Integrating cellular and organismic aspects of vascular differentiation

Vascular differentiation can be studied at two levels, and they should complement one another: as an aspect of integrated plant development and as cellular processes. The differentiation of organized strands that connect between organs is induced by polar auxin flow, towards the roots. Anatomy, therefore, can be a complementary method of observing polarity and its changes. As expected for a self-correcting and essential system, vascular patterning mutations are relatively rare and have pleiotropic effects, including modifications of responses to auxin and its transport. Tissue polarity both expresses and depends on auxin transport, a feedback that could account for the determined nature of polarity as well as the gradual canalization of differentiation to vascular strands. This predicts that the molecules responsible for polarity will be localized gradually as differentiation proceeds. Further, a modified location of these molecules can be expected to precede anatomical expressions of a new, regenerated, polarity. Tracheary differentiation is probably the best studied example of cell differentiation. Within the plant, however, this differentiation is coupled to oriented cell growth either along or at right angles to the axis of auxin flow, depending on tissue competence. Differentiation is also coupled to the differentiation of the other components of the vascular system. There are, presumably, early joint stages to these differentiation processes, but what they are remains an intriguing problem.     

Stochastic Collective Movement of Cells and Fingering Morphology: No Maverick Cells

The classical approach to model collective biological cell movement is through coupled nonlinear reaction-diffusion equations for biological cells and diffusive chemicals that interact with the biological cells. This approach takes into account the diffusion of cells, proliferation, death of cells, and chemotaxis. Whereas the classical approach has many advantages, it fails to consider many factors that affect multicell movement. In this work, a multiscale approach, the Glazier-Graner-Hogeweg model, is used. This model is implemented for biological cells coupled with the finite element method for a diffusive chemical. The Glazier-Graner-Hogeweg model takes the biological cell state as discrete and allows it to include cohesive forces between biological cells, deformation of cells, following the path of a single cell, and stochastic behavior of the cells. Where the continuity of the tissue at the epidermis is violated, biological cells regenerate skin to heal the wound. We assume that the cells secrete a diffusive chemical when they feel a wounded region and that the cells are attracted by the chemical they release (chemotaxis). Under certain parameters, the front encounters a fingering morphology, and two fronts progressing against each other are attracted and correlated. Cell flow exhibits interesting patterns, and a drift effect on the chemical may influence the cells' motion. The effects of a polarized substrate are also discussed.     

Enzyme reactions at the surface of living cells. I. Electric repulsion of charged ligands and recognition of signals from the external milieu

The dynamic behaviour of a polyelectrolyte-bound enzyme is studied when diffusion of substrate or diffusion of product is coupled to electric repulsion and to Michaelis-Menten enzyme reaction. The definition of the classical concepts of electric partition coefficients and Donnan potential of a polyelectrolyte membrane has been extended under global non-equilibrium conditions. This extension is permissible when a strong repulsion exists of substrate and product by the fixed negative charges of the membrane. Coupling between product diffusion, electric repulsion and enzyme reaction at constant advancement may result in a hysteresis loop of the partition coefficient as the product concentration is increased in the reservoir. This hysteresis loop vanishes as the rate of product diffusion increases. No hysteresis loop may occur when electric repulsion effects are coupled to substrate diffusion and reaction. The existence of multiple values of the partition coefficient for a fixed concentration of product implies that the membrane may store short-term memory of the former product concentration present in the external milieu. The occurrence of hysteresis generated by coupling enzyme reaction, product diffusion, electric partition effects at constant advancement of the reaction may be viewed as a sensing device of product concentration in the external milieu. Surprisingly, non-linearities required to generate this sensing device come from electrostatic effects and not from enzyme kinetics.     

Numerical simulation of the flow and concentration fields for oxygen delivery systems

The flow and concentration fields for various medical oxygen delivery devices are numerically investigated. Simulations are performed for a classical Venturi mask and two new OxyArm portable devices. The velocity and oxygen concentration fields are investigated for: (i) a constant (steady-state) inhalation and (ii) a complete respiratory cycle (unsteady). The numerical results are qualitatively compared with clinical trials. It is found that the optimal functioning of these medical devices implies a balance between oxygen delivery by advection and the mixing process that allows for reliable CO2 monitoring (capnographic capability). Also, at the typical scales associated with these devices the flow is found to be Reynolds number dependent.     

