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Register a new userA quantitative model for refilling of the sarcoplasmic reticulum during vascular smooth muscle asynchronous [Ca2+] oscillations
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We have developed a quantitative model for the creation of cytoplasmic Ca2+ gradients near the inner surface of the plasma membrane (PM). In particular we simulated the refilling of the sarcoplasmic reticulum (SR) via PM-SR junctions during asynchronous [Ca2+] oscillations in smooth muscle cells of the rabbit inferior vena cava. We have combined confocal microscopy data on the [Ca2+] oscillations, force transduction data from cell contraction studies and electron microscopic images to build a basis for computational simulations that model the transport of calcium ions from Na+/Ca2+ exchangers (NCX) on the PM to sarcoplasmic/endoplasmic reticulum Ca2+ ATPase (SERCA) pumps on the SR as a three-dimensional random walk through the PM-SR junctional cytoplasmic spaces. Electron microscopic ultrastructural images of the smooth muscle cells were elaborated with software algorithms to produce a very clear and dimensionally accurate picture of the PM-SR junctions. From this study, we conclude that it is plausible and possible for enough Ca2+ to pass through the PM-SR junctions to replete the SR during the regenerative Ca2+ release, which underlies agonist induced asynchronous Ca2+ oscillations in vascular smooth muscle.
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Muscle uses Ca2+ as a messenger to control contraction and relies on ATP to maintain the intracellular Ca2+ homeostasis. Mitochondria are the major sub-cellular organelle of ATP production. With a negative inner membrane potential, mitochondria take up Ca2+ from their surroundings, a process called mitochondrial Ca2+ uptake. Under physiological conditions, Ca2+ uptake into mitochondria promotes ATP production. Excessive uptake causes mitochondrial Ca2+ overload, which activates downstream adverse responses leading to cell dysfunction. Moreover, mitochondrial Ca2+ uptake could shape spatio-temporal patterns of intracellular Ca2+ signaling. Malfunction of mitochondrial Ca2+ uptake is implicated in muscle degeneration. Unlike non-excitable cells, mitochondria in muscle cells experience dramatic changes of intracellular Ca2+ levels. Besides the sudden elevation of Ca2+ level induced by action potentials, Ca2+ transients in muscle cells can be as short as a few milliseconds during a single twitch or as long as minutes during tetanic contraction, which raises the question whether mitochondrial Ca2+ uptake is fast and big enough to shape intracellular Ca2+ signaling during excitation-contraction coupling and creates technical challenges for quantification of the dynamic changes of Ca2+ inside mitochondria. This review focuses on characterization of mitochondrial Ca2+ uptake in skeletal muscle and its role in muscle physiology and diseases.
Coordination in circular and longitudinal muscle motions are of crucial importance in the motor function of gastrointestinal (GI) tract. Intestinal wall motions depend on myogenic-active properties of smooth muscles layers of intestinal wall, which is the ability to create active contractile forces in response to distension. Considering the stress in the circular and longitudinal smooth muscles as a sum of passive, depending on muscle deformations, and active, depending on muscle tone, components, and also assuming that the change in the muscle tone depends on the current stress-strain condition, the system of four ordinary differential equations (ODE) is obtained, which describes filling-emptying cycle of intestinal segment as a process of coordinated activities of circular and longitudinal muscles of intestinal wall. A general approach in formulating the modelling conditions is based on the previously described model restricted to the circularly distensible reservoir of constant length. Obtained results illustrate the character of coordinated activities of two orthogonal muscle layers, which are alternating phases of reciprocally and uniformly changing modalities such as stretching of the wall and muscle tone. The results also contribute to the existing understanding of the roles of Auerbachs and Meisners intermuscular and submucous neural plexuses in regulations of autonomous intestinal motility, as well as clarify functional mechanisms of the interstitial cells of Cajal (ICC) in triggering of smooth muscle contractions.
A quantitative description of the flagellar dynamics in the procyclic T. brucei is presented in terms of stationary oscillations and traveling waves. By using digital video microscopy to quantify the kinematics of trypanosome flagellar waveforms. A theoretical model is build starting from a Bernoulli-Euler flexural-torsional model of an elastic string with internal distribution of force and torque. The dynamics is internally driven by the action of the molecular motors along the string, which is proportional to the local shift and consequently to the local curvature. The model equation is a nonlinear partial differential wave equation of order four, containing nonlinear terms specific to the Korteweg-de Vries (KdV) equation and the modified-KdV equation. For different ranges of parameters we obtained kink-like solitons, breather solitons, and a new class of solutions constructed by smoothly piece-wise connected conic functions arcs (e.g. ellipse). The predicted amplitude and wavelengths are in good match with experiments. We also present the hypotheses for a step-wise kinematical model of swimming of procyclic African trypanosome.
Intratumor heterogeneity is often manifested by vascular compartments with distinct pharmacokinetics that cannot be resolved directly by in vivo dynamic imaging. We developed tissue-specific compartment modeling (TSCM), an unsupervised computational method of deconvolving dynamic imaging series from heterogeneous tumors that can improve vascular phenotyping in many biological contexts. Applying TSCM to dynamic contrast-enhanced MRI of breast cancers revealed characteristic intratumor vascular heterogeneity and therapeutic responses that were otherwise undetectable.
The positions of nucleosomes in eukaryotic genomes determine which parts of the DNA sequence are readily accessible for regulatory proteins and which are not. Genome-wide maps of nucleosome positions have revealed a salient pattern around transcription start sites, involving a nucleosome-free region (NFR) flanked by a pronounced periodic pattern in the average nucleosome density. While the periodic pattern clearly reflects well-positioned nucleosomes, the positioning mechanism is less clear. A recent experimental study by Mavrich et al. argued that the pattern observed in S. cerevisiae is qualitatively consistent with a `barrier nucleosome model, in which the oscillatory pattern is created by the statistical positioning mechanism of Kornberg and Stryer. On the other hand, there is clear evidence for intrinsic sequence preferences of nucleosomes, and it is unclear to what extent these sequence preferences affect the observed pattern. To test the barrier nucleosome model, we quantitatively analyze yeast nucleosome positioning data both up- and downstream from NFRs. Our analysis is based on the Tonks model of statistical physics which quantifies the interplay between the excluded-volume interaction of nucleosomes and their positional entropy. We find that although the typical patterns on the two sides of the NFR are different, they are both quantitatively described by the same physical model, with the same parameters, but different boundary conditions. The inferred boundary conditions suggest that the first nucleosome downstream from the NFR (the +1 nucleosome) is typically directly positioned while the first nucleosome upstream is statistically positioned via a nucleosome-repelling DNA region. These boundary conditions, which can be locally encoded into the genome sequence, significantly shape the statistical distribution of nucleosomes over a range of up to ~1000 bp to each side.
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