cell plate in dividing plant cells.It is known that microfilaments (MFs) are involved in constituting phragmoplast structure, but the dynamic distribution and role of phragmoplast MFs are far from being understood. In this study, the precise structure and dynamics of MFs during the initiation and the late lateral expansion of the phragmoplast were observed by using a tobacco BY-2 cell line stably expressing the microfilament reporter construct GFP-f ABD2. Three-dimensional imaging showed that the phragmoplast MFs were initiated by two populations of MFs emerging between the reconstituting daughter nuclei at anaphase, which migrated to the mid-zone and gave rise to two layers of microfilament arrays. FM4-64 stained vesicles accumulated and fused with the cell plate between the two populations of MFs. The two layers of microfilament arrays of phragmoplast with ends overlapped always surrounded the centrifugally expanding cell plate. Partial disruption of MFs at metaphase by low concentration of latrunculin B resulted in the inhibition of the cell plate consolidation and the blockage of cell plate lateral expansion,whereas high concentration of latrunculin B restrained the progression of the cell cycle. Treating the cell after the initiation of phragmoplast led to the cease of the expansion of the cell plate. Our observations provide new insights into the precise structure and dynamics of phragmoplast MFs during cytokinesis and suggest that dynamic phragmoplast MFs are important in cell plate formation.

  19. Bidirectional control of the inner dynamics of focal adhesions promotes cell migration

    OpenAIRE

    2009-01-01

    Focal adhesions (FA) are bidirectional mechanical biosensors that allow cells to integrate intracellular and extracellular cues. Their function is tightly regulated by changes in molecular composition and also by variation in the spatio-temporal dynamics of FA components within this structure. A closely regulated turnover of FA proteins within FA sites allows cells to respond appropriately to their environment, thereby impacting on cell shape and function. FA protein dynamics are linked to FA...

  20. Polyubiquitin chain assembly and organisation determine the dynamics of protein activation and degradation

    Directory of Open Access Journals (Sweden)

    Lan K. Nguyen

    2014-01-01

    Full Text Available Protein degradation via ubiquitination is a major proteolytic mechanism in cells. Once a protein is destined for degradation, it is tagged by multiple ubiquitin molecules. The synthesised polyubiquitin chains can be recognised by the 26S proteosome where proteins are degraded. These chains form through multiple ubiquitination cycles that are similar to multi-site phosphorylation cycles. As kinases and phosphatases, two opposing enzymes (E3 ligases and deubiquitinases DUBs catalyse (deubiquitination cycles. Although multi-ubiquitination cycles are fundamental mechanisms of controlling protein concentrations within a cell, their dynamics have never been explored. Here, we fill this knowledge gap. We show that under permissive physiological conditions, the formation of polyubiquitin chain of length greater than two and subsequent degradation of the ubiquitinated protein, which is balanced by protein synthesis, can display bistable, switch-like responses. Interestingly, the occurrence of bistability becomes pronounced, as the chain grows, giving rise to all-or-none regulation at the protein levels. We give predictions of protein distributions under bistable regime awaiting experimental verification. Importantly, we show for the first time that sustained oscillations can robustly arise in the process of formation of ubiquitin chain, largely due to the degradation of the target protein. This new feature is opposite to the properties of multi-site phosphorylation cycles, which are incapable of generating oscillation if the total abundance of interconverted protein forms is conserved. We derive structural and kinetic constraints for the emergence of oscillations, indicating that a competition between different substrate forms and the E3 and DUB is critical for oscillation. Our work provides the first detailed elucidation of the dynamical features brought about by different molecular setups of the polyubiquitin chain assembly process responsible for

  1. Determination of individual cell Michaelis-Menten constants.

    Science.gov (United States)

    Sunray, Merav; Zurgil, Naomi; Shafran, Yana; Deutsch, Mordechai

    2002-01-01

    A novel methodology for the measurement and analysis of apparent K(M) (Michaelis-Menten constant) and V(MAX) values of individual cells is suggested. It is based on a mathematical model that considers substrate influx into the cell, its intracellular enzymatic hydrolysis, and the product efflux. The mathematical formulation was approximated linearly in order to analyze intracellular substrate conversion characteristics via Michaelis-Menten theory. Utilizing static cytometry, the time dependence of the fluorescence intensity [FI(t)] emitted from prelocalized and defined FDA stained cells was recorded. This required frequent periodical measurements of the same cells, which are sequentially exposed to various fluorogenic substrate concentrations. Model simulations correlated with experimental results. Differences in distributions of individual K(M) and V(MAX) values of cells incubated with and without PHA were evident. Average K(M) and V(MAX) values of PHA-stimulated cells increased by 99% and 540%, respectively. This study may provide a tool for assessing intracellular enzymatic activity in individual intact cells under defined physiologic conditions. This may open new vistas in various areas, giving answers to critical questions arising in the field of cell and developmental biology, immunology, oncology, and pharmacology. Copyright 2001 Wiley-Liss, Inc.

  2. Fast spatiotemporal correlation spectroscopy to determine protein lateral diffusion laws in live cell membranes.

    Science.gov (United States)

    Di Rienzo, Carmine; Gratton, Enrico; Beltram, Fabio; Cardarelli, Francesco

    2013-07-23

    Spatial distribution and dynamics of plasma-membrane proteins are thought to be modulated by lipid composition and by the underlying cytoskeleton, which forms transient barriers to diffusion. So far this idea was probed by single-particle tracking of membrane components in which gold particles or antibodies were used to individually monitor the molecules of interest. Unfortunately, the relatively large particles needed for single-particle tracking can in principle alter the very dynamics under study. Here, we use a method that makes it possible to investigate plasma-membrane proteins by means of small molecular labels, specifically single GFP constructs. First, fast imaging of the region of interest on the membrane is performed. For each time delay in the resulting stack of images the average spatial correlation function is calculated. We show that by fitting the series of correlation functions, the actual protein "diffusion law" can be obtained directly from imaging, in the form of a mean-square displacement vs. time-delay plot, with no need for interpretative models. This approach is tested with several simulated 2D diffusion conditions and in live Chinese hamster ovary cells with a GFP-tagged transmembrane transferrin receptor, a well-known benchmark of membrane-skeleton-dependent transiently confined diffusion. This approach does not require extraction of the individual trajectories and can be used also with dim and dense molecules. We argue that it represents a powerful tool for the determination of kinetic and thermodynamic parameters over very wide spatial and temporal scales.

  3. Chromatographic behaviour of single cells in a microchannel with dynamic geometry.

    Science.gov (United States)

    Gerhardt, Thomas; Woo, Sangpil; Ma, Hongshen

    2011-08-21

    We present the design of a microchannel with dynamic geometry that imparts different flow rates to different cells based on their physical properties. This dynamic microchannel is formed between a textured surface and a flexible membrane. As cells flow through the microchannel, the height of the channel oscillates causing periodic entrapment of the larger cells, and as a result, attenuating their velocity relative to the bulk liquid. The smaller cells are not slowed by the moving microstructure, and move synchronously with the bulk liquid. The ability of the dynamic microchannel to selectively attenuate the flow rate of eukaryotic cells is similar to a size-exclusion chromatography column, but with the opposite behavior. The speed of smaller substances is attenuated relative to the larger substances in traditional size-exclusion chromatography columns, whereas the speed of the larger substances that is attenuated in the dynamic microchannel. We verified this property by tracking the flow of single cells through the dynamic microchannel. L1210 mouse lymphoma cells (MLCs), peripheral blood mononuclear cells (PBMCs), and red blood cells (RBCs) were used as model cells. We showed that the flow rate of MLC is slowed by more than 50% compared to PBMCs and RBCs. We characterized the operation of the microchannel by measuring the velocity of each of the three cell types as a function of the pressures used to oscillate the membrane position, as well as the duty cycle of the oscillation.

  4. On the origins of the universal dynamics of endogenous granules in mammalian cells.

    Science.gov (United States)

    Vanapalli, Siva A; Li, Yixuan; Mugele, Frieder; Duits, Michel H G

    2009-12-01

    Endogenous granules (EGs) that consist of lipid droplets and mitochondria have been commonly used to assess intracellular mechanical properties via multiple particle tracking microrheology (MPTM). Despite their widespread use, the nature of interaction of EGs with the cytoskeletal network and the type of forces driving their dynamics--both of which are crucial for the interpretation of the results from MPTM technique--are yet to be resolved. In this report, we study the dynamics of endogenous granules in mammalian cells using particle tracking methods. We find that the ensemble dynamics of EGs is diffusive in three types of mammalian cells (endothelial cells, smooth muscle cells and fibroblasts), thereby suggesting an apparent universality in their dynamical behavior. Moreover, in a given cell, the amplitude of the mean-squared displacement for EGs is an order of magnitude larger than that of injected particles. This observation along with results from ATP depletion and temperature intervention studies suggests that cytoskeletal active forces drive the dynamics of EGs. To elucidate the dynamical origin of the diffusive-like nonthermal motion, we consider three active force generation mechanisms--molecular motor transport, actomyosin contractility and microtubule polymerization forces. We test these mechanisms using pharmacological interventions. Experimental evidence and model calculations suggest that EGs are intimately linked to microtubules and that microtubule polymerization forces drive their dynamics. Thus, endogenous granules could serve as non-invasive probes for microtubule network dynamics in mammalian cells.

  5. A theoretical framework for determining cerebral vascular function and heterogeneity from dynamic susceptibility contrast MRI.

    Science.gov (United States)

    Digernes, Ingrid; Bjørnerud, Atle; Vatnehol, Svein Are S; Løvland, Grete; Courivaud, Frédéric; Vik-Mo, Einar; Meling, Torstein R; Emblem, Kyrre E

    2017-06-01

    Mapping the complex heterogeneity of vascular tissue in the brain is important for understanding cerebrovascular disease. In this translational study, we build on previous work using vessel architectural imaging (VAI) and present a theoretical framework for determining cerebral vascular function and heterogeneity from dynamic susceptibility contrast magnetic resonance imaging (MRI). Our tissue model covers realistic structural architectures for vessel branching and orientations, as well as a range of hemodynamic scenarios for blood flow, capillary transit times and oxygenation. In a typical image voxel, our findings show that the apparent MRI relaxation rates are independent of the mean vessel orientation and that the vortex area, a VAI-based parameter, is determined by the relative oxygen saturation level and the vessel branching of the tissue. Finally, in both simulated and patient data, we show that the relative distributions of the vortex area parameter as a function of capillary transit times show unique characteristics in normal-appearing white and gray matter tissue, whereas tumour-voxels in comparison display a heterogeneous distribution. Collectively, our study presents a comprehensive framework that may serve as a roadmap for in vivo and per-voxel determination of vascular status and heterogeneity in cerebral tissue.

  6. Determination of the protonation state of the Asp dyad: conventional molecular dynamics versus thermodynamic integration.

    Science.gov (United States)

    Huang, Jinfeng; Zhu, Yali; Sun, Bin; Yao, Yuan; Liu, Junjun

    2016-03-01

    The protonation state of the Asp dyad is important as it can reveal enzymatic mechanisms, and the information this provides can be used in the development of drugs for proteins such as memapsin 2 (BACE-1), HIV-1 protease, and rennin. Conventional molecular dynamics (MD) simulations have been successfully used to determine the preferred protonation state of the Asp dyad. In the present work, we demonstrate that the results obtained from conventional MD simulations can be greatly influenced by the particular force field applied or the values used for control parameters. In principle, free-energy changes between possible protonation states can be used to determine the protonation state. We show that protonation state prediction by the thermodynamic integration (TI) method is insensitive to force field version or to the cutoff for calculating nonbonded interactions (a control parameter). In the present study, the protonation state of the Asp dyad predicted by TI calculations was the same regardless of the force field and cutoff value applied. Contrary to the intuition that conventional MD is more efficient, our results clearly show that the TI method is actually more efficient and more reliable for determining the protonation state of the Asp dyad.

  7. Methodology to determine failure characteristics of planar soft tissues using a dynamic tensile test.

    Science.gov (United States)

    Jacquemoud, C; Bruyere-Garnier, K; Coret, M

    2007-01-01

    Predicting the injury risk in automotive collisions requires accurate knowledge of human tissues, more particularly their mechanical properties under dynamic loadings. The present methodology aims to determine the failure characteristics of planar soft tissues such as skin, hollow organs and large vessel walls. This consists of a dynamic tensile test, which implies high-testing velocities close to those in automotive collisions. To proceed, I-shaped tissue samples are subjected to dynamic tensile tests using a customized tensile device based on the drop test principle. Data acquisition has especially been adapted to heterogeneous and soft biological tissues given that standard measurement systems (considered to be global) have been completed with a non-contact and full-field strain measurement (considered to be local). This local measurement technique, called the Image Correlation Method (ICM) provides an accurate strain analysis by revealing strain concentrations and avoids damaging the tissue. The methodology has first been applied to human forehead skin and can be further expanded to other planar soft tissues. The failure characteristics for the skin in terms of ultimate stress are 3 MPa +/- 1.5 MPa. The ultimate global longitudinal strains are equal to 9.5%+/-1.9% (Green-Lagrange strain), which contrasts with the ultimate local longitudinal strain values of 24.0%+/-5.3% (Green-Lagrange strain). This difference is a consequence of the tissue heterogeneity, clearly illustrated by the heterogeneous distribution of the local strain field. All data will assist in developing the tissue constitutive law that will be implemented in finite element models.

