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  • American Society for Cell Biology (ASCB)  (80)
  • 1
    Online Resource
    Online Resource
    American Society for Cell Biology (ASCB) ; 2017
    In:  Molecular Biology of the Cell Vol. 28, No. 23 ( 2017-11-07), p. 3457-3470
    In: Molecular Biology of the Cell, American Society for Cell Biology (ASCB), Vol. 28, No. 23 ( 2017-11-07), p. 3457-3470
    Abstract: Migrating cells often exhibit signal relay, a process in which cells migrating in response to a chemotactic gradient release a secondary chemoattractant to enhance directional migration. In neutrophils, signal relay toward the primary chemoattractant N-­formylmethionyl-leucyl-phenylalanine (fMLP) is mediated by leukotriene B 4 (LTB 4 ). Recent evidence suggests that the release of LTB 4 from cells occurs through packaging in exosomes. Here we present a mathematical model of neutrophil signal relay that focuses on LTB 4 and its exosome-mediated secretion. We describe neutrophil chemotaxis in response to a combination of a defined gradient of fMLP and an evolving gradient of LTB 4 , generated by cells in response to fMLP. Our model enables us to determine the gradient of LTB 4 arising either through directed secretion from cells or through time-varying release from exosomes. We predict that the secondary release of LTB 4 increases recruitment range and show that the exosomes provide a time delay mechanism that regulates the development of LTB 4 gradients. Additionally, we show that under decaying primary gradients, secondary gradients are more stable when secreted through exosomes as compared with direct secretion. Our chemotactic model, calibrated from observed responses of cells to gradients, thereby provides insight into chemotactic signal relay in neutrophils during inflammation.
    Type of Medium: Online Resource
    ISSN: 1059-1524 , 1939-4586
    Language: English
    Publisher: American Society for Cell Biology (ASCB)
    Publication Date: 2017
    detail.hit.zdb_id: 1474922-1
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    American Society for Cell Biology (ASCB) ; 2013
    In:  Molecular Biology of the Cell Vol. 24, No. 3 ( 2013-02), p. 421-432
    In: Molecular Biology of the Cell, American Society for Cell Biology (ASCB), Vol. 24, No. 3 ( 2013-02), p. 421-432
    Abstract: The Rho GTPases—Rho, Rac, and Cdc42—control an enormous variety of processes, many of which reflect activation of these GTPases in spatially confined and mutually exclusive zones. By using mathematical models and experimental results to establish model parameters, we analyze the formation and segregation of Rho and Cdc42 zones during Xenopus oocyte wound repair and the role played by Abr, a dual guanine nucleotide exchange factor–GTPase-activating protein, in this process. The Rho and Cdc42 zones are found to be best represented as manifestations of spatially modulated bistability, and local positive feedback between Abr and Rho can account for the maintenance and dynamic properties of the Rho zone. In contrast, the invocation of an Abr-independent positive feedback loop is required to account for Cdc42 spatial bistability. In addition, the model replicates the results of previous in vivo experiments in which Abr activity is manipulated. Further, simulating the model with two closely spaced wounds made nonintuitive predictions about the Rho and Cdc42 patterns; these predictions were confirmed by experiment. We conclude that the model is a useful tool for analysis of Rho GTPase signaling and that the Rho GTPases can be fruitfully considered as components of intracellular pattern formation systems.
