scholarly journals Robustness of the microtubule network self-organization in epithelia

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Aleksandra Z Płochocka ◽  
Miguel Ramirez Moreno ◽  
Alexander M Davie ◽  
Natalia A Bulgakova ◽  
Lyubov Chumakova
Keyword(s):  
Large Scale ◽  
Stochastic Simulations ◽  
Self Organization ◽  
Microtubule Network ◽  
Biologically Relevant ◽  
Genetic Manipulations ◽  
Microtubule Networks ◽  
Open Question ◽  
Cellular Components

Robustness of biological systems is crucial for their survival, however, for many systems its origin is an open question. Here, we analyze one subcellular level system, the microtubule cytoskeleton. Microtubules self-organize into a network, along which cellular components are delivered to their biologically relevant locations. While the dynamics of individual microtubules is sensitive to the organism’s environment and genetics, a similar sensitivity of the overall network would result in pathologies. Our large-scale stochastic simulations show that the self-organization of microtubule networks is robust in a wide parameter range in individual cells. We confirm this robustness in vivo on the tissue-scale using genetic manipulations of Drosophila epithelial cells. Finally, our minimal mathematical model shows that the origin of robustness is the separation of time-scales in microtubule dynamics rates. Altogether, we demonstrate that the tissue-scale self-organization of a microtubule network depends only on cell geometry and the distribution of the microtubule minus-ends.

scholarly journals Robustness of bidirectional microtubule network self-organization

2019 ◽  
Author(s):  
Aleksandra Z. Płochocka ◽  
Alexander M. Davie ◽  
Natalia. A. Bulgakova ◽  
Lyubov Chumakova
Keyword(s):  
Tissue Level ◽  
Cellular Level ◽  
Self Organization ◽  
Level System ◽  
Microtubule Network ◽  
Biologically Relevant ◽  
Genetic Manipulations ◽  
Network Sensitivity ◽  
Open Question ◽  
Cellular Components

Robustness of biological systems is crucial for their survival, however, for many systems its origin is an open question. Here we analyze one sub-cellular level system, the microtubule cytoskeleton. Microtubules self-organize into a network, along which cellular components are delivered to their biologically relevant locations. While individual microtubule are highly dynamic with their dynamics depends on the organism environment and genetics, network sensitivity to this dynamics would result in pathologies. Combining mathematical modelling with genetic manipulations in Drosophila, we show that the microtubule self-organization indeed does not depend on dynamics of individual microtubules, and thus is robust on the tissue level. We demonstrate the origin of this robustness via a mathematical model, suggesting this being a generic mechanism.

scholarly journals In-cell SHAPE reveals that free 30S ribosome subunits are in the inactive state

2015 ◽  
Vol 112 (8) ◽  
pp. 2425-2430 ◽  
Author(s):  
Jennifer L. McGinnis ◽  
Qi Liu ◽  
Christopher A. Lavender ◽  
Aishwarya Devaraj ◽  
Sean P. McClory ◽  
...  
Keyword(s):  
Energy Barrier ◽  
Cell Shape ◽  
Large Scale ◽  
Neck Region ◽  
Active Conformation ◽  
Conformational Switch ◽  
Biologically Relevant ◽  
Inactive State ◽  
Active Subunits

It was shown decades ago that purified 30S ribosome subunits readily interconvert between “active” and “inactive” conformations in a switch that involves changes in the functionally important neck and decoding regions. However, the physiological significance of this conformational change had remained unknown. In exponentially growing Escherichia coli cells, RNA SHAPE probing revealed that 16S rRNA largely adopts the inactive conformation in stably assembled, mature 30S subunits and the active conformation in translating (70S) ribosomes. Inactive 30S subunits bind mRNA as efficiently as active subunits but initiate translation more slowly. Mutations that inhibited interconversion between states compromised translation in vivo. Binding by the small antibiotic paromomycin induced the inactive-to-active conversion, consistent with a low-energy barrier between the two states. Despite the small energetic barrier between states, but consistent with slow translation initiation and a functional role in vivo, interconversion involved large-scale changes in structure in the neck region that likely propagate across the 30S body via helix 44. These findings suggest the inactive state is a biologically relevant alternate conformation that regulates ribosome function as a conformational switch.

scholarly journals Active contraction of microtubule networks

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Peter J Foster ◽  
Sebastian Fürthauer ◽  
Michael J Shelley ◽  
Daniel J Needleman
Keyword(s):  
Large Scale ◽  
Quantitative Agreement ◽  
Self Organization ◽  
Cellular Processes ◽  
Network Geometry ◽  
Initial Network ◽  
Fluid Theory ◽  
Scale Structures ◽  
Density Inhomogeneities ◽  
Microtubule Networks