  8. Root responses to soil physical conditions; growth dynamics from field to cell.

    Science.gov (United States)

    Bengough, A Glyn; Bransby, M Fraser; Hans, Joachim; McKenna, Stephen J; Roberts, Tim J; Valentine, Tracy A

    2006-01-01

    Root growth in the field is often slowed by a combination of soil physical stresses, including mechanical impedance, water stress, and oxygen deficiency. The stresses operating may vary continually, depending on the location of the root in the soil profile, the prevailing soil water conditions, and the degree to which the soil has been compacted. The dynamics of root growth responses are considered in this paper, together with the cellular responses that underlie them. Certain root responses facilitate elongation in hard soil, for example, increased sloughing of border cells and exudation from the root cap decreases friction; and thickening of the root relieves stress in front of the root apex and decreases buckling. Whole root systems may also grow preferentially in loose versus dense soil, but this response depends on genotype and the spatial arrangement of loose and compact soil with respect to the main root axes. Decreased root elongation is often accompanied by a decrease in both cell flux and axial cell extension, and recent computer-based models are increasing our understanding of these processes. In the case of mechanical impedance, large changes in cell shape occur, giving rise to shorter fatter cells. There is still uncertainty about many aspects of this response, including the changes in cell walls that control axial versus radial extension, and the degree to which the epidermis, cortex, and stele control root elongation. Optical flow techniques enable tracking of root surfaces with time to yield estimates of two-dimensional velocity fields. It is demonstrated that these techniques can be applied successfully to time-lapse sequences of confocal microscope images of living roots, in order to determine velocity fields and strain rates of groups of cells. In combination with new molecular approaches this provides a promising way of investigating and modelling the mechanisms controlling growth perturbations in response to environmental stresses.

  9. Determination of Original Infection Source of H7N9 Avian Influenza by Dynamical Model

    Science.gov (United States)

    Zhang, Juan; Jin, Zhen; Sun, Gui-Quan; Sun, Xiang-Dong; Wang, You-Ming; Huang, Baoxu

    2014-05-01

    H7N9, a newly emerging virus in China, travels among poultry and human. Although H7N9 has not aroused massive outbreaks, recurrence in the second half of 2013 makes it essential to control the spread. It is believed that the most effective control measure is to locate the original infection source and cut off the source of infection from human. However, the original infection source and the internal transmission mechanism of the new virus are not totally clear. In order to determine the original infection source of H7N9, we establish a dynamical model with migratory bird, resident bird, domestic poultry and human population, and view migratory bird, resident bird, domestic poultry as original infection source respectively to fit the true dynamics during the 2013 pandemic. By comparing the date fitting results and corresponding Akaike Information Criterion (AIC) values, we conclude that migrant birds are most likely the original infection source. In addition, we obtain the basic reproduction number in poultry and carry out sensitivity analysis of some parameters.

  10. Dynamic light scattering and atomic force microscopy techniques for size determination of polyurethane nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Giehl Zanetti-Ramos, Betina [Laboratorio de Bioenergetica e Bioquimica de Macromoleculas, Departamento de Ciencias Farmaceuticas (Brazil)], E-mail: betinagzramos@pq.cnpq.br; Beddin Fritzen-Garcia, Mauricia [Laboratorio de Bioenergetica e Bioquimica de Macromoleculas, Departamento de Ciencias Farmaceuticas (Brazil); Schweitzer de Oliveira, Cristian; Avelino Pasa, Andre [Laboratorio de Filmes Finos e Superficie, Departamento de Fisica (Brazil); Soldi, Valdir [Grupo de Estudos em Materiais Polimericos, Departamento de Quimica, Universidade Federal de Santa Catarina, 88040-900, Florianopolis, SC (Brazil); Borsali, Redouane [Centre de Recherche sur les Macromolecules Vegetales CERMAV/CNRS, 38041 - Grenoble (France); Creczynski-Pasa, Tania Beatriz [Laboratorio de Bioenergetica e Bioquimica de Macromoleculas, Departamento de Ciencias Farmaceuticas (Brazil)

    2009-03-01

    Nanoparticles have applications in various industrial fields principally in drug delivery. Nowadays, there are several processes for manufacturing colloidal polymeric systems and methods of preparation as well as of characterization. In this work, Dynamic Light Scattering and Atomic Force Microscopy techniques were used to characterize polyurethane nanoparticles. The nanoparticles were prepared by miniemulsion technique. The lipophilic monomers, isophorone diisocyanate (IPDI) and natural triol, were emulsified in water containing surfactant. In some formulations the poly(ethylene glycol) was used as co-monomer to obtain the hydrophilic and pegylated nanoparticles. Polyurethane nanoparticles observed by atomic force microscopy (AFM) were spherical with diameter around 209 nm for nanoparticles prepared without PEG. From AFM imaging two populations of nanoparticles were observed in the formulation prepared with PEG (218 and 127 nm) while dynamic light scattering (DLS) measurements showed a monodisperse size distribution around 250 nm of diameters for both formulations. The polydispersity index of the formulations and the experimental procedures could influence the particle size determination with these techniques.

  11. Inquiring the niche determinants of social media websites in dynamically mobile hypercompetitive communication era

    Directory of Open Access Journals (Sweden)

    Chih-Cheng Huang

    2016-03-01

    Full Text Available This research cross-employs the information communication distribution transaction and analytic network process models to effectively institute the hierarchical evaluated model and utilizes, in specific, fuzzy theory and the grey relation analysis approaches of multiple criteria decision-making methodology into the weight measurements of expert’s questionnaires from three analytical perspectives (user’s satisfaction, corporate commitment, and social trust of relationship quality in order to explore the niche determinants of the social media websites in the contemporarily hypercompetitive and dynamic online era. Consequently, as for the measured consequences after a series of complicated and systematical calculations, the most valuable findings in this research are (1 the technological interfaces of social media websites is a positive niche in the dynamically mobile hypercompetitive communication era and (2 the “social media websites” is in a position of becoming one of the social media mainstreams in the online technology field based on the measured weights from the detailed survey data collected from experts in this research.

  12. Measuring and Modeling Sonoporation Dynamics in Mammalian Cells via Calcium Imaging

    Science.gov (United States)

    Kumon, R. E.; Parikh, P.; Sabens, D.; Aehle, M.; Kourennyi, D.; Deng, C. X.

    2007-05-01

    In this study, calcium imaging via the fluorescent indicator Fura-2 is used to characterize the sonoporation of Chinese Hamster Ovarian (CHO) cells in the presence of Optison™ microbubbles. Evolution of the calcium concentration within cells is determined from real-time fluorescence intensity measurements before, during, and after exposure to a 1 MHz ultrasound tone burst (0.2 s, 0.45 MPa). To relate microscopic sonoporation parameters to the measurements, an analytical model that includes sonoporation and plasma membrane transport is developed, assuming rapid mixing (uniform spatial distribution) in the cell. Fitting the measured data to the model provides estimated values for the poration area as a function of poration relaxation rate as well as plasma membrane pump and leakage rates. A modified compartment model that includes the effects of sonoporation, buffering proteins, and transport across the plasma membrane, endoplasmic reticulum, and mitochondria is also investigated. Numerical 3solutions of this model show a variety of behaviors for the calcium dynamics of the cell.

  13. Quantitative analysis of organelle distribution and dynamics in Physcomitrella patens protonemal cells

    Directory of Open Access Journals (Sweden)

    Furt Fabienne

    2012-05-01

    Full Text Available Abstract Background In the last decade, the moss Physcomitrella patens has emerged as a powerful plant model system, amenable for genetic manipulations not possible in any other plant. This moss is particularly well suited for plant polarized cell growth studies, as in its protonemal phase, expansion is restricted to the tip of its cells. Based on pollen tube and root hair studies, it is well known that tip growth requires active secretion and high polarization of the cellular components. However, such information is still missing in Physcomitrella patens. To gain insight into the mechanisms underlying the participation of organelle organization in tip growth, it is essential to determine the distribution and the dynamics of the organelles in moss cells. Results We used fluorescent protein fusions to visualize and track Golgi dictyosomes, mitochondria, and peroxisomes in live protonemal cells. We also visualized and tracked chloroplasts based on chlorophyll auto-fluorescence. We showed that in protonemata all four organelles are distributed in a gradient from the tip of the apical cell to the base of the sub-apical cell. For example, the density of Golgi dictyosomes is 4.7 and 3.4 times higher at the tip than at the base in caulonemata and chloronemata respectively. While Golgi stacks are concentrated at the extreme tip of the caulonemata, chloroplasts and peroxisomes are totally excluded. Interestingly, caulonemata, which grow faster than chloronemata, also contain significantly more Golgi dictyosomes and fewer chloroplasts than chloronemata. Moreover, the motility analysis revealed that organelles in protonemata move with low persistency and average instantaneous speeds ranging from 29 to 75 nm/s, which are at least three orders of magnitude slower than those of pollen tube or root hair organelles. Conclusions To our knowledge, this study reports the first quantitative analysis of organelles in Physcomitrella patens and will make possible

  14. Definition of molecular determinants of prostate cancer cell bone extravasation.

    Science.gov (United States)

    Barthel, Steven R; Hays, Danielle L; Yazawa, Erika M; Opperman, Matthew; Walley, Kempland C; Nimrichter, Leonardo; Burdick, Monica M; Gillard, Bryan M; Moser, Michael T; Pantel, Klaus; Foster, Barbara A; Pienta, Kenneth J; Dimitroff, Charles J

    2013-01-15

    Advanced prostate cancer commonly metastasizes to bone, but transit of malignant cells across the bone marrow endothelium (BMEC) remains a poorly understood step in metastasis. Prostate cancer cells roll on E-selectin(+) BMEC through E-selectin ligand-binding interactions under shear flow, and prostate cancer cells exhibit firm adhesion to BMEC via β1, β4, and αVβ3 integrins in static assays. However, whether these discrete prostate cancer cell-BMEC adhesive contacts culminate in cooperative, step-wise transendothelial migration into bone is not known. Here, we describe how metastatic prostate cancer cells breach BMEC monolayers in a step-wise fashion under physiologic hemodynamic flow. Prostate cancer cells tethered and rolled on BMEC and then firmly adhered to and traversed BMEC via sequential dependence on E-selectin ligands and β1 and αVβ3 integrins. Expression analysis in human metastatic prostate cancer tissue revealed that β1 was markedly upregulated compared with expression of other β subunits. Prostate cancer cell breaching was regulated by Rac1 and Rap1 GTPases and, notably, did not require exogenous chemokines as β1, αVβ3, Rac1, and Rap1 were constitutively active. In homing studies, prostate cancer cell trafficking to murine femurs was dependent on E-selectin ligand, β1 integrin, and Rac1. Moreover, eliminating E-selectin ligand-synthesizing α1,3 fucosyltransferases in transgenic adenoma of mouse prostate mice dramatically reduced prostate cancer incidence. These results unify the requirement for E-selectin ligands, α1,3 fucosyltransferases, β1 and αVβ3 integrins, and Rac/Rap1 GTPases in mediating prostate cancer cell homing and entry into bone and offer new insight into the role of α1,3 fucosylation in prostate cancer development.

  15. High frequency dynamics of BMG determined by synchrotron radiation: A microscopic picture

    Energy Technology Data Exchange (ETDEWEB)

    Serrano, Jorge, E-mail: jserrano@fa.upc.ed [Institucio Catalana de Recerca i Estudis Avancats (ICREA), Univ. Politecnica de Catalunya, Avda. del Canal Olimpic 15, Castelldefels (Spain); Dept. de Fisica Aplicada, EPSC, Univ. Politecnica de Catalunya, Avda. del Canal Olimpic 15, 08860 Castelldefels (Spain); Pineda, Eloi [Dept. de Fisica i Enginyeria Nuclear, ESAB, Univ. Politecnica de Catalunya, Avda. del Canal Olimpic 15, 08860 Castelldefels (Spain); Bruna, Pere [Dept. de Fisica Aplicada, EPSC, Univ. Politecnica de Catalunya, Avda. del Canal Olimpic 15, 08860 Castelldefels (Spain); Labrador, Ana [LLS, BM16-ESRF, BP 220, 38043 Grenoble Cedex 9 (France); Le Tacon, Mathieu; Krisch, Michael; Monaco, Giulio [European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, BP 220, 38043 Grenoble Cedex 9 (France); Crespo, Daniel [Dept. de Fisica Aplicada, EPSC, Univ. Politecnica de Catalunya, Avda. del Canal Olimpic 15, 08860 Castelldefels (Spain)

    2010-04-16

    Mechanical properties are becoming the focus in research on bulk metallic glasses (BMG), as they are the limiting factor for structural applications. A wide range of experimental techniques gives complementary macroscopic data that are often difficult to correlate with the microscopic structural knowledge of the same materials. Recently, high resolution inelastic X-ray scattering (IXS) was applied to determine the high frequency dynamics of BMG [T. Scopigno, J.-B. Suck, R. Angelini, F. Albergamo, G. Ruocco, Phys. Rev. Lett. 96 (2006) 135501]. This technique offers a new approach to the mechanic properties helping to bridge the gap between the microscopic and the macroscopic picture. Here we will present results of IXS experiments on bulk metallic glasses with different fragility values, obtained at the European Synchrotron Radiation Facility (ESRF) in Grenoble (France).