    Type of Medium: Online Resource
    ISSN: 1059-1524 , 1939-4586
    Language: English
    Publisher: American Society for Cell Biology (ASCB)
    Publication Date: 2013
    detail.hit.zdb_id: 1474922-1
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  • 3
    Online Resource
    Online Resource
    American Society for Cell Biology (ASCB) ; 2010
    In:  Molecular Biology of the Cell Vol. 21, No. 24 ( 2010-12-15), p. 4418-4427
    In: Molecular Biology of the Cell, American Society for Cell Biology (ASCB), Vol. 21, No. 24 ( 2010-12-15), p. 4418-4427
    Abstract: The centrosome position in many types of interphase cells is actively maintained in the cell center. Our previous work indicated that the centrosome is kept at the center by pulling force generated by dynein and actin flow produced by myosin contraction and that an unidentified factor that depends on microtubule dynamics destabilizes position of the centrosome. Here, we use modeling to simulate the centrosome positioning based on the idea that the balance of three forces—dyneins pulling along microtubule length, myosin-powered centripetal drag, and microtubules pushing on organelles—is responsible for the centrosome displacement. By comparing numerical predictions with centrosome behavior in wild-type and perturbed interphase cells, we rule out several plausible hypotheses about the nature of the microtubule-based force. We conclude that strong dynein- and weaker myosin-generated forces pull the microtubules inward competing with microtubule plus-ends pushing the microtubule aster outward and that the balance of these forces positions the centrosome at the cell center. The model also predicts that kinesin action could be another outward-pushing force. Simulations demonstrate that the force-balance centering mechanism is robust yet versatile. We use the experimental observations to reverse engineer the characteristic forces and centrosome mobility.
    Type of Medium: Online Resource
    ISSN: 1059-1524 , 1939-4586
    Language: English
    Publisher: American Society for Cell Biology (ASCB)
    Publication Date: 2010
    detail.hit.zdb_id: 1474922-1
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    American Society for Cell Biology (ASCB) ; 2015
    In:  Molecular Biology of the Cell Vol. 26, No. 22 ( 2015-11-05), p. 3954-3965
    In: Molecular Biology of the Cell, American Society for Cell Biology (ASCB), Vol. 26, No. 22 ( 2015-11-05), p. 3954-3965
    Abstract: High-fidelity chromosome segregation during cell division depends on a series of concerted interdependent interactions. Using a systems biology approach, we built a robust minimal computational model to comprehend mitotic events in dividing budding yeasts of two major phyla: Ascomycota and Basidiomycota. This model accurately reproduces experimental observations related to spindle alignment, nuclear migration, and microtubule (MT) dynamics during cell division in these yeasts. The model converges to the conclusion that biased nucleation of cytoplasmic microtubules (cMTs) is essential for directional nuclear migration. Two distinct pathways, based on the population of cMTs and cortical dyneins, differentiate nuclear migration and spindle orientation in these two phyla. In addition, the model accurately predicts the contribution of specific classes of MTs in chromosome segregation. Thus we present a model that offers a wider applicability to simulate the effects of perturbation of an event on the concerted process of the mitotic cell division.
    Type of Medium: Online Resource
    ISSN: 1059-1524 , 1939-4586
    Language: English
    Publisher: American Society for Cell Biology (ASCB)
    Publication Date: 2015
    detail.hit.zdb_id: 1474922-1
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    American Society for Cell Biology (ASCB) ; 2017
    In:  Molecular Biology of the Cell Vol. 28, No. 24 ( 2017-11-15), p. 3480-3488
    In: Molecular Biology of the Cell, American Society for Cell Biology (ASCB), Vol. 28, No. 24 ( 2017-11-15), p. 3480-3488
    Abstract: Dynamics of endocytic clathrin-coated structures can be remarkably divergent across different cell types, cells within the same culture, or even distinct surfaces of the same cell. The origin of this astounding heterogeneity remains to be elucidated. Here we show that cellular processes associated with changes in effective plasma membrane tension induce significant spatiotemporal alterations in endocytic clathrin coat dynamics. Spatiotemporal heterogeneity of clathrin coat dynamics is also observed during morphological changes taking place within developing multicellular organisms. These findings suggest that tension gradients can lead to patterning and differentiation of tissues through mechanoregulation of clathrin-mediated endocytosis.
