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Workshop 5 Titles and Abstracts
Abstract: Worddoc Presentation materials: PPT Streaming Video: Real Media
Presentation materials: PPT Streaming Video: Real Media Renal autoregulatory mechanisms are not only characterized by their dynamic nature, but the nature of their dynamics varies over time, leading to transient signals. These time-varying dynamics are often nonlinear and have different time scale oscillations (fast and slow), with each oscillation exhibiting its own transient dynamics. Our recent application of high-resolution, time-varying spectral and transfer function methods has revealed substantial differences between hypertensive and normotensive rats in the dynamics of the two principal autoregulatory mechanisms, tubuloglomerular feedback (TGF) and the myogenic mechanism. Despite the major progress made, the fundamental determinants that underlie differences in the renal autoregulatory dynamics between normotensive and hypertensive rats remain unresolved. For example, it remains to be determined why either time-invariant or time-varying spectral densities associated with hypertensive rats are more complicated than those of normotensive rats. A recent modeling study by Layton and Moore have predicted this in part due to the TGF system exhibiting multi-stability which can result in rapid switching between the dynamic modes which can consequently lead to a complicated spectral behavior. We will provide preliminary data from SHR that are consistent with the prediction of the Layton and Moore TGF model, including TGF waveform shape, switching between multiple stable modes of TGF oscillation, increased parameter variability relative to controls, and the presence of low frequency modulation of the TGF system. In addition, we will show data using time-varying nonlinear methods that complicated and additional spectral peaks associated with SHR arise because of nonlinear interactions between the autoregulatory mechanisms. Work done in collaboration with Kin Siu and Leon C. Moore.
Renal function is crucially dependent on renal microstructure providing the basis for the mechanisms that control the transport of water and solutes between filtrate and plasma and the urinary concentration. This study provides, detailed information on mouse renal architecture, including the spatial course of the tubules, lengths of different segments of nephrons, histotopography of tubules and vascular bundles, epithelial ultrastructure at well-defined positions along Henle's loop and the distal convolution of nephrons, and the exact distribution of AQP-1 and the urea transporter UT-A2. Three-dimensional reconstruction of 200 nephrons and collecting ducts was performed on aligned digital images, obtained from 2.5-\mu m-thick serial sections of mouse kidneys. Important new findings include: (1) A tortuous course of the descending thin limbs of long-looped nephrons and a winding course of the thick ascending limbs of short-looped nephrons contribute to a 27% average increase in the lengths of the corresponding segments, (2) the thick-walled tubules incorporated in the central part of the vascular bundles in the inner stripe of the outer medulla were identified as thick ascending limbs of long-looped nephrons, and (3) three types of short-looped nephron bends were identified related to the length and the position of the nephron and its corresponding glomerulus. The ultrastructure of the tubule segments was identified and correlated to the localization of AQP-1 and UT-A2. Our new findings suggest important implications for renal transport mechanisms that should be considered when evaluating the segmental distribution of water and solute transporters within the normal and diseased kidney. Work done in collaboration with Xiao-Yue Zhai.
Abstract: Worddoc Abstract: Worddoc Streaming Video: Real Media
Presentation materials: PDF A 3D "virtual kidney" interface has been developed for access to experimental data and parameter values abstracted within the Quantitative Kidney Database (QKDB) described by S Randall Thomas and to a repository of mathematical models of kidney function. At the gross anatomy level a translucent 3D reconstruction of a rat kidney shows contours of the renal capsule, inner and outer medullas, and the ureter, as well as renal arteries and veins to several levels of branching. Within the kidney are superficial and juxtamedullary nephrons. Using the mouse buttons the user can rotate the kidney, display or hide individual structures, and zoom in on any portion. Selection of a structure provides a link to the search facility of QKDB and thence to relevant parameter values and extracts from the literature. A menu lists the repository of mathematical models, such as segmental (e.g., proximal or distal tubule) or medullary transport models, which may be run on the local machine or, via a Grid Portal (KidneyGrid), simultaneously on several remote machines. The use of a grid resource broker demonstrates the ability to compose, schedule, monitor and visualize the results of the simulation and simplifies the development of application, credential and resource management while decoupling the launch platform from the underlying grid middleware. The simulation results (e.g., solute concentrations or local flow rates) are visible on the virtual kidney structures as scaled colour gradients, thus allowing a visual and quantitative appreciation of the effects of simulated parameter changes. A separate panel shows x-y plots of the results. The underlying models are implemented via CellML descriptions and are consistent, as far as possible, with standards and ontologies being developed for other organs under the Physiome initiative.