Hard-sphere/pseudo-particle modelling (HS-PPM) for efficient and scalable molecular simulation of dilute gaseous flow and transport

Continuum methods are not accurate enough for flows at high Knudsen numbers, whereas rigorous molecular dynamics (MD) methods are too costly for simulations at practical dimensions. Hard-sphere (HS) model is a simplified MD method efficient for dilute gaseous flow but is of poor parallelism due to its event-driven nature, which sets a strong limitation to its large-scale applications. In this work, pseudo-particle modelling, a time-driven modelling approach is coupled with HS model to construct a scalable parallel method capable of simulating flows and transport processes at high Knudsen numbers without losing necessary molecular details in describing their macro-scale behaviours. The method is validated in several classical simulation cases and its performance is evaluated to be favourable. To demonstrate the potential applications of this method, we also simulate the diffusion of small molecules in multi-scale porous media which is related to catalysis, material preparation and micro chemical engineering in the long term.     

Pressure profile along the microvascular network and its control

The distribution of pressures within the arcading microvessels in numerous tissues is described and evaluated relative to potential sites for the control of blood flow and/or pressure. In various tissues a large fraction of the total systemic pressure is dissipated by small arteries and/or large arterioles and by small arterioles, the classical high-resistance vessels. Thus, these sites must be linked to the regulation and distribution of blood flow and pressure within the network as evidenced by the shifts in the profiles of pressures in these vessels after vasoactive stimuli. In fact, there may be some coupling of vasoactivity between these areas of vascular resistance. The vasodilator activity may predominate in small arterioles whereas the neural control may be directed to the small arteries and large arterioles. Thus, physiological, pharmacological, and pathological influences may affect the control of blood flow and/or pressure at one or both of these sites.     

Ectoglycosyltransferase activities at the surface of cultured neurons

Glycosyltransferase activities (ectogalactosyl, ectofucosyl and ectosialyl) were studied at the external surface of exclusively neuronal cultures. An appropriate methodology gave the possibility to eliminate sources of errors due to the hydrolysis of nucleotide sugar substrates or due to cellular uptake of free sugars. Ovomucoïd and asialofetuin coupled to Sepharose and Ultrogel beads were used as exogenous substrate to circumvent possible substrates pinocytosis. Ectoglycosyltransferase activities were studied as function of protein concentration, incubation time and amount of bead coupled exogenous acceptors. The data show that these enzymes are present at the external surface of the neuronal membrane; their possible role in cell — cell interactions is suggested.     

Testing hypotheses of population structuring in the Northeast Atlantic Ocean and Mediterranean Sea using the common cuttlefish Sepia officinalis

Population structuring in species inhabiting marine environments such as the Northeast Atlantic Ocean (NEA) and Mediterranean Sea (MS) has usually been explained based on past and present physical barriers to gene flow and isolation by distance (IBD). Here, we examined the relative importance of these factors on population structuring of the common cuttlefish Sepia officinalis by using methods of phylogenetic inference and hypothesis testing coupled with coalescent and classical population genetic parameter estimation. Individuals from 10 Atlantic and 15 Mediterranean sites were sequenced for 659 bp of the mitochondrial COI gene (259 sequences). IBD seems to be the main factor driving present and past genetic structuring of Sepia populations across the NEA-MS, both at large and small geographical scales. Such an evolutionary process agrees well with some of the biological features characterizing this cuttlefish species (short migrations, nektobenthic habit, benthic eggs hatching directly to benthic juveniles). Despite the many barriers to migration/gene flow suggested in the NEA-MS region, genetic population fragmentation due to past isolation of water masses (Pleistocene; 0.56 million years ago) and/or present-day oceanographic currents was only detected between the Aegean-Ionian and western Mediterranean Seas. Restricted gene flow associated with the Almería-Oran hydrographic front was also suggested between southern and eastern Spanish populations. Distinct population boundaries could not be clearly determined, except for the Aegean-Ionian stock. Two Atlantic and five Mediterranean samples showed evidence of current decline in genetic diversity, which may indicate over-exploitation of Sepia in both marine regions.     