    Type of Medium: Online Resource
    ISSN: 1059-1524 , 1939-4586
    Language: English
    Publisher: American Society for Cell Biology (ASCB)
    Publication Date: 2017
    detail.hit.zdb_id: 1474922-1
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    American Society for Cell Biology (ASCB) ; 2018
    In:  Molecular Biology of the Cell Vol. 29, No. 11 ( 2018-06), p. 1318-1331
    In: Molecular Biology of the Cell, American Society for Cell Biology (ASCB), Vol. 29, No. 11 ( 2018-06), p. 1318-1331
    Abstract: Cytokinesis in many eukaryotic cells is orchestrated by a contractile actomyosin ring. While many of the proteins involved are known, the mechanism of constriction remains unclear. Informed by the existing literature and new three-dimensional (3D) molecular details from electron cryotomography, here we develop 3D coarse-grained models of actin filaments, unipolar and bipolar myosins, actin cross-linkers, and membranes and simulate their interactions. Assuming that local force on the membrane results in inward growth of the cell wall, we explored a matrix of possible actomyosin configurations and found that node-based architectures like those presently described for ring assembly result in membrane puckers not seen in electron microscope images of real cells. Instead, the model that best matches data from fluorescence microscopy, electron cryotomography, and biochemical experiments is one in which actin filaments transmit force to the membrane through evenly distributed, membrane-attached, unipolar myosins, with bipolar myosins in the ring driving contraction. While at this point this model is only favored (not proven), the work highlights the power of coarse-grained biophysical simulations to compare complex mechanistic hypotheses.
    Type of Medium: Online Resource
    ISSN: 1059-1524 , 1939-4586
    Language: English
    Publisher: American Society for Cell Biology (ASCB)
    Publication Date: 2018
    detail.hit.zdb_id: 1474922-1
    SSG: 12
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  • 7
    Online Resource
    Online Resource
    American Society for Cell Biology (ASCB) ; 2019
    In:  Molecular Biology of the Cell Vol. 30, No. 16 ( 2019-07-22), p. 2014-2024
    In: Molecular Biology of the Cell, American Society for Cell Biology (ASCB), Vol. 30, No. 16 ( 2019-07-22), p. 2014-2024
    Abstract: We formulated a spatially resolved model to estimate forces exerted by a polymerizing actin meshwork on an invagination of the plasma membrane during endocytosis in yeast cells. The model, which approximates the actin meshwork as a visco-active gel exerting forces on a rigid spherocylinder representing the endocytic invagination, is tightly constrained by experimental data. Simulations of the model produce forces that can overcome resistance of turgor pressure in yeast cells. Strong forces emerge due to the high density of polymerized actin in the vicinity of the invagination and because of entanglement of the meshwork due to its dendritic structure and cross-linking. The model predicts forces orthogonal to the invagination that are consistent with formation of a flask shape, which would diminish the net force due to turgor pressure. Simulations of the model with either two rings of nucleation-promoting factors (NPFs) as in fission yeast or a single ring of NPFs as in budding yeast produce enough force to elongate the invagination against the turgor pressure.
    Type of Medium: Online Resource
    ISSN: 1059-1524 , 1939-4586
    Language: English
    Publisher: American Society for Cell Biology (ASCB)
    Publication Date: 2019
    detail.hit.zdb_id: 1474922-1
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    American Society for Cell Biology (ASCB) ; 2020
    In:  Molecular Biology of the Cell Vol. 31, No. 7 ( 2020-03-19), p. 640-654
    In: Molecular Biology of the Cell, American Society for Cell Biology (ASCB), Vol. 31, No. 7 ( 2020-03-19), p. 640-654
    Abstract: Neurofilaments are abundant space-filling cytoskeletal polymers in axons that are transported along microtubule tracks. Neurofilament transport is accelerated at nodes of Ranvier, where axons are locally constricted. Strikingly, these constrictions are accompanied by sharp decreases in neurofilament number, no decreases in microtubule number, and increases in the packing density of these polymers, which collectively bring nodal neurofilaments closer to their microtubule tracks. We hypothesize that this leads to an increase in the proportion of time that the filaments spend moving and that this can explain the local acceleration. To test this, we developed a stochastic model of neurofilament transport that tracks their number, kinetic state, and proximity to nearby microtubules in space and time. The model assumes that the probability of a neurofilament moving is dependent on its distance from the nearest available microtubule track. Taking into account experimentally reported numbers and densities for neurofilaments and microtubules in nodes and internodes, we show that the model is sufficient to explain the local acceleration of neurofilaments within nodes of Ranvier. This suggests that proximity to microtubule tracks may be a key regulator of neurofilament transport in axons, which has implications for the mechanism of neurofilament accumulation in development and disease.