Abstract: Worddoc
Spectral frequencies arising from harmonics and from heterodyning have been reported in both experimental and modeling studies. Both harmonic and heterodyne frequencies have been attributed to the nonlinear properties of the tubuloglomerular (TGF) loop. However, the detailed mechanisms by which particular renal components generate harmonic and heterodyne frequencies have not been elucidated. Elementary mathematics can be used to show that signal transduction in a model of the thick ascending limb, of tubular flow rate to NaCl concentration at the macula densa, can, in principle, produce infinite series of both harmonic and heterodyne frequencies. Other nonlinear processes (e.g., the sigmoidal TGF response at the juxtaglomerular apparatus) can also introduce harmonic and heterodyne frequencies. Harmonic and heterodyne frequencies may be important components of the complex power spectra which arise from the irregular oscillations that are found in intratubular pressure records obtained from spontaneously hypertensive rats. Supported by NIH Grant DK-42091 and NSF Grant DMS-0340654. Collaborators: Anita Layton, Bruce Pitman, Paula Grajdeanu, Kevin Kesseler, Leon Moore, and Lauren Shareshian Streaming Video: Real Media Glucose is actively transported across the apical membrane of proximal tubular cells by Na+/glucose cotransporters (SGLT's). SGLT1, the model for this class of transporter, functions by an alternating access mechanism via a series of conformational changes induced by substrate-binding and membrane voltage. We have examined the conformations of human SGLT1 mutant G507C (expressed in Xenopus oocytes) during sugar transport using simultaneous electrical and optical measurements. The mutant exhibited similar kinetics as wild-type SGLT1, and labeling of Cys507 by tetramethylrhodamine-6-maleimide had no effect on function. We recorded changes in presteady-state currents (charge movement) and fluorescence in response to rapid-jumps in membrane potential in the presence and absence of glucose. Simulations based on an 8-state kinetic model for SGLT1 indicate that external sugar increases the occupancy probability of inward-facing conformations at the expense of outward-facing conformations. The simulations predict, and we have observed experimentally, that presteady-state currents are blocked by saturating sugar, but not the changes in fluorescence. Thus the conformational change associated with the rate-limiting step is electroneutral: at maximal inward Na+/sugar cotransport (saturating voltage and external Na+ and sugar concentrations), it is the slow release of Na+ from the internal surface of SGLT1.
Abstract: PDF Nephrons signal to each other over the vascular wall; the strength of this signalling increases 3-fold in hypertension. We developed a model that includes a single cortical radial artery, and 22 nephrons, of which 14 are cortical; of the remaining 8, 4 are short medullary nephrons, 3 intermediate length, and 1 a longer length medullary nephron. The nephron models are a 3rd order set of ODE's that predict tubular pressure and arteriolar diameter, with a 3rd order lag to simulate the various physical delays that occur in transmitting a change in proximal tubular outflow into a signal that reaches the afferent arteriole via TGF. The model does not have an independent myogenic component. Cortical nephrons synchronize at a single frequency, but the medullary nephrons cluster at frequencies incommensurate with the cortical frequency. The result is that cortical nephrons operating at normal blood pressure and normal vascular coupling, develop quasiperiodic dynamics, a well known route to chaos. The simulation shows that medullary nephrons operate in a chaotic mode even when arterial pressures and coupling coefficients are normal, and the chaotic domain increases to include cortical nephrons as the arterial blood pressure and the vascular coupling strength are made to increase. The results of these simulations suggest that there is more than one possible cause of the bifurcation to chaos that has been observed. The simulated synchronization, whether in normotensive or hypertensive states, provides the possibility that nephrons could react to perturbations in arterial pressure as an organized ensemble. The formation of a chaotic state, however, can lead to reduced synchronization despite the increase of coupling strength, because such states are inherently more likely to become desynchronized. The functional significance of synchronization and of its reduction in hypertension, remain to be understood.