  16. System Dynamics Modeling for Determining Optimal Ship Sizes and Types in Coastal Liner Services

    Directory of Open Access Journals (Sweden)

    Sung-il Park

    2014-04-01

    Full Text Available The problem of determining the required ship investment for deployment is an ongoing problem faced by governments and ship operators. The nature of ship investment is capital-intensive and the return on investment is often take long time. This paper attempts to establish system dynamics modeling (SDM to simulate and solve this problem in order to help ship operators make effective strategic decisions. A case study of coastal liner services between Incheon and Baengnyeong Island in South Korea was performed. Using scenario analysis, the possible ship sizes (small: 350 tons; large: 2,500 tons and types (new or used were considered by comparing potential revenue with costs. The results indicated that putting a used large-sized ship into operation would accommodate the increasing passenger and cargo volumes, and improve customer services.

  17. Robust and Irreversible Development in Cell Society as a General Consequence of Intra-Inter Dynamics

    CERN Document Server

    Kaneko, K; Kaneko, Kunihiko; Furusawa, Chikara

    1999-01-01

    A dynamical systems scenario for developmental cell biology is proposed, based on numerical studies of a system with interacting units with internal dynamics and reproduction. Diversification, formation of discrete and recursive types, and rules for differentiation are found as a natural consequence of such a system. "Stem cells" that either proliferate or differentiate to different types stochastically are found to appear when intra-cellular dynamics are chaotic. Robustness of the developmental process against microscopic and macroscopic perturbations is shown to be a natural consequence of such intra-inter dynamics, while irreversibility in developmental process is discussed in terms of the gain of stability, loss of diversity and chaotic instability.

  18. A Comprehensive Fluid Dynamic-Diffusion Model of Blood Microcirculation with Focus on Sickle Cell Disease

    Science.gov (United States)

    Le Floch, Francois; Harris, Wesley L.

    2009-11-01

    A novel methodology has been developed to address sickle cell disease, based on highly descriptive mathematical models for blood flow in the capillaries. Our investigations focus on the coupling between oxygen delivery and red blood cell dynamics, which is crucial to understanding sickle cell crises and is unique to this blood disease. The main part of our work is an extensive study of blood dynamics through simulations of red cells deforming within the capillary vessels, and relies on the use of a large mathematical system of equations describing oxygen transfer, blood plasma dynamics and red cell membrane mechanics. This model is expected to lead to the development of new research strategies for sickle cell disease. Our simulation model could be used not only to assess current researched remedies, but also to spur innovative research initiatives, based on our study of the physical properties coupled in sickle cell disease.

  19. Molecular determinants of epidermal growth factor binding: a molecular dynamics study.

    Directory of Open Access Journals (Sweden)

    Jeffrey M Sanders

    Full Text Available The epidermal growth factor receptor (EGFR is a member of the receptor tyrosine kinase family that plays a role in multiple cellular processes. Activation of EGFR requires binding of a ligand on the extracellular domain to promote conformational changes leading to dimerization and transphosphorylation of intracellular kinase domains. Seven ligands are known to bind EGFR with affinities ranging from sub-nanomolar to near micromolar dissociation constants. In the case of EGFR, distinct conformational states assumed upon binding a ligand is thought to be a determining factor in activation of a downstream signaling network. Previous biochemical studies suggest the existence of both low affinity and high affinity EGFR ligands. While these studies have identified functional effects of ligand binding, high-resolution structural data are lacking. To gain a better understanding of the molecular basis of EGFR binding affinities, we docked each EGFR ligand to the putative active state extracellular domain dimer and 25.0 ns molecular dynamics simulations were performed. MM-PBSA/GBSA are efficient computational approaches to approximate free energies of protein-protein interactions and decompose the free energy at the amino acid level. We applied these methods to the last 6.0 ns of each ligand-receptor simulation. MM-PBSA calculations were able to successfully rank all seven of the EGFR ligands based on the two affinity classes: EGF>HB-EGF>TGF-α>BTC>EPR>EPG>AR. Results from energy decomposition identified several interactions that are common among binding ligands. These findings reveal that while several residues are conserved among the EGFR ligand family, no single set of residues determines the affinity class. Instead we found heterogeneous sets of interactions that were driven primarily by electrostatic and Van der Waals forces. These results not only illustrate the complexity of EGFR dynamics but also pave the way for structure-based design of

  20. Automatic cell cloning assay for determining the clonogenic capacity of cancer and cancer stem-like cells.

    Science.gov (United States)

    Fedr, Radek; Pernicová, Zuzana; Slabáková, Eva; Straková, Nicol; Bouchal, Jan; Grepl, Michal; Kozubík, Alois; Souček, Karel

    2013-05-01

    The clonogenic assay is a well-established in vitro method for testing the survival and proliferative capability of cells. It can be used to determine the cytotoxic effects of various treatments including chemotherapeutics and ionizing radiation. However, this approach can also characterize cells with different phenotypes and biological properties, such as stem cells or cancer stem cells. In this study, we implemented a faster and more precise method for assessing the cloning efficiency of cancer stem-like cells that were characterized and separated using a high-speed cell sorter. Cell plating onto a microplate using an automatic cell deposition unit was performed in a single-cell or dilution rank mode by the fluorescence-activated cell sorting method. We tested the new automatic cell-cloning assay (ACCA) on selected cancer cell lines and compared it with the manual approach. The obtained results were also compared with the results of the limiting dilution assay for different cell lines. We applied the ACCA to analyze the cloning capacity of different subpopulations of prostate and colon cancer cells based on the expression of the characteristic markers of stem (CD44 and CD133) and cancer stem cells (TROP-2, CD49f, and CD44). Our results revealed that the novel ACCA is a straightforward approach for determining the clonogenic capacity of cancer stem-like cells identified in both cell lines and patient samples. Copyright © 2013 International Society for Advancement of Cytometry.

  1. Cell fate determination during tooth development and regeneration.

    Science.gov (United States)

    Mitsiadis, Thimios A; Graf, Daniel

    2009-09-01

    Teeth arise from sequential and reciprocal interactions between the oral epithelium and the underlying cranial neural crest-derived mesenchyme. Their formation involves a precisely orchestrated series of molecular and morphogenetic events, and gives us the opportunity to discover and understand the nature of the signals that direct cell fates and patterning. For that reason, it is important to elucidate how signaling factors work together in a defined number of cells to generate the diverse and precise patterned structures of the mature functional teeth. Over the last decade, substantial research efforts have been directed toward elucidating the molecular mechanisms that control cell fate decisions during tooth development. These efforts have contributed toward the increased knowledge on dental stem cells, and observation of the molecular similarities that exist between tooth development and regeneration.

  2. Manufacturing of Human Umbilical Cord Mesenchymal Stromal Cells on Microcarriers in a Dynamic System for Clinical Use

    Directory of Open Access Journals (Sweden)

    Florian Petry

    2016-01-01

    Full Text Available The great properties of human mesenchymal stromal cells (hMSCs make these cells an important tool in regenerative medicine. Because of the limitations of hMSCs derived from the bone marrow during isolation and expansion, hMSCs derived from the umbilical cord stroma are a great alternative to overcome these issues. For a large expansion of these cells, we performed a process transfer from static culture to a dynamic system. For this reason, a microcarrier selection out of five microcarrier types was made to achieve a suitable growth surface for the cells. The growth characteristics and metabolite consumption and production were used to compare the cells growth in 12-well plate and spinner flask. The goal to determine relevant process parameters to transfer the expansion process into a stirred tank bioreactor was achieved.

  3. Manufacturing of Human Umbilical Cord Mesenchymal Stromal Cells on Microcarriers in a Dynamic System for Clinical Use

    Science.gov (United States)

    Petry, Florian; Smith, J. Robert; Leber, Jasmin; Salzig, Denise; Czermak, Peter; Weiss, Mark L.

    2016-01-01

    The great properties of human mesenchymal stromal cells (hMSCs) make these cells an important tool in regenerative medicine. Because of the limitations of hMSCs derived from the bone marrow during isolation and expansion, hMSCs derived from the umbilical cord stroma are a great alternative to overcome these issues. For a large expansion of these cells, we performed a process transfer from static culture to a dynamic system. For this reason, a microcarrier selection out of five microcarrier types was made to achieve a suitable growth surface for the cells. The growth characteristics and metabolite consumption and production were used to compare the cells growth in 12-well plate and spinner flask. The goal to determine relevant process parameters to transfer the expansion process into a stirred tank bioreactor was achieved. PMID:26977155

  4. A phenomenological model for the dynamics of cell cycle in responding to X-rays

    Institute of Scientific and Technical Information of China (English)

    Zhang Sheng; Ao Bin; Ye Caiyong; Yang Lei; Zhou Guangming

    2015-01-01

    Objective To establish a model to predict the cell-cycle process in response to ionizing radiation.Methods Human choroidal malignant melanoma 92-1 cells were used and the cell cycle distribution of cells was analyzed in 0-96 h after exposure to X-rays.A phenomenological model was constructed based on biological knowledge to describe the cell cycle dynamics in experiments.Results In the present study,a phenomenological model was constructed to describe the cellcycle dynamics of synchronized 92-1 cells in responding to various doses of ionizing radiation.The simulation results obtained with the model were consistent with the experimental data,demonstrating that the model had a good expansibility and could be used to predict the dynamics of cell cycle in responding to ionizing radiation.Further theoretical modeling of the cellcycle dynamics was made and the results were consistent with the simulation.Conclusions A phenomenological model was constructed which could be used to describe the dynamics of cell cycle of cells exposed to ionizing radiation and was supported by the experimental data.Because this model is easy to run by the written code,it has a good expansibility for studying the behaviors of cell populations under various conditions.

  5. Dynamics of p53: A Master Decider of Cell Fate.

    Science.gov (United States)

    Luo, Qingyin; Beaver, Jill M; Liu, Yuan; Zhang, Zunzhen

    2017-02-09

    Cellular stress-induced temporal alterations-i.e., dynamics-are typically exemplified  by the dynamics of p53 that serve as a master to determine cell fate. p53 dynamics were initially  identified as the variations of p53 protein levels. However, a growing number of studies have  shown that p53 dynamics are also manifested in variations in the activity, spatial location, and  posttranslational modifications of p53 proteins, as well as the interplay among all p53 dynamical  features. These are essential in determining a specific outcome of cell fate. In this review, we  discuss the importance of the multifaceted features of p53 dynamics and their roles in the cell fate  decision process, as well as their potential applications in p53-based cancer therapy. The review  provides new insights into p53 signaling pathways and their potentials in the development of new  strategies in p53-based cancer therapy.

  6. Suppression of microtubule dynamics by discodermolide by a novel mechanism is associated with mitotic arrest and inhibition of tumor cell proliferation.

    Science.gov (United States)

    Honore, Stéphane; Kamath, Kathy; Braguer, Diane; Wilson, Leslie; Briand, Claudette; Jordan, Mary Ann

    2003-12-01

    Discodermolide is a new microtubule-targeted drug in Phase I clinical trials that inhibits tumor growth and induces G(2)-M cell cycle arrest. It is effective against paclitaxel-resistant cell lines and acts synergistically in combination with paclitaxel. Suppression of microtubule dynamics by microtubule-targeted drugs has been hypothesized to be responsible for their ability to inhibit mitotic progression and cell proliferation. To determine whether discodermolide blocks mitosis by an effect on microtubule dynamics, we analyzed the effects of discodermolide on microtubule dynamics in living A549 human lung cancer cells during interphase at concentrations that block mitosis and inhibit cell proliferation. We found that discodermolide (7-166 nM) significantly suppressed microtubule dynamic instability. At the IC(50) for proliferation (7 nM discodermolide, 72 h), overall dynamicity was reduced by 23%. The principal parameters of dynamic instability suppressed by discodermolide were the microtubule shortening rate and length shortened. In addition, discodermolide markedly increased the frequency of rescued catastrophes. At the discodermolide concentration that resulted in 50% of maximal mitotic block (83 nM, 20 h), most microtubules were completely non-dynamic, no anaphases occurred, and all spindles were abnormal. The dynamicity of the remaining dynamic microtubules was reduced by 62%. The results indicate that a principal mechanism of inhibition of cell proliferation and mitotic block by discodermolide is suppression of microtubule dynamics. Importantly, the results indicate significant additional stabilizing effects of discodermolide on microtubule dynamics as compared with those of paclitaxel that may in turn reflect differences in their binding sites and their effects on tubulin conformation.