河西走廊山地-荒漠-绿洲复合生态系统耦合模式及耦合宏观经济价值分析——以肃南山地-张掖北山地区荒漠-临泽绿洲为例

应用合作对策理论提出河西走廊山地 -荒漠 -绿洲复合生态系统的 4个可行的耦合模式 ,在现有能值投入水平和科学管理力度下 ,4种耦合模式分别增加肃南山地 -张掖北山荒漠 -临泽绿洲动物生产系统和绿洲植物生产系统的宏观经济价值 3.6 7、4 .0 2、1.0 3和 4 .6倍。用能值概念和度量标准 ,以耦合后新增宏观经济价值为对策论中合作对策的特征函数 ,筛选出模式 是 4种耦合模式中的最佳策略组合即最优的耦合模式。该模式下 ,家畜对高山草地的压力减小 ,退化的山地子系统得以恢复 ,脆弱的荒漠子系统得到保护 ,绿洲种植业系统也因为家畜的加入、系统多样性提高 ,系统稳定性加强。研究方法避免了传统的纯货币评价分析方法对耦合产出所含环境资源评价的缺失 ,使得对耦合效应的评价值较为客观真实     

On the potentialities of 3D–1D coupled models in hemodynamics simulations

This work comprises a step towards the quantitative and qualitative analysis of coupled local and global hemodynamics phenomena in the arterial system. The aim of this work is to present some numerical examples to put in evidence the importance of the use of 3D–1D coupled models in hemodynamics problems when carrying out simulations of rather complex situations. Accordingly, some cases for which classical modeling cannot be applied are identified and solved. The results obtained here allow us to assess some interrelations between local pointwise quantities (defined at the level of the 3D model) and global mean quantities (defined at the level of the 1D model).     

AGS proteins, GPR motifs and the signals processed by heterotrimeric G proteins

A long term objective of our research effort is to define factors that influence the specificity and efficiency of signal propagation by heterotrimeric G-proteins (G). G-proteins play a central role in cellular communication mediating the cell response to numerous hormones and neurotransmitters. A major determinant of signalling specificity for heterotrimeric G-proteins is the cell specific expression of the subtypes of the primary signalling entities, receptor, G and effector (E). Another major site for regulating signalling specificity lies at the R-G or G-E interface where these interactions are influenced by cell architecture, the stoichiometry of signalling components and accessory proteins that may segregate the receptor to microdomains of the cell, regulate the efficiency and/or specificity of signal transfer and/or influence the activation state of G-protein independent of a classical G-protein coupled receptor. One strategy to address these issues in our laboratory involves the identification of cellular proteins that regulate the transfer of signal from receptor to G or directly influence the activation state of G independent of a classical G-protein coupled receptor. We identified three proteins, AGS1, AGS2 and AGS3 (for Activators of G-protein Signaling), that activated heterotrimeric G-protein signalling pathways in the absence of a typical receptor. AGS1, 2 and 3 interact with different subunits and/or conformations of heterotrimeric G-proteins, selectively activate different G-proteins, provide unexpected mechanisms for regulation of the G-protein activation cycle and have opened up a new area of research related to the cellular role of G-proteins as signal transducers.     

Increase of desensitization as an additional mode of action for classical NMDA receptor channel blockers

It is well known that not all effects of such classical NMDA receptor channel blockers as spermine and phylantotoxins are madiated via channel blockade. To determine if these side effects have any functional role we studied inhibition of NMDA receptors by derivatives of phenylcyclohexyl and clinically approved memantine. We showed that these drugs not only blocked the channel pore but also potentiated desensitization of NMDA receptors. Apparently, these effects are not interrelated because there was no correlation between a degree of “trapping” and a level of channel desensitization induced by these blockers. Yet, in contrast to channel blockade, which was strongly voltage-dependent, these compounds affected NMDA receptor desensitization in a voltage-independent manner. Based on these facts, we suppose the existence of two different binding sites for memantine and functionally related compounds, one being responsible for channel blockade and another being coupled to channel desensitization. This possibility should be taken into account when interpreting experimental and clinical effects of these channel blockers.     

An innovative approach for locating and evaluating subsurface pathways for nitrogen loss

Fundamental watershed-scale processes governing chemical flux to neighboring ecosystems are so poorly understood that effective strategies for mitigating chemical contamination cannot be formulated. Characterization of evapotranspiration, surface runoff, plant uptake, subsurface preferential flow, behavior of the chemicals in neighboring ecosystems, and an understanding of how crop management practices influence these processes are needed. Adequate characterization of subsurface flow has been especially difficult because conventional sampling methods are ineffective for measuring preferential flow of water and solutes. A sampling strategy based on ground-penetrating radar (GPR) mapping of subsurface structures coupled with near real-time soil moisture data, surface topography, remotely sensed imagery, and a geographic information system (GIS) appears to offer a means of accurately identifying subsurface preferential flow pathways. Four small adjacent watersheds draining into a riparian wetland and first-order stream at the USDA-ARS Beltsville Agricultural Research Center, Beltsville, MD are being studied with this protocol. The spatial location of some preferential flow pathways for chemicals exiting these agricultural watersheds to the neighboring ecosystems have been identified. Confirmation of the pathways is via examination of patterns in yield monitor data and remote sensing imagery.     