    Type of Medium: Online Resource
    ISSN: 1059-1524 , 1939-4586
    Language: English
    Publisher: American Society for Cell Biology (ASCB)
    Publication Date: 2020
    detail.hit.zdb_id: 1474922-1
    SSG: 12
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  • 9
    Online Resource
    Online Resource
    American Society for Cell Biology (ASCB) ; 2023
    In:  Molecular Biology of the Cell Vol. 34, No. 6 ( 2023-05-15)
    In: Molecular Biology of the Cell, American Society for Cell Biology (ASCB), Vol. 34, No. 6 ( 2023-05-15)
    Abstract: Biosynthesis of organelle precursors is a central part of the organelle size control problem, but what systems are required to control precursor production? Genes encoding flagellar proteins are up-regulated during flagellar regeneration in Chlamydomonas, and this up-regulation is critical for flagella to reach their final length, but it not known how the cell triggers these genes during regeneration. We present two models based on transcriptional repressor that is produced either in the flagellum or in the cell body and sequestered in the growing flagellum. Both models lead to stable flagellar length control and can reproduce the observed dynamics of gene expression. The two models make opposite predictions regarding the effect of mutations that block intraflagellar transport (IFT). Using quantitative measurements of gene expression, we show that gene expression during flagellar regeneration is greatly reduced in mutations of the heterotrimeric kinesin-2 that drives IFT. This result is consistent with the predictions of the model in which a repressor is sequestered in the flagellum by IFT. Inhibiting axonemal assembly has a much smaller effect on gene expression. The repressor sequestration model allows precursor production to occur when flagella are growing rapidly, representing a form of derivative control.
    Type of Medium: Online Resource
    ISSN: 1059-1524 , 1939-4586
    Language: English
    Publisher: American Society for Cell Biology (ASCB)
    Publication Date: 2023
    detail.hit.zdb_id: 1474922-1
    SSG: 12
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  • 10
    Online Resource
    Online Resource
    American Society for Cell Biology (ASCB) ; 2018
    In:  Molecular Biology of the Cell Vol. 29, No. 11 ( 2018-06), p. 1400-1409
    In: Molecular Biology of the Cell, American Society for Cell Biology (ASCB), Vol. 29, No. 11 ( 2018-06), p. 1400-1409
    Abstract: Biological systems are endowed with two fundamental but seemingly contradictory properties: robustness, the ability to withstand environmental fluctuations and genetic variability; and evolvability, the ability to acquire selectable and heritable phenotypic changes. Cell populations with heterogeneous genetic makeup, such as those of infectious microbial organisms or cancer, rely on their inherent robustness to maintain viability and fitness, but when encountering environmental insults, such as drug treatment, these populations are also poised for rapid adaptation through evolutionary selection. In this study, we develop a general mathematical model that allows us to explain and quantify this fundamental relationship between robustness and evolvability of heterogeneous cell populations. Our model predicts that robustness is, in fact, essential for evolvability, especially for more adverse environments, a trend we observe in aneuploid budding yeast and breast cancer cells. Robustness also compensates for the negative impact of the systems’ complexity on their evolvability. Our model also provides a mathematical means to estimate the number of independent processes underlying a system’s performance and identify the most generally adapted subpopulation, which may resemble the multi-drug-resistant “persister” cells observed in cancer.
    Type of Medium: Online Resource
    ISSN: 1059-1524 , 1939-4586
    Language: English
    Publisher: American Society for Cell Biology (ASCB)
    Publication Date: 2018
    detail.hit.zdb_id: 1474922-1
    SSG: 12
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