  7. A dynamic course of T cell defects in individuals at risk for mood disorders

    NARCIS (Netherlands)

    Snijders, G.; Schiweck, C.; Mesman, E.; Grosse, L.; De Wit, H.; Nolen, W. A.; Drexhage, H. A.; Hillegers, M. H. J.

    2016-01-01

    Objectives: T cell abnormalities have been repeatedly reported in adult patients with mood disorders, suggesting a role of these cells in the pathogenesis of these disorders. In the present study, we explored the dynamics of circulating T cell subsets over time in a population at high familial risk

  8. Application of Vehicle Dynamic Modeling in Uavs for Precise Determination of Exterior Orientation

    Science.gov (United States)

    Khaghani, M.; Skaloud, J.

    2016-06-01

    Advances in unmanned aerial vehicles (UAV) and especially micro aerial vehicle (MAV) technology together with increasing quality and decreasing price of imaging devices have resulted in growing use of MAVs in photogrammetry. The practicality of MAV mapping is seriously enhanced with the ability to determine parameters of exterior orientation (EO) with sufficient accuracy, in both absolute and relative senses (change of attitude between successive images). While differential carrier phase GNSS satisfies cm-level positioning accuracy, precise attitude determination is essential for both direct sensor orientation (DiSO) and integrated sensor orientation (ISO) in corridor mapping or in block configuration imaging over surfaces with low texture. Limited cost, size, and weight of MAVs represent limitations on quality of onboard navigation sensors and puts emphasis on exploiting full capacity of available resources. Typically short flying times (10-30 minutes) also limit the possibility of estimating and/or correcting factors such as sensor misalignment and poor attitude initialization of inertial navigation system (INS). This research aims at increasing the accuracy of attitude determination in both absolute and relative senses with no extra sensors onboard. In comparison to classical INS/GNSS setup, novel approach is presented here to integrated state estimation, in which vehicle dynamic model (VDM) is used as the main process model. Such system benefits from available information from autopilot and physical properties of the platform in enhancing performance of determination of trajectory and parameters of exterior orientation consequently. The navigation system employs a differential carrier phase GNSS receiver and a micro electro-mechanical system (MEMS) grade inertial measurement unit (IMU), together with MAV control input from autopilot. Monte-Carlo simulation has been performed on trajectories for typical corridor mapping and block imaging. Results reveal

  9. Dynamics of cell polarity in tissue morphogenesis: a comparative view from Drosophila and Ciona.

    Science.gov (United States)

    Veeman, Michael T; McDonald, Jocelyn A

    2016-01-01

    Tissues in developing embryos exhibit complex and dynamic rearrangements that shape forming organs, limbs, and body axes. Directed migration, mediolateral intercalation, lumen formation, and other rearrangements influence the topology and topography of developing tissues. These collective cell behaviors are distinct phenomena but all involve the fine-grained control of cell polarity. Here we review recent findings in the dynamics of polarized cell behavior in both the Drosophila ovarian border cells and the Ciona notochord. These studies reveal the remarkable reorganization of cell polarity during organ formation and underscore conserved mechanisms of developmental cell polarity including the Par/atypical protein kinase C (aPKC) and planar cell polarity pathways. These two very different model systems demonstrate important commonalities but also key differences in how cell polarity is controlled in tissue morphogenesis. Together, these systems raise important, broader questions on how the developmental control of cell polarity contributes to morphogenesis of diverse tissues across the metazoa.

  10. Dynamics and Regulation of Actin Cytoskeleton in Plant Cells

    Institute of Scientific and Technical Information of China (English)

    Ren Haiyun

    2007-01-01

    @@ The actin cytoskeleton constituted of globular actin (G-actin) is a ubiquitous component of eukaryotic cells and plays crucial roles in diverse physiological processes in plant cells, such as cytoplasmic streaming, organelle and nucleus positioning, cell morphogenesis, cell division, tip growth, etc.

  11. Neoantigen landscape dynamics during human melanoma-T cell interactions

    DEFF Research Database (Denmark)

    Verdegaal, Els M. E.; De Miranda, Noel F. C. C.; Visser, Marten

    2016-01-01

    Recognition of neoantigens that are formed as a consequence of DNA damage is likely to form a major driving force behind the clinical activity of cancer immunotherapies such as T-cell checkpoint blockade and adoptive T-cell therapy. Therefore, strategies to selectively enhance T-cell reactivity...... is constant over time is unclear. Here we analyse the stability of neoantigen-specific T-cell responses and the antigens they recognize in two patients with stage IV melanoma treated by adoptive T-cell transfer. The T-cell-recognized neoantigens can be selectively lost from the tumour cell population, either...

  12. An independent determination of Fomalhaut b's orbit and the dynamical effects on the outer dust belt

    CERN Document Server

    Beust, Hervé; Bonsor, Amy; Graham, J; Kalas, Paul; Lebreton, J; Lagrange, Anne-Marie; Ertel, Steve; Faramaz, Virginie; Thebault, Philippe

    2013-01-01

    The nearby star Fomalhaut harbours a cold, moderately eccentric dust belt with a sharp inner edge near 133 au. A low-mass, common proper motion companion (Fom b), was discovered near the inner edge and was identified as a planet candidate that could account for the belt morphology. However, the most recent orbit determination based on four epochs of astrometry over eight years reveals a highly eccentric orbit that appears to cross the belt in the sky plane projection. We perform here a full orbital determination based on the available astrometric data to independently validate the orbit estimates previously presented. Adopting our values for the orbital elements and their associated uncertainties, we then study the dynamical interaction between the planet and the dust ring, to check whether the proposed disk sculpting scenario by Fom b is plausible. We used a dedicated MCMC code to derive the statistical distributions of the orbital elements of Fom b. Then we used symplectic N-body integration to investigate ...

  13. Temporal dynamics and determinants of whole brain tissue volume changes during recovery from alcohol dependence.

    Science.gov (United States)

    Gazdzinski, Stefan; Durazzo, Timothy C; Meyerhoff, Dieter J

    2005-06-01

    Brain shrinkage and its partial reversibility with abstinence is a common neuroimaging finding in alcohol dependent individuals. We used an automated three-dimensional whole brain magnetic resonance imaging method (boundary shift integral) in 23 alcohol dependent individuals to measure the temporal dynamics of cerebral tissue and spinal fluid volume changes over a 12-month interval and to examine the major determinants of brain tissue change rates during abstinence and non-abstinence. We found more rapid brain tissue gain during the first month of sobriety than in the following months. The most rapid volume recovery was observed in abstinent individuals with the greatest baseline brain shrinkage and drinking severity. The rapid reversal of brain volume gains in non-abstinent individuals and tissue volume changes are modulated by duration of abstinence and non-abstinence periods, as well as recency of non-abstinence. Age, family history density of alcoholism, relapse severity, and duration or age of onset of heavy drinking were not major determinants of brain shrinkage and brain volume recovery rates. Treatment providers may use this tangible information to reinforce the biomedical benefits of sobriety. Previous quantitative measurements of brain volumes in alcohol dependent individuals performed after several weeks of abstinence likely underestimated the full extent of chronic alcohol-associated brain shrinkage.

  14. Using Maximal Isometric Force to Determine the Optimal Load for Measuring Dynamic Muscle Power

    Science.gov (United States)

    Spiering, Barry A.; Lee, Stuart M. C.; Mulavara, Ajitkumar P.; Bentley, Jason R.; Nash, Roxanne E.; Sinka, Joseph; Bloomberg, Jacob J.

    2009-01-01

    Maximal power output occurs when subjects perform ballistic exercises using loads of 30-50% of one-repetition maximum (1-RM). However, performing 1-RM testing prior to power measurement requires considerable time, especially when testing involves multiple exercises. Maximal isometric force (MIF), which requires substantially less time to measure than 1-RM, might be an acceptable alternative for determining the optimal load for power testing. PURPOSE: To determine the optimal load based on MIF for maximizing dynamic power output during leg press and bench press exercises. METHODS: Twenty healthy volunteers (12 men and 8 women; mean +/- SD age: 31+/-6 y; body mass: 72 +/- 15 kg) performed isometric leg press and bench press movements, during which MIF was measured using force plates. Subsequently, subjects performed ballistic leg press and bench press exercises using loads corresponding to 20%, 30%, 40%, 50%, and 60% of MIF presented in randomized order. Maximal instantaneous power was calculated during the ballistic exercise tests using force plates and position transducers. Repeated-measures ANOVA and Fisher LSD post hoc tests were used to determine the load(s) that elicited maximal power output. RESULTS: For the leg press power test, six subjects were unable to be tested at 20% and 30% MIF because these loads were less than the lightest possible load (i.e., the weight of the unloaded leg press sled assembly [31.4 kg]). For the bench press power test, five subjects were unable to be tested at 20% MIF because these loads were less than the weight of the unloaded aluminum bar (i.e., 11.4 kg). Therefore, these loads were excluded from analysis. A trend (p = 0.07) for a main effect of load existed for the leg press exercise, indicating that the 40% MIF load tended to elicit greater power output than the 60% MIF load (effect size = 0.38). A significant (p . 0.05) main effect of load existed for the bench press exercise; post hoc analysis indicated that the effect of

  15. Impact of release dynamics of laser-irradiated polymer micropallets on the viability of selected adherent cells

    Science.gov (United States)

    Ma, Huan; Mismar, Wael; Wang, Yuli; Small, Donald W.; Ras, Mat; Allbritton, Nancy L.; Sims, Christopher E.; Venugopalan, Vasan

    2012-01-01

    We use time-resolved interferometry, fluorescence assays and computational fluid dynamics (CFD) simulations to examine the viability of confluent adherent cell monolayers to selection via laser microbeam release of photoresist polymer micropallets. We demonstrate the importance of laser microbeam pulse energy and focal volume position relative to the glass–pallet interface in governing the threshold energies for pallet release as well as the pallet release dynamics. Measurements using time-resolved interferometry show that increases in laser pulse energy result in increasing pallet release velocities that can approach 10 m s−1 through aqueous media. CFD simulations reveal that the pallet motion results in cellular exposure to transient hydrodynamic shear stress amplitudes that can exceed 100 kPa on microsecond timescales, and which produces reduced cell viability. Moreover, CFD simulation results show that the maximum shear stress on the pallet surface varies spatially, with the largest shear stresses occurring on the pallet periphery. Cell viability of confluent cell monolayers on the pallet surface confirms that the use of larger pulse energies results in increased rates of necrosis for those cells situated away from the pallet centre, while cells situated at the pallet centre remain viable. Nevertheless, experiments that examine the viability of these cell monolayers following pallet release show that proper choices for laser microbeam pulse energy and focal volume position lead to the routine achievement of cell viability in excess of 90 per cent. These laser microbeam parameters result in maximum pallet release velocities below 6 m s−1 and cellular exposure of transient hydrodynamic shear stresses below 20 kPa. Collectively, these results provide a mechanistic understanding that relates pallet release dynamics and associated transient shear stresses with subsequent cellular viability. This provides a quantitative, mechanistic basis for determining

  16. Swimming motility plays a key role in the stochastic dynamics of cell clumping

    Science.gov (United States)

    Qi, Xianghong; Nellas, Ricky B.; Byrn, Matthew W.; Russell, Matthew H.; Bible, Amber N.; Alexandre, Gladys; Shen, Tongye

    2013-04-01

    Dynamic cell-to-cell interactions are a prerequisite to many biological processes, including development and biofilm formation. Flagellum induced motility has been shown to modulate the initial cell-cell or cell-surface interaction and to contribute to the emergence of macroscopic patterns. While the role of swimming motility in surface colonization has been analyzed in some detail, a quantitative physical analysis of transient interactions between motile cells is lacking. We examined the Brownian dynamics of swimming cells in a crowded environment using a model of motorized adhesive tandem particles. Focusing on the motility and geometry of an exemplary motile bacterium Azospirillum brasilense, which is capable of transient cell-cell association (clumping), we constructed a physical model with proper parameters for the computer simulation of the clumping dynamics. By modulating mechanical interaction (‘stickiness’) between cells and swimming speed, we investigated how equilibrium and active features affect the clumping dynamics. We found that the modulation of active motion is required for the initial aggregation of cells to occur at a realistic time scale. Slowing down the rotation of flagellar motors (and thus swimming speeds) is correlated to the degree of clumping, which is consistent with the experimental results obtained for A. brasilense.