Numerical models for the simulation of flexible artificial heart valves: part I--computational methods

A numerical model of the coupled motion of a flexing surface in a high Reynolds number flow is presented for the simulation of flexible polyurethane heart valves in the aortic position. This is achieved by matching a Lagrangian dynamic leaflet model with a panel method based flow solver. The two models are coupled via the time-dependent pressure field using the unsteady Bernoulli equation. Incorporation of sub-cycling in the dynamic model equations and fast pre conditioning techniques in the panel method solver yields efficient convergence and near real-time simulations of valve motion. The generality of dynamic model allows different material properties and/or geometries to be studied easily and interactively. This interactivity is realized by embedding the models within a design environment created using the software IRIS Explorer. Two flow domains are developed, an infinite domain and an internal domain using conformal mapping theory. In addition bending stress on the valve is computed using a simple stress model based on spline and circle equation techniques.     

Signal Transduction by Growth Factor Receptors: Signaling in an Instant

Phosphorylation-based signaling events happening within the first minute of receptor stimulation have so far only been analyzed by classical cell biological approaches like live-cell microscopy. The development of a quench flow system with a time resolution of one second coupled to a read-out by mass spectrometry-based proteomics has allowed exciting views on the very early events in signal transduction. Activation profiles of regulated phosphorylation sites on epidermal growth factor receptor and downstream signal transducers showed different kinetics within the first ten seconds of stimulation. This new technique opens the perspectives for accurate analysis of rapid cellular processes and will help to establish models describing signal initiation at the plasma membrane.     

Determination of the upper and lower limits of the mechanistic stoichiometry of incompletely coupled fluxes. Stoichiometry of incompletely coupled reactions

A rationale is formulated for the design of experiments to determine the upper and lower limits of the mechanistic stoichiometry of any two incompletely coupled fluxes J1 and J2. Incomplete coupling results when there is a branch at some point in the sequence of reactions or processes coupling the two fluxes. The upper limit of the mechanistic stoichiometry is given by the minimum value of dJ2/dJ1 obtained when the fluxes are systematically varied by changes in steps after the branch point. The lower limit is given by the maximum value of dJ2/dJ1 obtained when the fluxes are varied by changes in steps prior to the branch point. The rationale for determining these limits is developed from both a simple kinetic model and from a linear nonequilibrium thermodynamic treatment of coupled fluxes, using the mechanistic approach [Westerhoff, H. V. & van Dam, K. (1979) Curr. Top. Bioenerg. 9, 1-62]. The phenomenological stoichiometry, the flux ratio at level flow and the affinity ratio at static head of incompletely coupled fluxes are defined in terms of mechanistic conductances and their relationship to the mechanistic stoichiometry is discussed. From the rationale developed, experimental approaches to determine the mechanistic stoichiometry of mitochondrial oxidative phosphorylation are outlined. The principles employed do not require knowledge of the pathway or the rate of transmembrane leaks or slippage and may also be applied to analysis of the stoichiometry of other incompletely coupled systems, including vectorial H+/O and K+/O translocation coupled to mitochondrial electron transport.     

Coupled oxygen transport analysis in the avascular wall of a post-angioplasty coronary artery stenosis

The coupled oxygen transport in the avascular wall of a coronary artery stenosis is studied by numerically solving the convection-diffusion equations. Geometry, replicating residual stenosis after percutaneous transluminal coronary angioplasty (PTCA), is used for the analysis. Important physiological aspects, such as oxygen consumption in the wall, oxygen carried by the hemoglobin, non-Newtonian viscosity of the blood, and supply of oxygen from the vasa vasorum are included. Mean blood flow rate in the lumen is varied from basal to hyperemic conditions. The results show that the P(O2) in the medial region of the arterial wall is approximately 10 mmHg. The oxygen flux to the wall increases in the flow acceleration region, whereas it decreases at the flow reattachment zone. Near the location of flow separation there is a small rise and a sharp fall in the oxygen flux. The minimum P(O2) in the avascular wall, P(O2, min ), at the point of flow reattachment reduces to approximately 6 mmHg for a 300 micron wall thickness. For a thinner wall of 200 micron, the P(O2, min ) at the location of flow reattachment increases to 6 times that of a 300 micron wall. The P(O2, min ) in the wall decreases by 60% when volumetric oxygen consumption is increased by 30% for the same avascular wall thickness.