Presentation materials: PDF Streaming Video: Real Media Our aim is to simulate the behaviour of clusters of nephrons and to understand how this behaviour arises from the activities of individual tubule segments. Further, we aim to create models that are capable of predicting kidney function and the effects of renal disease. Ultimately, we are interested in investigating the behaviour of the kidney at a level of abstraction that is relevant to clinicians.We approach the problem of renal modelling by assuming that the kidney is a complex network and applying techniques from Dynamical Networks (a form of Graph Automata) and methods from Statistical Mechanics and Machine Learning. We present a model of the nephron as a Graph Automata, where each node models a tubule segment, and difference equations model solute transport between tubule segments, the surrounding renal fluid, and peritubular capillaries. This network will form the basis of multi-nephron models, allowing us to study interactions and patterns of behaviour across groups of nephrons. Our current system of simple transport equations makes simulation of large clusters of nephrons computationally tractable. The model, though simple and still incomplete, is able to construct and maintain a salt gradient in the medullary fluid, and to regulate water and sodium reabsorption in response to ADH levels. The model also allows us to introduce stochastic failures into the nodes to mimic the onset of renal diseases (such as scar tissue in Bowman's Capsule) and so facilitate the analysis of the effects that diseased nephrons have on neighbouring nephrons. DVR 12 - 15 micron vessels to which contractility is imparted by smooth muscle remnants called pericytes. Much controversy has surrounded the ion channel architecture of the afferent and efferent circulations of the kidney. The roles of voltage gated calcium channels and membrane potential changes in vasoconstriction has been uncertain. To test their roles, we have isolated DVR by microdissection and performed patch clamp experiments on the pericytes and endothelium. The data shows that vasoactive agonists depolarize the pericyte cell membrane through a combination of calcium dependent chloride channel activation and potassium channel deactivation. Several classes of potassium channels are involved. Voltage gated calcium channel activity can be demonstrated in the pericytes, and, surprisingly, fast voltage gated sodium channels yield prominent currents. Finally, we have demonstrated that both pericytes and endothelial cells are electrically coupled via gap junctions. The pericytes appear to be weakly coupled while the endothelium forms low resistance syncytium. My talk will describe our current knowledge of the channel architecture of the DVR wall and compare it to that of other renal arteriolar segments. Abstract: Worddoc
Presentation materials: PPT Streaming Video: Real Media Urea transport, mediated by the UT-A1 and/or UT-A3 urea transporters, is important for the production of concentrated urine. Vasopressin rapidly increases urea transport in rat terminal inner medullary collecting ducts (IMCDs). UT-A1 is expressed in the apical plasma membrane of inner medullary collecting ducts (IMCDs). The localization of UT-A3 is controversial: it is apical in rat but basolateral in mice. Two mechanisms have been identified by which vasopressin may rapidly increase urea permeability in rat IMCDs: 1) increases in UT-A1 phosphorylation; and 2) increases in UT-A1 plasma membrane accumulation. The fold-increase in urea transport following vasopressin is larger than the fold-increase in either UT-A1 phosphorylation or plasma membrane accumulation alone. This suggests that vasopressin increases urea permeability through increases in both UT-A1 accumulation and phosphorylation.
Presentation materials: PPT Streaming Video: Real Media Framework models are designed to incorporate information from molecular dynamics simulations of ion channels in order to calculate their conductance properties on much longer time scales than can be achieved by the simulations. They provide a comparison between the simulations and conductance data. This talk describes three different steady state framework models. The single particle model was originally developed by Levitt, and describes a channel whose pore can be occupied by only one ion at a time. It has been used to model Na+ conduction through gramicidin. Transport is described by a Smoluchowski equation with non-local boundary conditions enforcing the single occupancy constraint. The Grotthuss conduction model describes proton conduction through gramicidin. It incorporates potentials of mean force for proton occupation and water reorientation calculated by Pomes and Roux. Model parameters were optimized against an extensive set of conductance data taken by Busath and his colleagues. Berneche and Roux developed a framework model for conduction through the narrow pore of the KcsA potassium channel, using a potential of mean force for occupation of the pore by two or three potassium ions. Finally, the problem of constructing time-dependent framework models is addressed.