  17. Delaunay-Object-Dynamics: cell mechanics with a 3D kinetic and dynamic weighted Delaunay-triangulation.

    Science.gov (United States)

    Meyer-Hermann, Michael

    2008-01-01

    Mathematical methods in Biology are of increasing relevance for understanding the control and the dynamics of biological systems with medical relevance. In particular, agent-based methods turn more and more important because of fast increasing computational power which makes even large systems accessible. An overview of different mathematical methods used in Theoretical Biology is provided and a novel agent-based method for cell mechanics based on Delaunay-triangulations and Voronoi-tessellations is explained in more detail: The Delaunay-Object-Dynamics method. It is claimed that the model combines physically realistic cell mechanics with a reasonable computational load. The power of the approach is illustrated with two examples, avascular tumor growth and genesis of lymphoid tissue in a cell-flow equilibrium.

  18. Dynamic Simulation of Carbonate Fuel Cell-Gas Turbine Hybrid Systems

    Energy Technology Data Exchange (ETDEWEB)

    Roberts, R.A. (U. of California, Irvine, CA); Brouwer, J. (U. of California, Irvine, CA); Liese, E.A.; Gemmen, R.S.

    2006-04-01

    Hybrid fuel cell/gas turbine systems provide an efficient means of producing electricity from fossil fuels with ultra low emissions. However, there are many significant challenges involved in integrating the fuel cell with the gas turbine and other components of this type of system. The fuel cell and the gas turbine must maintain efficient operation and electricity production while protecting equipment during perturbations that may occur when the system is connected to the utility grid or in stand-alone mode. This paper presents recent dynamic simulation results from two laboratories focused on developing tools to aid in the design and dynamic analyses of hybrid fuel cell systems. The simulation results present the response of a carbonate fuel cell/gas turbine, or molten carbonate fuel cell/gas turbine, (MCFC/GT) hybrid system to a load demand perturbation. Initial results suggest that creative control strategies will be needed to ensure a flexible system with wide turndown and robust dynamic operation.

  19. Collective migration models: Dynamic monitoring of leader cells in migratory/invasive disease processes

    Science.gov (United States)

    Dean, Zachary Steven

    Leader cells are a fundamental biological process that have only been investigated since the early 2000s. These cells have often been observed emerging at the edge of an artificial wound in 2D epithelial cell collective invasion, created with either a mechanical scrape from a pipette tip or from the removal of a plastic, physical blocker. During migration, the moving cells maintain cell-cell contacts, an important quality of collective migration; the leader cells originate from either the first or the second row, they increase in size compared to other cells, and they establish ruffled lamellipodia. Recent studies in 3D have also shown that cells emerging from an invading collective group that also exhibit leader-like properties. Exactly how leader cells influence and interact with follower cells as well as other cells types during collective migration, however, is another matter, and is a subject of intense investigation between many different labs and researchers. The majority of leader cell research to date has involved epithelial cells, but as collective migration is implicated in many different pathogenic diseases, such as cancer and wound healing, a better understanding of leader cells in many cell types and environments will allow significant improvement to therapies and treatments for a wide variety of disease processes. In fact, more recent studies on collective migration and invasion have broadened the field to include other cell types, including mesenchymal cancer cells and fibroblasts. However, the proper technology for picking out dynamic, single cells within a moving and changing cell population over time has severely limited previous investigation into leader cell formation and influence over other cells. In line with these previous studies, we not only bring new technology capable of dynamically monitoring leader cell formation, but we propose that leader cell behavior is more than just an epithelial process, and that it is a critical physiological

  20. Molecular determinants of treatment response in human germ cell tumors

    NARCIS (Netherlands)

    F. Mayer; J.A. Stoop (Hans); G.L. Scheffer (George); R. Scheper; J.W. Oosterhuis (Wolter); L.H.J. Looijenga (Leendert); C. Bokemeyer

    2003-01-01

    textabstractPURPOSE: Germ cell tumors (GCTs) are highly sensitive to cisplatin-based chemotherapy. This feature is unexplained, as is the intrinsic chemotherapy resistance of mature teratomas and the resistant phenotype of a minority of refractory GCTs. Various cellular pathways ma

  1. Time constant determination for electrical equivalent of biological cells

    Science.gov (United States)

    Dubey, Ashutosh Kumar; Dutta-Gupta, Shourya; Kumar, Ravi; Tewari, Abhishek; Basu, Bikramjit

    2009-04-01

    The electric field interactions with biological cells are of significant interest in various biophysical and biomedical applications. In order to study such important aspect, it is necessary to evaluate the time constant in order to estimate the response time of living cells in the electric field (E-field). In the present study, the time constant is evaluated by considering the hypothesis of electrical analog of spherical shaped cells and assuming realistic values for capacitance and resistivity properties of cell/nuclear membrane, cytoplasm, and nucleus. In addition, the resistance of cytoplasm and nucleoplasm was computed based on simple geometrical considerations. Importantly, the analysis on the basis of first principles shows that the average values of time constant would be around 2-3 μs, assuming the theoretical capacitance values and the analytically computed resistance values. The implication of our analytical solution has been discussed in reference to the cellular adaptation processes such as atrophy/hypertrophy as well as the variation in electrical transport properties of cellular membrane/cytoplasm/nuclear membrane/nucleoplasm.

  2. STRIPAK components determine mode of cancer cell migration and metastasis

    DEFF Research Database (Denmark)

    Madsen, Chris D; Hooper, Steven; Tozluoglu, Melda;

    2015-01-01

    and MST4 kinases, which promote the co-localization of the contractile actomyosin machinery with the Ezrin/Radixin/Moesin family proteins by phosphorylating the inhibitors of PPP1CB, PPP1R14A-D. Using computational modelling, in vitro cell migration assays and in vivo breast cancer metastasis assays we...

  3. Molecular determinants of treatment response in human germ cell tumors

    NARCIS (Netherlands)

    F. Mayer; J.A. Stoop (Hans); G.L. Scheffer (George); R. Scheper; J.W. Oosterhuis (Wolter); L.H.J. Looijenga (Leendert); C. Bokemeyer

    2003-01-01

    textabstractPURPOSE: Germ cell tumors (GCTs) are highly sensitive to cisplatin-based chemotherapy. This feature is unexplained, as is the intrinsic chemotherapy resistance of mature teratomas and the resistant phenotype of a minority of refractory GCTs. Various cellular pathways

  4. Dynamics of dye release from nanocarriers of different types in model cell membranes and living cells

    Directory of Open Access Journals (Sweden)

    Tkacheva T. N.

    2014-07-01

    Full Text Available Aim. To study the dynamics of lipophilic content release from nanocarriers of different types, organic molecular ensembles and inorganic nanoparticles (NPs in vitro experiments. Methods. Two-channel ratiometric fluorescence detection method based on Forster Resonance Energy Transfer, fluorescent spectroscopy and micro-spectroscopy have been used. Results. It has been found that the profiles of lipophilic dyes release from organic nanocarriers (PC liposomes and SDS micelles and inorganic ones (GdYVO4:Eu3+ and CeO2 NPs are well fitted by the first-order reaction kinetics in both model cell membranes and living cells (rat hepatocytes. The dye release constants (K and half-lives (t1/2 were analyzed. Conclusions. GdYVO4:Eu3+ and CeO2 NPs have been shown to provide faster lipophilic content release in model cell membranes as compared to PC liposomes. Negatively charged or lipophilic compounds added into nanocarriers can decrease the rate of lipophilic dyes release. Specific interaction of GdYVO4:Eu3+ NPs with rat hepatocytes has been observed.

  5. Dynamic quantitative microscopy and nanoscopy of red blood cells in sickle cell disease

    Science.gov (United States)

    Shaked, Natan T.; Satterwhite, Lisa L.; Telen, Marilyn J.; Truskey, George A.; Wax, Adam

    2012-03-01

    We have applied wide-field digital interferometric techniques to quantitatively image sickle red blood cells (RBCs) [1] in a noncontact label-free manner, and measure the nanometer-scale fluctuations in their thickness as an indication of their stiffness. The technique can simultaneously measure the fluctuations for multiple spatial points on the RBC and thus yields a map describing the stiffness of each RBC in the field of view. Using this map, the local rigidity regions of the RBC are evaluated quantitatively. Since wide-field digital interferometry is a quantitative holographic imaging technique rather than one-point measurement, it can be used to simultaneously evaluate cell transverse morphology plus thickness in addition to its stiffness profile. Using this technique, we examine the morphology and dynamics of RBCs from individuals who suffer from sickle cell disease, and find that the sickle RBCs are significantly stiffer than healthy RBCs. Furthermore, we show that the technique is sensitive enough to distinguish various classes of sickle RBCs, including sickle RBCs with visibly-normal morphology, compared to the stiffer crescent-shaped sickle RBCs.

  6. Quantitative Determination of Ceramide Molecular Species in Dendritic Cells

    Directory of Open Access Journals (Sweden)

    Samar Al Makdessi

    2016-09-01

    Full Text Available Background/Aims: The activation of acid sphingomyelinase by cellular stress or receptors or the de novo synthesis lead to the formation of ceramide (N-acylsphingosine, which in turn modifies the biophysical properties of cellular membrane and greatly amplifies the intensity of the initial signal. Ceramide, which acts by re-organizing a given signalosome rather than being a second messenger, has many functions in infection biology, cancer, cardiovascular syndromes, and immune regulation. Experimental studies on the infection of human cells with different bacterial agents demonstrated the activation of the acid sphingomyelinase/ceramide system. Moreover, the release of ceramide was found to be a requisite for the uptake of the pathogen. Considering the particular importance of the cellular role of ceramide, it was necessary to develop sensitive and accurate methods for its quantification. Methods: Here, we describe a method quantifying ceramide in dendritic cells and defining the different fatty acids (FA bound to sphingosine. The main steps of the method include extraction of total lipids, separation of the ceramide by thin-layer chromatography, derivatization of ceramide-fatty acids (Cer-FA, and quantitation of these acids in their methyl form by gas chromatography on polar capillary columns. The identification of FA was achieved by means of known standards and confirmed by mass spectrometry. Results: FA ranging between C10 and C24 could be detected and quantified. The concentration of the sum of Cer-FA amounted to 14.88 ± 8.98 nmol/106 cells (n=10. Oleic acid, which accounted for approximately half of Cer-FA (7.73 ± 6.52 nmol/106 cells was the predominant fatty acid followed by palmitic acid (3.47 ± 1.54 nmol/106 cells. Conclusion: This highly sensitive method allows the quantification of different molecular species of ceramides.

  7. Environmental determinants of severity in sickle cell disease.

    Science.gov (United States)

    Tewari, Sanjay; Brousse, Valentine; Piel, Frédéric B; Menzel, Stephan; Rees, David C

    2015-09-01

    Sickle cell disease causes acute and chronic illness, and median life expectancy is reduced by at least 30 years in all countries, with greater reductions in low-income countries. There is a wide spectrum of severity, with some patients having no symptoms and others suffering frequent, life-changing complications. Much of this variability is unexplained, despite increasingly sophisticated genetic studies. Environmental factors, including climate, air quality, socio-economics, exercise and infection, are likely to be important, as demonstrated by the stark differences in outcomes between patients in Africa and USA/Europe. The effects of weather vary with geography, although most studies show that exposure to cold or wind increases hospital attendance with acute pain. Most of the different air pollutants are closely intercorrelated, and increasing overall levels seem to correlate with increased hospital attendance, although higher concentrations of atmospheric carbon monoxide may offer some benefit for patients with sickle cell disease. Exercise causes some adverse physiological changes, although this may be off-set by improvements in cardiovascular health. Most sickle cell disease patients live in low-income countries and socioeconomic factors are undoubtedly important, but little studied beyond documenting that sickle cell disease is associated with decreases in some measures of social status. Infections cause many of the differences in outcomes seen across the world, but again these effects are relatively poorly understood. All the above factors are likely to account for much of the pathology and variability of sickle cell disease, and large prospective studies are needed to understand these effects better.

  8. On higher ground: how well can dynamic body acceleration determine speed in variable terrain?

    Directory of Open Access Journals (Sweden)

    Owen R Bidder

    Full Text Available INTRODUCTION: Animal travel speed is an ecologically significant parameter, with implications for the study of energetics and animal behaviour. It is also necessary for the calculation of animal paths by dead-reckoning. Dead-reckoning uses heading and speed to calculate an animal's path through its environment on a fine scale. It is often used in aquatic environments, where transmission telemetry is difficult. However, its adoption for tracking terrestrial animals is limited by our ability to measure speed accurately on a fine scale. Recently, tri-axial accelerometers have shown promise for estimating speed, but their accuracy appears affected by changes in substrate and surface gradients. The purpose of the present study was to evaluate four metrics of acceleration; Overall dynamic body acceleration (ODBA, vectorial dynamic body acceleration (VDBA, acceleration peak frequency and acceleration peak amplitude, as proxies for speed over hard, soft and inclined surfaces, using humans as a model species. RESULTS: A general linear model (GLM showed a significant difference in the relationships between the metrics and speed depending on substrate or surface gradient. When the data from all surface types were considered together, VeDBA had the highest coefficient of determination. CONCLUSIONS: All of the metrics showed some variation in their relationship with speed according to the surface type. This indicates that changes in the substrate or surface gradient during locomotion by animals would produce errors in speed estimates, and also in dead-reckoned tracks if they were calculated from speeds based entirely on a priori calibrations. However, we describe a method by which the relationship between acceleration metrics and speed can be corrected ad hoc, until tracks accord with periodic ground truthed positions, obtained via a secondary means (e.g. VHF or GPS telemetry. In this way, dead-reckoning provides a means to obtain fine scale movement data

  9. Fluid dynamics and noise in bacterial cell—cell and cell—surface scattering

    National Research Council Canada - National Science Library

    Knut Drescher; Jörn Dunkel; Luis H. Cisneros; Sujoy Ganguly; Raymond E. Goldstein

    2011-01-01

    .... While the importance of stochastic fluctuations has been appreciated for chemotaxis, it is currently believed that deterministic long-range fluid dynamical effects govern cell—cell and cell—surface scattering...

  10. Simple method of dynamic Young’s modulus determination in lime and cement mortars

    Directory of Open Access Journals (Sweden)

    Rosell, J. R.

    2011-03-01

    Full Text Available The present work explains a simple method to determine the dynamic Young module (MOE by inducing a set of small mechanical perturbation to samples of lime and cement mortars and correlating the results obtained with results determined using other techniques and methods. The procedure described herein follows the instructions stated in the UNE-EN ISO 12680-1 standard for refractory products although in this study the instructions are applied to standardized RILEM 4x4x16 cm test samples made of lime and cement mortars. In addition, MOE determinations are obtained by using ultrasonic impulse velocity while static Young's modulus determinations are obtained by performing conventional bending tests. The ability of this procedure to correlate with results from other techniques, along with its simplicity, suggests that it can be widely adapted to determine the deformability of mortars under load using standardized samples.

    El presente trabajo muestra un método simple para determinar el módulo de Young dinámico (MOE a partir de pequeñas perturbaciones mecánicas producidas a probetas de mortero de cal y de cemento, correlacionando los resultados obtenidos con las correspondientes mediciones realizadas con otras técnicas. El procedimiento sigue básicamente las instrucciones fijadas en la norma UNE-EN ISO 12680-1 de productos refractarios, pero aplicándolo a probetas normalizadas RILEM 4x4x16 de morteros confeccionados con cal y cemento. Paralelamente se realizan determinaciones del MOE a partir de la velocidad de paso de impulsos ultrasónicos y determinaciones del módulo de Young estático a partir de ensayos de flexión convencionales. La simplicidad del método aplicado y la correlación de los resultados obtenidos con las variables medidas permiten concluir que esta metodología es de aplicación directa para determinar la deformabilidad bajo carga de los morteros a partir de probetas normalizadas.

  11. Universal Features of Electron Dynamics in Solar Cells with TiO2 Contact: From Dye Solar Cells to Perovskite Solar Cells.

    Science.gov (United States)

    Todinova, Anna; Idígoras, Jesús; Salado, Manuel; Kazim, Samrana; Anta, Juan A

    2015-10-01

    The electron dynamics of solar cells with mesoporous TiO2 contact is studied by electrochemical small-perturbation techniques. The study involved dye solar cells (DSC), solid-state perovskite solar cells (SSPSC), and devices where the perovskite acts as sensitizer in a liquid-junction device. Using a transport-recombination continuity equation we found that mid-frequency time constants are proper lifetimes that determine the current-voltage curve. This is not the case for the SSPSC, where a lifetime of ∼1 μs, 1 order of magnitude longer, is required to reproduce the current-voltage curve. This mismatch is attributed to the dielectric response on the mid-frequency component. Correcting for this effect, lifetimes lie on a common exponential trend with respect to open-circuit voltage. Electron transport times share a common trend line too. This universal behavior of lifetimes and transport times suggests that the main difference between the cells is the power to populate the mesoporous TiO2 contact with electrons.

  12. Dynamic rupture simulation with an experimentally-determined friction law leads to slip-pulse propagation

    Science.gov (United States)

    Liao, Z.; Chang, J. C.; Reches, Z.

    2013-12-01

    We simulate the dynamic rupture along a vertical, strike-slip fault in an elastic half-space. The fault has frictional properties that were determined in high-velocity, rotary shear apparatus Sierra-White granite. The experimental fault was abruptly loaded by a massive flywheel, which is assumed to simulate the loading of a fault patch during an earthquake, and termed Earthquake-Like-Slip Event (ELSE) (Chang et al., 2012). The experiments revealed systematic alteration between slip-weakening and slip-strengthening (Fig. 1A), and were considered as proxies of fault-patch behavior during earthquakes of M = 4-8. We used the friction-distance relations of these experiments to form an empirical slip-dependent friction model, ELSE-model (Fig. 1B). For the dynamic rupture simulation, we used the program of Ampuero (2002) (2D spectral boundary integral elements) designed for anti-plane (mode III) shear fracturing. To compare with published works, the calculations used a crust with mechanical properties and stress state of Version 3 benchmark of SCEC (Harris et al., 2004). The calculations with a fault of ELSE-model friction revealed: (1) Rupture propagation in a slip-pulse style with slip cessation behind the pulse; (2) Systematic decrease of slip distance away from the nucleation zone; and (3) Spontaneous arrest of the dynamic rupture without a barrier. These features suggest a rupture of a self-healing slip-pulse mode (Fig. 1C), in contrast to rupturing of a fault with linear slip-weakening friction (Fig. 1B) (Rojas et al., 2008) in crack-like mode and no spontaneous arrest. We deduce that the slip-pulse in our simulation results from the fast recovery of shear strength as observed in ELSE experiments, and argue that incorporating this experimentally-based friction model to rupture modeling produces realistic propagation style of earthquake rupture. Figure 1 Fault patch behavior during an earthquake. (A) Experimental evolution of frictional stress, slip velocity, and

  13. Tracking the big ones : novel dynamics of organelles and macromolecular complexes during cell division and aging

    NARCIS (Netherlands)

    Deventer, Sjoerd Jan van

    2015-01-01

    In this Thesis we address two important aspects of protein dynamics: protein synthesis and distribution upon cell division and dynamics of the protein degradation machinery. In Chapter 2, we present novel technology (Recombination-Induced Tag Exchange)to distinguish and simultaneously track old and

  14. Direct simulation of liquid water dynamics in the gas channel of a polymer electrolyte fuel cell

    NARCIS (Netherlands)

    Qin, C.; Rensink, D.; Hassanizadeh, S.M.; Fell, S.

    2012-01-01

    For better water management in gas channels (GCs) of polymer electrolyte fuel cells (PEFCs), a profound understanding of the liquid water dynamics is needed. In this study, we propose a novel geometrical setup to conduct a series of direct simulations of the liquid water dynamics in a GC. The conduc

  15. NKCC1 Regulates Migration Ability of Glioblastoma Cells by Modulation of Actin Dynamics and Interacting with Cofilin

    Directory of Open Access Journals (Sweden)

    Paula Schiapparelli

    2017-07-01

    Full Text Available Glioblastoma (GBM is the most aggressive primary brain tumor in adults. The mechanisms that confer GBM cells their invasive behavior are poorly understood. The electroneutral Na+-K+-2Cl− co-transporter 1 (NKCC1 is an important cell volume regulator that participates in cell migration. We have shown that inhibition of NKCC1 in GBM cells leads to decreased cell migration, in vitro and in vivo. We now report on the role of NKCC1 on cytoskeletal dynamics. We show that GBM cells display a significant decrease in F-actin content upon NKCC1 knockdown (NKCC1-KD. To determine the potential actin-regulatory mechanisms affected by NKCC1 inhibition, we studied NKCC1 protein interactions. We found that NKCC1 interacts with the actin-regulating protein Cofilin-1 and can regulate its membrane localization. Finally, we analyzed whether NKCC1 could regulate the activity of the small Rho-GTPases RhoA and Rac1. We observed that the active forms of RhoA and Rac1 were decreased in NKCC1-KD cells. In summary, we report that NKCC1 regulates GBM cell migration by modulating the cytoskeleton through multiple targets including F-actin regulation through Cofilin-1 and RhoGTPase activity. Due to its essential role in cell migration NKCC1 may serve as a specific therapeutic target to decrease cell invasion in patients with primary brain cancer.

  16. GADD45β Determines Chemoresistance and Invasive Growth of Side Population Cells of Human Embryonic Carcinoma

    Directory of Open Access Journals (Sweden)

    Toshihiko Inowa

    2010-01-01

    Full Text Available Side population (SP cells are an enriched population of stem, and the existence of SP cells has been reported in human cancer cell lines. In this study, we performed an SP analysis using 11 human cancer cell lines and confirmed the presence of SP cells in an embryonic carcinoma cell line, NEC8. NEC8 SP cells showed characteristics of cancer stem cells, such as high growth rate, chemoresistance and high invasiveness. To further characterize the NEC8 SP cells, we used DNA microarrays. Among 38,500 genes, we identified 12 genes that were over-expressed in SP cells and 1 gene that was over-expressed in non-SP cells. Among these 13 genes, we focused on GADD45b. GADD45b was over-expressed in non-SP cells, but the inhibition of GADD45b had no effect on non-SP cells. Paradoxically, the inhibition of GADD45b significantly reduced the viability of NEC8 SP cells. The inhibition of ABCG2, which determines the SP phenotype, had no effect on the invasiveness of NEC8 SP cells, but the inhibition of GADD45b significantly reduced invasiveness. These results suggest that GADD45b, but not ABCG2, might determine the cancer stem cell-like phenotype, such as chemoresistance and the high invasiveness of NEC8 SP cells, and might be a good therapeutic target.

  17. Dynamical Modes of Deformed Red Blood Cells and Lipid Vesicles in Flows

    Science.gov (United States)

    Noguchi, H.

    Red blood cells and lipid vesicles exhibit rich behaivor in flows.Their dynamics were studied using a particle-based hydrodynamic simulation method, multi-particle collision dynamics. Rupture of lipid vesicles in simple shear flow was simulated by meshless membrane model. Several shape transitions of lipid vesicles and red blood cells are induced by flows. Transition of a lipid vesicle from budded to prolate shapes with increasing shear rate and ordered alignments of deformed elastic vesicles in high density are presented.

  18. Catalysis of Protein Folding by Chaperones Accelerates Evolutionary Dynamics in Adapting Cell Populations

    OpenAIRE

    Murat Cetinbaş; Shakhnovich, Eugene I.

    2013-01-01

    Although molecular chaperones are essential components of protein homeostatic machinery, their mechanism of action and impact on adaptation and evolutionary dynamics remain controversial. Here we developed a physics-based ab initio multi-scale model of a living cell for population dynamics simulations to elucidate the effect of chaperones on adaptive evolution. The 6-loci genomes of model cells encode model proteins, whose folding and interactions in cellular milieu can be evaluated exactly f...

  19. Cell Adhesion on Dynamic Supramolecular Surfaces Probed by Fluid Force Microscopy-Based Single-Cell Force Spectroscopy.

    Science.gov (United States)

    Sankaran, Shrikrishnan; Jaatinen, Leena; Brinkmann, Jenny; Zambelli, Tomaso; Vörös, Janos; Jonkheijm, Pascal

    2017-04-25

    Biomimetic and stimuli-responsive cell-material interfaces are actively being developed to study and control various cell-dynamics phenomena. Since cells naturally reside in the highly dynamic and complex environment of the extracellular matrix, attempts are being made to replicate these conditions in synthetic biomaterials. Supramolecular chemistry, dealing with noncovalent interactions, has recently provided possibilities to incorporate such dynamicity and responsiveness in various types of architectures. Using a cucurbit[8]uril-based host-guest system, we have successfully established a dynamic and electrochemically responsive interface for the display of the integrin-specific ligand, Arg-Gly-Asp (RGD), to promote cell adhesion. Due to the weak nature of the noncovalent forces by which the components at the interface are held together, we expected that cell adhesion would also be weaker in comparison to traditional interfaces where ligands are usually immobilized by covalent linkages. To assess the stability and limitations of our noncovalent interfaces, we performed single-cell force spectroscopy studies using fluid force microscopy. This technique enabled us to measure rupture forces of multiple cells that were allowed to adhere for several hours on individual substrates. We found that the rupture forces of cells adhered to both the noncovalent and covalent interfaces were nearly identical for up to several hours. We have analyzed and elucidated the reasons behind this result as a combination of factors including the weak rupture force between linear Arg-Gly-Asp and integrin, high surface density of the ligand, and increase in effective concentration of the supramolecular components under spread cells. These characteristics enable the construction of highly dynamic biointerfaces without compromising cell-adhesive properties.