In the interest of developing a global approach to biomedical data integration and interpretation, the Renal Physiome effort is exploring possibilities for multiscale modeling and simulation explicitly targeting questions of physiopathology. To this end, the first resource that has been developed is a quantitative kidney database (QKDB) to provide centralized access to measured parameter values, anatomical features, and functional characteristics at all scales from membrane transporters to the whole organ, both in human, when available, and in animal models. An interactive World-Wide-Web interface to legacy mathematical models at all levels of kidney physiology is also underway. Integral to the project is the development of ontologies, necessary to resolve issues of semantic ambiguity, consistency of descriptions, relational descriptions, and the like, and to enable integration with related resources in other fields. I will present current Physiome efforts internationally, will mention funding opportunities in this direction, and will give an indication of how the renal research community can participate in this communal effort.
Streaming Video: Real Media Phenotype analysis of transgenic mice lacking various components of the urinary concentrating system, such as aquaporins, urea transporters and the V2 receptor, have provided useful information on their role in generating a concentrating urine. Selective small-molecule inhibitors of these proteins have potential utility for chemical knock-out studies that are not confounded by compensatory changes in transgenic mice, as well as for development of clinical therapies. We have established a small molecule discovery program with high-throughput screening, a collection of >300,000 drug-like chemicals, and pharmacology/small animal testing resources. The program has been successful in identifying small-molecule CFTR activators and inhibitors for therapy of cystic fibrosis and secretory diarrheas, and recently, for identification of nanomolar potency inhibitors of urea transporter UT-B, the V2 receptor, and cyclic nucleotide signaling. Small-molecule modulators of protein function are likely to have great utility in post-genomic renal physiology.
Streaming Video: Real Media Renal autoregulation (AR) is the vasoconstriction and dilation of the renal microvasculature in response to changes in systemic blood pressure (BP) that maintains renal blood flow (RBF), glomerular filtration rate, and the glomerular capillary pressure approximately constant. This regulatory effect is believed to simultaneously insulate renal function from variations in BP and to protect glomerular capillaries from hypertensive injury. The dynamics of renal AR informs one about the operational characteristics of its underlying mechanisms and potentially enables the study of AR in vivo. These dynamics have been investigated using spectral analysis of RBF and BP recordings, time-frequency analysis of RBF recordings, and the fitting of exponential curves to the RBF and the afferent arteriolar diameter (AAD) time responses following step changes in pressure. We developed simple dynamic models for the myogenic mechanism of renal AR that take BP waveforms as inputs and produce RBF or AAD waveforms as outputs. Simulation studies of model behavior when driven by BP waveforms measured in rats and by various test waveforms provide insight into the interpretation of results of the various analysis techniques. We have used these models to connect alterations in AR response that are observed during experimental interventions to characteristics of the AR dynamics. In particular, changes in model parameters related to AR strength cause effects similar to those from AR impairment via calcium channel blockers, and changes in parameters related to AR capacity match effects from impairments after renal mass reduction. Our models also enable simulation of (myogenic-based) AR when triggered either by mean or by systolic pressure changes. Empirical observations of AAD responses in the hydronephrotic kidney, when presented with a variety of pressure waveforms, are better matched by model behavior with AR triggered by systolic pressure.
Streaming Video: Real Media
The Quantitative Kidney Database (QKDB, http://physiome.ibisc.fr/qkdb/) is accessible to all for consultation and is open to the renal research community for (password protected) data entry. It contains, for human kidneys where known, but especially in experimentally studied species (mammalian, amphibian, avian, ) and in model epithelia such as cultured cells and amphibian skin and urinary bladder: transport parameters (permeabilities to water and solutes, kinetics of transporters and channels, in all nephron and vessel segments and kidney regions); tubular concentrations and flow rates along nephrons and vessels; qualitative and quantitative anatomical details (e.g., tubule diameters and epithelial and cellular dimensions; relative placement of structures in each kidney region; and typical kidney sizes and weights for different species; dimensions of cortical and medullary regions and subregions).