  20. Dynamics of defense responses and cell fate change during Arabidopsis-Pseudomonas syringae interactions.

    Directory of Open Access Journals (Sweden)

    Safae Hamdoun

    picture of dynamic changes of defense phenotypes and cell fate determination during Arabidopsis-P. syringae interactions, contributing to a better understanding of plant defense mechanisms.

  1. Endothelial cells undergo morphological, biomechanical, and dynamic changes in response to tumor necrosis factor-α

    OpenAIRE

    Stroka, Kimberly M.; Vaitkus, Janina A.; Aranda-Espinoza, Helim

    2012-01-01

    The immune response triggers a complicated sequence of events, one of which is release of the cytokine tumor necrosis factor-α (TNF-α) from stromal cells such as monocytes and macrophages. In this work we explored the biophysical effects of TNF-α on endothelial cells (ECs), including changes in cell morphology, biomechanics, migration, and cytoskeletal dynamics. We found that TNF-α induces a wide distribution of cell area and aspect ratio, with these properties increasing on average during tr...

  2. Rationale for the real-time and dynamic cell death assays using propidium iodide

    OpenAIRE

    Zhao, Hong; Oczos, Jadwiga; Janowski, Pawel; Trembecka, Dominika; Dobrucki, Jurek; Darzynkiewicz, Zbigniew; Wlodkowic, Donald

    2010-01-01

    We have recently reported an innovative approach to use charged fluorochromes such as propidium iodide (PI) in the real-time, dynamic cell viability assays. The present study was designed to provide a mechanistic rationale for the kinetic assays using cell permeability markers. Uptake of PI by live cells, effect on the cell cycle, long term proliferation capacity, DNA damage response and pharmacologic interactions with anticancer drugs were studied using both laser scanning microscopy and las...

  3. In vivo protein synthesis determinations in human immune cells

    OpenAIRE

    Januszkiewicz, Anna

    2005-01-01

    Intact immune responses are essential for defeating severe infections in individual patients. Insufficient function of the immune system contributes to a poor prognosis in these patients, in particular the ICU patients. Nevertheless, the immune system function is not easily monitored and evaluated. The ongoing metabolic activity of immune competent cells is reflected by their in vivo protein synthesis rate. The aim of this thesis was to apply in vivo protein synthesis measur...

  4. Determination of Activation Energy of Relaxation Events in Composite Solid Propellants by Dynamic Mechanical Analysis

    Directory of Open Access Journals (Sweden)

    B. K Bihari

    2014-03-01

    Full Text Available The shelf life of a composite solid propellant is one of the critical aspects for the usage of solid propellants. To assess the ageing behavior of the composite solid propellant, the activation energy is a key parameter. The activation energy is determined by analysis of visco-elastic response of the composite solid propellant when subjected to sinusoidal excitation. In the present study, dynamic mechanical analyzer was used to characterize six different types of propellants based on hydroxyl terminated polybutadiene, aluminium, ammonium perchlorate cured with toluene diisocyanate having burning rates varying from 5 mm/s to 25 mm/s at 7000 kPa. Each propellant sample was given a multi-frequency strain of 0.01 percent at three discrete frequencies (3.5 Hz, 11 Hz, 35 Hz in the temperature range -80 °C to + 80 °C. It was observed that all the propellants have shown two relaxation events (α- and β- transition in the temperature range -80 °C to +80 °C. The α-transition was observed between -66 °C and -51 °C and β-transition between 7 °C and 44 °C for the propellants studied. The activation energy for both transitions was determined by Arrhenius plot from dynamic properties measured at different frequencies and also by time temperature superposition principle using Williams-Landel-Ferry and Arrhenius temperature dependence equations. The data reveal that the activation energy corresponding to α-transition varies from 90 kJ/mol to 125 kJ/mol for R-value between 0.7 to 0.9 while for β-transition the values are from 75 kJ/mol to 92 kJ/mol. The activation energy corresponding to β-transition may be used to predict the useful life of solid propellant.Defence Science Journal, 2014, 64(2, pp. 173-178. DOI: http://dx.doi.org/10.14429/dsj.64.3818

  5. Plant cortical microtubule dynamics and cell division plane orientation

    NARCIS (Netherlands)

    Chakrabortty, Bandan

    2017-01-01

    This thesis work aimed at a better understanding of the molecular basis of oriented cell division in plant cell. As, the efficiency of plant morphogenesis depends on oriented cell division, this work should contribute  towards a fundamental understanding of the  molecular basis of

  6. STRIPAK components determine mode of cancer cell migration and metastasis

    Science.gov (United States)

    Madsen, Chris D.; Hooper, Steven; Tozluoglu, Melda; Bruckbauer, Andreas; Fletcher, Georgina; Erler, Janine T.; Bates, Paul A.; Thompson, Barry; Sahai, Erik

    2017-01-01

    The contractile actomyosin cytoskeleton and its connection to the plasma membrane are critical for control of cell shape and migration. We identify three STRIPAK complex components, FAM40A, FAM40B, and STRN3, as regulators of the actomyosin cortex. We show that FAM40A negatively regulates the MST3 and MST4 kinases, which promote the co-localisation of the contractile actomyosin machinery with the Ezrin/Radixin/Moesin family proteins by phosphorylating the inhibitors of PPP1CB, PPP1R14A-D. Using computational modelling, in vitro cell migration assays and in vivo breast cancer metastasis assays we demonstrate that co-localisation of contractile activity and actin-plasma membrane linkage reduces cell speed on planar surfaces, but favours migration in confined environments similar to those observed in vivo. We further show that FAM40B mutations found in human tumours uncouple it from PP2A and enable it to drive a contractile phenotype, which may underlie its role in human cancer. PMID:25531779

  7. Determinants of action potential propagation in cerebellar Purkinje cell axons.

    Science.gov (United States)

    Monsivais, Pablo; Clark, Beverley A; Roth, Arnd; Häusser, Michael

    2005-01-12

    Axons have traditionally been viewed as highly faithful transmitters of action potentials. Recently, however, experimental evidence has accumulated to support the idea that under some circumstances axonal propagation may fail. Cerebellar Purkinje neurons fire highfrequency simple spikes, as well as bursts of spikes in response to climbing fiber activation (the "complex spike"). Here we have visualized the axon of individual Purkinje cells to directly investigate the relationship between somatic spikes and axonal spikes using simultaneous somatic whole-cell and cell-attached axonal patch-clamp recordings at 200-800 microm from the soma. We demonstrate that sodium action potentials propagate at frequencies up to approximately 260 Hz, higher than simple spike rates normally observed in vivo. Complex spikes, however, did not propagate reliably, with usually only the first and last spikes in the complex spike waveform being propagated. On average, only 1.7 +/- 0.2 spikes in the complex spike were propagated during resting firing, with propagation limited to interspike intervals above approximately 4 msec. Hyperpolarization improved propagation efficacy without affecting total axonal spike number, whereas strong depolarization could abolish propagation of the complex spike. These findings indicate that the complex spike waveform is not faithfully transmitted to downstream synapses and that propagation of the climbing fiber response may be modulated by background activity.

  8. Robustness of MEK-ERK Dynamics and Origins of Cell-to-Cell Variability in MAPK Signaling

    Directory of Open Access Journals (Sweden)

    Sarah Filippi

    2016-06-01

    Full Text Available Cellular signaling processes can exhibit pronounced cell-to-cell variability in genetically identical cells. This affects how individual cells respond differentially to the same environmental stimulus. However, the origins of cell-to-cell variability in cellular signaling systems remain poorly understood. Here, we measure the dynamics of phosphorylated MEK and ERK across cell populations and quantify the levels of population heterogeneity over time using high-throughput image cytometry. We use a statistical modeling framework to show that extrinsic noise, particularly that from upstream MEK, is the dominant factor causing cell-to-cell variability in ERK phosphorylation, rather than stochasticity in the phosphorylation/dephosphorylation of ERK. We furthermore show that without extrinsic noise in the core module, variable (including noisy signals would be faithfully reproduced downstream, but the within-module extrinsic variability distorts these signals and leads to a drastic reduction in the mutual information between incoming signal and ERK activity.

  9. Modeling reveals bistability and low-pass filtering in the network module determining blood stem cell fate.

    Directory of Open Access Journals (Sweden)

    Jatin Narula

    2010-05-01

    Full Text Available Combinatorial regulation of gene expression is ubiquitous in eukaryotes with multiple inputs converging on regulatory control elements. The dynamic properties of these elements determine the functionality of genetic networks regulating differentiation and development. Here we propose a method to quantitatively characterize the regulatory output of distant enhancers with a biophysical approach that recursively determines free energies of protein-protein and protein-DNA interactions from experimental analysis of transcriptional reporter libraries. We apply this method to model the Scl-Gata2-Fli1 triad-a network module important for cell fate specification of hematopoietic stem cells. We show that this triad module is inherently bistable with irreversible transitions in response to physiologically relevant signals such as Notch, Bmp4 and Gata1 and we use the model to predict the sensitivity of the network to mutations. We also show that the triad acts as a low-pass filter by switching between steady states only in response to signals that persist for longer than a minimum duration threshold. We have found that the auto-regulation loops connecting the slow-degrading Scl to Gata2 and Fli1 are crucial for this low-pass filtering property. Taken together our analysis not only reveals new insights into hematopoietic stem cell regulatory network functionality but also provides a novel and widely applicable strategy to incorporate experimental measurements into dynamical network models.

  10. Golgi localization and dynamics of hyaluronan binding protein 1 (HABP1/p32/C1QBP) during the cell cycle

    Institute of Scientific and Technical Information of China (English)

    Aniruddha SENGUPTA; Bhaswati BANERJEE; Rakesh K. TYAGI; Kasturi DATTA

    2005-01-01

    Hyaluronan binding protein 1 (HABP1) is a negatively charged multifunctional mammalian protein with a unique structural fold. Despite the fact that HABP1 possesses mitochondrial localization signal, it has also been localized to other cellular compartments. Using indirect immunofluorescence, we examined the sub-cellular localization of HABP1 and its dynamics during mitosis. We wanted to determine whether it distributes in any distinctive manner after mitotic nuclear envelope disassembly or is dispersed randomly throughout the cell. Our results reveal the golgi localization of HABP1 and demonstrate its complete dispersion throughout the cell during mitosis. This distinctive distribution pattern of HABP1 during mitosis resembles its ligand hyaluronan, suggesting that in concert with each other the two molecules play critical roles in this dynamic process.

  11. Modest Interference with Actin Dynamics in Primary T Cell Activation by Antigen Presenting Cells Preferentially Affects Lamellal Signaling.

    Directory of Open Access Journals (Sweden)

    Kole T Roybal

    Full Text Available Dynamic subcellular distributions of signaling system components are critical regulators of cellular signal transduction through their control of molecular interactions. Understanding how signaling activity depends on such distributions and the cellular structures driving them is required for comprehensive insight into signal transduction. In the activation of primary murine T cells by antigen presenting cells (APC signaling intermediates associate with various subcellular structures, prominently a transient, wide, and actin-associated lamellum extending from an interdigitated T cell:APC interface several micrometers into the T cell. While actin dynamics are well established as general regulators of cellular organization, their role in controlling signaling organization in primary T cell:APC couples and the specific cellular structures driving it is unresolved. Using modest interference with actin dynamics with a low concentration of Jasplakinolide as corroborated by costimulation blockade we show that T cell actin preferentially controls lamellal signaling localization and activity leading downstream to calcium signaling. Lamellal localization repeatedly related to efficient T cell function. This suggests that the transient lamellal actin matrix regulates T cell signaling associations that facilitate T cell activation.

  12. Runx Family Genes in Tissue Stem Cell Dynamics.

    Science.gov (United States)

    Wang, Chelsia Qiuxia; Mok, Michelle Meng Huang; Yokomizo, Tomomasa; Tergaonkar, Vinay; Osato, Motomi

    2017-01-01

    The Runx family genes play important roles in development and cancer, largely via their regulation of tissue stem cell behavior. Their involvement in two organs, blood and skin, is well documented. This review summarizes currently known Runx functions in the stem cells of these tissues. The fundamental core mechanism(s) mediated by Runx proteins has been sought; however, it appears that there does not exist one single common machinery that governs both tissue stem cells. Instead, Runx family genes employ multiple spatiotemporal mechanisms in regulating individual tissue stem cell populations. Such specific Runx requirements have been unveiled by a series of cell type-, developmental stage- or age-specific gene targeting studies in mice. Observations from these experiments revealed that the regulation of stem cells by Runx family genes turned out to be far more complex than previously thought. For instance, although it has been reported that Runx1 is required for the endothelial-to-hematopoietic cell transition (EHT) but not thereafter, recent studies clearly demonstrated that Runx1 is also needed during the period subsequent to EHT, namely at perinatal stage. In addition, Runx1 ablation in the embryonic skin mesenchyme eventually leads to complete loss of hair follicle stem cells (HFSCs) in the adult epithelium, suggesting that Runx1 facilitates the specification of skin epithelial stem cells in a cell extrinsic manner. Further in-depth investigation into how Runx family genes are involved in stem cell regulation is warranted.