Work done in collaboration with Sylvain Demey and S. Randall Thomas.
The Quantitative Kidney Database (QKDB, http://physiome.ibisc.fr/qkdb/) is accessible to all for consultation and is open to the renal research community for (password protected) data entry. It contains, for human kidneys where known, but especially in experimentally studied species (mammalian, amphibian, avian, ) and in model epithelia such as cultured cells and amphibian skin and urinary bladder: transport parameters (permeabilities to water and solutes, kinetics of transporters and channels, in all nephron and vessel segments and kidney regions); tubular concentrations and flow rates along nephrons and vessels; qualitative and quantitative anatomical details (e.g., tubule diameters and epithelial and cellular dimensions; relative placement of structures in each kidney region; and typical kidney sizes and weights for different species; dimensions of cortical and medullary regions and subregions).
Work done in collaboration with Boubacar Benziane and S. Randall Thomas.
We use a generalized mathematical model of rat thick ascending limb (TAL) of the loop of Henle to investigate the impact of variable TAL inner radius and variable NaCl transport rate on the TGF-mediated oscillations. An analytic bifurcation analysis of the TGF minimal model with TAL backleak provides fundamental insight into how oscillatory states depend on the physiological parameters of the model. Several attempts has been made to formulate mathematical models of the TGF system that is able to reproduce both the regular oscillations (in normotensive rats), and the irregular fluctuations (in spontaneously hypertensive rats). However, in most cases the models have been successful in describing the regular oscillations, but have failed to reproduce the irregular fluctuations (but by coupling of two nephorns). We hypothise that, irregular oscillations in hypertensive rats are attributable, at least in part, to the tubule's spatial inhomogeneities.
A transient 1D mathematical model of whole-organ renal autoregulation in the rat is presented, with the current focus being the myogenic response on multiple levels of the renal vasculature. Morphological data derived from micro-CT imaging has been employed to divide the vasculature via a Strahler ordering scheme. A previously published model of the myogenic response based on wall tension is expanded upon and adapted to fit the response of each level, corresponding to a distally dominant resistance distribution with the highest contributions localized to the afferent arterioles and interlobular arteries. Computer simulation results of the autoregulatory response to pressure perturbations are examined. Furthermore, ongoing and future works to be presented incorporate spatial dependence at the level of the nephron via the inclusion of a system of coupled partial differential equations to model the tubuloglomerular feedback mechanism, and the influence of nitric oxide through flow-induced dilation and macula densa signaling. Work done in collaboration with Tim David, Mike Plank, and Zoltan Endre.
Abstract: Worddoc Our previous work using the auto-bispectrum revealed nonlinear interactions between the myogenic and TGF mechanisms in both the whole kidney and single nephron measurements from SDR and SHR. Our aim in this study was to investigate whether nephrons located on the same radial artery shows similar interactions. To this end, stop flow pressure (SFP) from two nephrons were simultaneously measured from both SDR (n=12) and SHR (n=18). Vascular connections between nephrons were confirmed with vascular cast. Interactions between the nephron measurements were assessed using the cross-bispectrum. The statistical significance of the presence of nonlinear interactions found via cross-bispectrum was tested against surrogate data realizations. Results show that most of the nephron pairs have significant coupling between the tubuloglomerular (TGF) and myogenic (MYO) mechanisms (10 out of 12 and 13 out of 18 SFP records for SDR and SHR, respectively), while only a few have MYO to MYO coupling (2/12 and 2/18) for both stains of rats. TGF to TGF coupling was more prevalent in SHR (10/18) than SDR (4/12). The true number of nephron to nephron coupling obtained from vascular cast measurements are 10 out of 12 and 13 out of 18 for SDR and SHR, respectively. This correlates well with the amount of coupling detected between the MYO and TGF mechanisms. The enhanced TGF to TGF coupling between nephrons in SHR may be an indication of enhanced autoregulatory function associated with SHR. Work done in collaboration with Kay-Pong Yip, Leon C. Moore, Donald J. Marsh, and Ki H. Chon.
Abstract for Poster: Worddoc Presentation materials: PDF
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