  13. Modeling Cancer Cell Growth Dynamics In vitro in Response to Antimitotic Drug Treatment

    Directory of Open Access Journals (Sweden)

    Alexander Lorz

    2017-08-01

    Full Text Available Investigating the role of intrinsic cell heterogeneity emerging from variations in cell-cycle parameters and apoptosis is a crucial step toward better informing drug administration. Antimitotic agents, widely used in chemotherapy, target exclusively proliferative cells and commonly induce a prolonged mitotic arrest followed by cell death via apoptosis. In this paper, we developed a physiologically motivated mathematical framework for describing cancer cell growth dynamics that incorporates the intrinsic heterogeneity in the time individual cells spend in the cell-cycle and apoptosis process. More precisely, our model comprises two age-structured partial differential equations for the proliferative and apoptotic cell compartments and one ordinary differential equation for the quiescent compartment. To reflect the intrinsic cell heterogeneity that governs the growth dynamics, proliferative and apoptotic cells are structured in “age,” i.e., the amount of time remaining to be spent in each respective compartment. In our model, we considered an antimitotic drug whose effect on the cellular dynamics is to induce mitotic arrest, extending the average cell-cycle length. The prolonged mitotic arrest induced by the drug can trigger apoptosis if the time a cell will spend in the cell cycle is greater than the mitotic arrest threshold. We studied the drug’s effect on the long-term cancer cell growth dynamics using different durations of prolonged mitotic arrest induced by the drug. Our numerical simulations suggest that at confluence and in the absence of the drug, quiescence is the long-term asymptotic behavior emerging from the cancer cell growth dynamics. This pattern is maintained in the presence of small increases in the average cell-cycle length. However, intermediate increases in cell-cycle length markedly decrease the total number of cells and can drive the cancer population to extinction. Intriguingly, a large

  14. Modeling Cancer Cell Growth Dynamics In vitro in Response to Antimitotic Drug Treatment

    KAUST Repository

    Lorz, Alexander

    2017-08-30

    Investigating the role of intrinsic cell heterogeneity emerging from variations in cell-cycle parameters and apoptosis is a crucial step toward better informing drug administration. Antimitotic agents, widely used in chemotherapy, target exclusively proliferative cells and commonly induce a prolonged mitotic arrest followed by cell death via apoptosis. In this paper, we developed a physiologically motivated mathematical framework for describing cancer cell growth dynamics that incorporates the intrinsic heterogeneity in the time individual cells spend in the cell-cycle and apoptosis process. More precisely, our model comprises two age-structured partial differential equations for the proliferative and apoptotic cell compartments and one ordinary differential equation for the quiescent compartment. To reflect the intrinsic cell heterogeneity that governs the growth dynamics, proliferative and apoptotic cells are structured in “age,” i.e., the amount of time remaining to be spent in each respective compartment. In our model, we considered an antimitotic drug whose effect on the cellular dynamics is to induce mitotic arrest, extending the average cell-cycle length. The prolonged mitotic arrest induced by the drug can trigger apoptosis if the time a cell will spend in the cell cycle is greater than the mitotic arrest threshold. We studied the drug\\'s effect on the long-term cancer cell growth dynamics using different durations of prolonged mitotic arrest induced by the drug. Our numerical simulations suggest that at confluence and in the absence of the drug, quiescence is the long-term asymptotic behavior emerging from the cancer cell growth dynamics. This pattern is maintained in the presence of small increases in the average cell-cycle length. However, intermediate increases in cell-cycle length markedly decrease the total number of cells and can drive the cancer population to extinction. Intriguingly, a large “switch-on/ switch-off” increase in the average

  15. Viscoelastic and dynamic properties of embryonic stem cells

    DEFF Research Database (Denmark)

    Ritter, Christine

    ofthe cells themselves. In this thesis, the viscoelastic properties of mouse embryonic stem cells primedeither toward the epiblast (Epi) or the primitive endoderm (PrE) lineage were investigated.Optical tweezers were used to measure the fluctuations of endogenous lipid granules and therebydraw......Stem cells are often referred to as the ‘holy grail’ of regenerative medicine, because they possessthe ability to develop into any cell type. The use of stem cells within medicine is currently limited bythe effectivity of differentiation and cell reprogramming protocols, making it therefore...... imperative tounderstand stem cells’ differentiation mechanisms better. Studies have shown that mechanical cuescan have an influence on stem cell fate decision. However, in order to understand the reaction of stemcells to mechanical input, one should first investigate and understand the mechanical properties...

  16. Viscoelastic and dynamic properties of embryonic stem cells

    DEFF Research Database (Denmark)

    Ritter, Christine

    Stem cells are often referred to as the ‘holy grail’ of regenerative medicine, because they possessthe ability to develop into any cell type. The use of stem cells within medicine is currently limited bythe effectivity of differentiation and cell reprogramming protocols, making it therefore...... imperative tounderstand stem cells’ differentiation mechanisms better. Studies have shown that mechanical cuescan have an influence on stem cell fate decision. However, in order to understand the reaction of stemcells to mechanical input, one should first investigate and understand the mechanical properties...... ofthe cells themselves. In this thesis, the viscoelastic properties of mouse embryonic stem cells primedeither toward the epiblast (Epi) or the primitive endoderm (PrE) lineage were investigated.Optical tweezers were used to measure the fluctuations of endogenous lipid granules and therebydraw...

  17. Factors determining cell killing by chemotherapeutic agents In Vivo-II : Melphalan, chlorambucil and nitrogen mustard

    NARCIS (Netherlands)

    Putten, L.M. van; Lelieveld, P.

    1971-01-01

    The sensitivity of resting spleen colony-forming cells in normal mouse bone marrow and of rapidly-proliferating spleen colony-forming cells in repopulating mouse spleen to a number of bis-chloro-aethyl-amines was determined. The rapidly-growing cells were more sensitive to each of the agents than

  18. Determination of optimum electrolyte composition for molten carbonate fuel cells

    Energy Technology Data Exchange (ETDEWEB)

    Yuh, C.Y.; Pigeaud, A.

    1987-01-01

    The goal of this program is the development of a molten carbonate fuel cell (MCFC) anode which is more tolerant of sulfur contaminants in the fuel than the current state-of-the-art nickel-based anode structures. This program addresses two different but related aspects of the sulfur contamination problem. The primary aspect is concerned with the development of a sulfur tolerant electrocatalyst for the fuel oxidation reaction. A secondary issue is the development of a sulfur tolerant water-gas-shift reaction catalyst and an investigation of potential steam reforming catalysts which also have some sulfur tolerant capabilities. These two aspects are being addressed as two separate tasks.

  19. Determination of the Antibiotic Resistance Profile of Student Cell Phones

    Directory of Open Access Journals (Sweden)

    Lisa Ann Blankinship

    2012-08-01

    Full Text Available Sampling of common use items (e.g., student cell phones for bacterial presence, identification, and antibiotic resistance profiling helps students to recognize the need for routine cleaning of personal items and encourages thoughtful use of currently available medications. This multilab period project can be used to teach or reinforce several methods from general microbiology including aseptic technique, isolation streak, serial dilution, spread plating, Kirby Bauer testing, unknown identification, and media production. The data generated can be saved and added to each semester, thus providing a data set that reflects a local trend of antibiotic resistance.      

  20. Phase equilibrium calculations of ternary liquid mixtures with binary interaction parameters and molecular size parameters determined from molecular dynamics.

    Science.gov (United States)

    Oh, Suk Yung; Bae, Young Chan

    2010-07-15

    The method presented in this paper was developed to predict liquid-liquid equilibria in ternary liquid mixtures by using a combination of a thermodynamic model and molecular dynamics simulations. In general, common classical thermodynamic models have many parameters which are determined by fitting a model with experimental data. This proposed method, however, provides a simple procedure for calculating liquid-liquid equilibria utilizing binary interaction parameters and molecular size parameters determined from molecular dynamics simulations. This method was applied to mixtures containing water, hydrocarbons, alcohols, chlorides, ketones, acids, and other organic liquids over various temperature ranges. The predicted results agree well with the experimental data without the use of adjustable parameters.

  1. Motivational dynamics of eating regulation: a self-determination theory perspective.

    Science.gov (United States)

    Verstuyf, Joke; Patrick, Heather; Vansteenkiste, Maarten; Teixeira, Pedro J

    2012-03-02

    Within Western society, many people have difficulties adequately regulating their eating behaviors and weight. Although the literature on eating regulation is vast, little attention has been given to motivational dynamics involved in eating regulation. Grounded in Self-Determination Theory (SDT), the present contribution aims to provide a motivational perspective on eating regulation. The role of satisfaction and thwarting of the basic psychological needs for autonomy, competence, and relatedness is introduced as a mechanism to (a) explain the etiology of body image concerns and disordered eating and (b) understand the optimal regulation of ongoing eating behavior for healthy weight maintenance. An overview of empirical studies on these two research lines is provided. In a final section, the potential relevance and value of SDT in relation to prevailing theoretical models in the domain of eating regulation is discussed. Although research on SDT in the domain of eating regulation is still in its early stages and more research is clearly needed, this review suggests that the SDT represents a promising framework to more thoroughly study and understand the motivational processes involved in eating regulation and associated problems.

  2. Determination of thermal properties pure ThO2 using classical molecular dynamics simulations

    Science.gov (United States)

    Ghosh, Partha S.; Kaur, Karamvir; Ali, K.; Arya, A.; Dey, G. K.

    2016-05-01

    This paper calculates lattice thermal expansion (LTE), thermal conductivity (TC) and melting temperature (MT) of ThO2 using classical molecular dynamic simulations. In this study we consider two set of interatomic potential consisting of Coulomb-Buckingham (Buck) and Coulomb-Buckingham-Morse-Many body (BMM) potential form. The MD calculated LTE of 10.29 × 10-6 and 10.61 × 10-6 K-1 using BMM and Buck potential, respectively, is slightly higher than the experimentally determined values (9.54 - 9.86 × 10-6 K-1). The MD calculated TC values in the high temperature range (600 to 1200 K) accords very well with the experimental measurements and at the low temperature range (300-500 K) our results are slightly different from experimental results as our presumption that the dominant mechanism for phonon scattering is the Umklapp process. The MD calculated MT of ThO2 using Buck and BMM potential model is 3662.5±12.5 K and 3812.5±12.5 K, respectively, and these values are in reasonable agreement with previous experimental values.

  3. Absolute densities, masses, and radii of the WASP-47 system determined dynamically

    CERN Document Server

    Almenara, J M; Bonfils, X; Udry, S

    2016-01-01

    We present a self-consistent modelling of the available light curve and radial velocity data of WASP-47 that takes into account the gravitational interactions between all known bodies in the system. The joint analysis of light curve and radial velocity data in a multi-planetary system allows deriving absolute densities, radii, and masses without the use of theoretical stellar models. For WASP-47 the precision is limited by the reduced dynamical information that is due to the short time span of the K2 light curve. We achieve a precision of around 22% for the radii of the star and the transiting planets, between 40% and 60% for their masses, and between 1.5% and 38% for their densities. All values agree with previously reported measurements. When theoretical stellar models are included, the system parameters are determined with a precision that exceeds that achieved by previous studies, thanks to the self-consistent modelling of light curve and radial velocity data.

  4. Vortices determine the dynamics of biodiversity in cyclical interactions with protection spillovers

    CERN Document Server

    Szolnoki, Attila

    2015-01-01

    If rock beats scissors and scissors beat paper, one might assume that rock beats paper too. But this is not the case for intransitive relationships that make up the famous rock-paper-scissors game. However, the sole presence of paper might prevent rock from beating scissors, simply because paper beats rock. This is the blueprint for the rock-paper-scissors game with protection spillovers, which has recently been introduced as a new paradigm for biodiversity in well-mixed microbial populations. Here we study the game in structured populations, demonstrating that protection spillovers give rise to spatial patterns that are impossible to observe in the classical rock-paper-scissors game. We show that the spatiotemporal dynamics of the system is determined by the density of stable vortices, which may ultimately transform to frozen states, to propagating waves, or to target waves with reversed propagation direction, depending further on the degree and type of randomness in the interactions among the species. If vo...

  5. Absolute densities, masses, and radii of the WASP-47 system determined dynamically

    Science.gov (United States)

    Almenara, J. M.; Díaz, R. F.; Bonfils, X.; Udry, S.

    2016-10-01