Many cellular processes are driven by cytoskeletal assemblies. It remains unclear how cytoskeletal filaments and motor proteins organize into cellular scale structures and how molecular properties of cytoskeletal components affect the large-scale behaviors of these systems. Here, we investigate the self-organization of stabilized microtubules in Xenopus oocyte extracts and find that they can form macroscopic networks that spontaneously contract. We propose that these contractions are driven by the clustering of microtubule minus ends by dynein. Based on this idea, we construct an active fluid theory of network contractions, which predicts a dependence of the timescale of contraction on initial network geometry, a development of density inhomogeneities during contraction, a constant final network density, and a strong influence of dynein inhibition on the rate of contraction, all in quantitative agreement with experiments. These results demonstrate that the motor-driven clustering of filament ends is a generic mechanism leading to contraction.

scholarly journals Thermodynamics of protein destabilization in live cells

2015 ◽  
Vol 112 (40) ◽  
pp. 12402-12407 ◽  
Author(s):  
Jens Danielsson ◽  
Xin Mu ◽  
Lisa Lang ◽  
Huabing Wang ◽  
Andres Binolfi ◽  
...  
Keyword(s):  
Self Organization ◽  
Live Cells ◽  
Heat Capacity Change ◽  
Bacterial Cells ◽  
Crowding Effects ◽  
Capacity Change ◽  
The Individual ◽  
Cellular Components

Although protein folding and stability have been well explored under simplified conditions in vitro, it is yet unclear how these basic self-organization events are modulated by the crowded interior of live cells. To find out, we use here in-cell NMR to follow at atomic resolution the thermal unfolding of a β-barrel protein inside mammalian and bacterial cells. Challenging the view from in vitro crowding effects, we find that the cells destabilize the protein at 37 °C but with a conspicuous twist: While the melting temperature goes down the cold unfolding moves into the physiological regime, coupled to an augmented heat-capacity change. The effect seems induced by transient, sequence-specific, interactions with the cellular components, acting preferentially on the unfolded ensemble. This points to a model where the in vivo influence on protein behavior is case specific, determined by the individual protein’s interplay with the functionally optimized “interaction landscape” of the cellular interior.

scholarly journals MPTH-18STREAMS, VORTICES, AND NEUROSPHERES: IN VIVO NON-RANDOM LARGE SCALE SELF-ORGANIZATION OF GLIOBLASTOMA MULTIFORME AND THE ROLE OF NOVEL HISTOPATHOLOGICAL STRUCTURES

2015 ◽  
Vol 17 (suppl 5) ◽  
pp. v142.1-v142
Author(s):  
Pedro Lowenstein ◽  
Sebastien Motsch ◽  
Carl Koschmann ◽  
Felipe Nuñez-Aguilera ◽  
Gregory Baker ◽  
...  
Keyword(s):  
Glioblastoma Multiforme ◽  
Large Scale ◽  
Self Organization

scholarly journals Extensile motor activity drives coherent motions in a model of interphase chromatin

2018 ◽  
Vol 115 (45) ◽  
pp. 11442-11447 ◽  
Author(s):  
David Saintillan ◽  
Michael J. Shelley ◽  
Alexandra Zidovska
Keyword(s):  
Molecular Motors ◽  
Large Scale ◽  
Fluid Flows ◽  
Coarse Grained ◽  
Polymeric Form ◽  
Nematic Ordering ◽  
Model Account ◽  
Active Motor ◽  
Open Question

The 3D spatiotemporal organization of the human genome inside the cell nucleus remains a major open question in cellular biology. In the time between two cell divisions, chromatin—the functional form of DNA in cells—fills the nucleus in its uncondensed polymeric form. Recent in vivo imaging experiments reveal that the chromatin moves coherently, having displacements with long-ranged correlations on the scale of micrometers and lasting for seconds. To elucidate the mechanism(s) behind these motions, we develop a coarse-grained active polymer model where chromatin is represented as a confined flexible chain acted upon by molecular motors that drive fluid flows by exerting dipolar forces on the system. Numerical simulations of this model account for steric and hydrodynamic interactions as well as internal chain mechanics. These demonstrate that coherent motions emerge in systems involving extensile dipoles and are accompanied by large-scale chain reconfigurations and nematic ordering. Comparisons with experiments show good qualitative agreement and support the hypothesis that self-organizing long-ranged hydrodynamic couplings between chromatin-associated active motor proteins are responsible for the observed coherent dynamics.

scholarly journals Extensile motor activity drives coherent motions in a model of interphase chromatin

2018 ◽  
Author(s):  
David Saintillan ◽  
Michael J. Shelley ◽  
Alexandra Zidovska
Keyword(s):  
Molecular Motors ◽  
Large Scale ◽  
Coarse Grained ◽  
Cellular Biology ◽  
Polymeric Form ◽  
Nematic Ordering ◽  
Model Account ◽  
Active Motor ◽  
Open Question

AbstractThe 3D spatiotemporal organization of the human genome inside the cell nucleus remains a major open question in cellular biology. In the time between two cell divisions, chromatin – the functional form of DNA in cells – fills the nucleus in its uncondensed polymeric form. Recent in-vivo imaging experiments reveal that the chromatin moves coherently, having displacements with long-ranged correlations on the scale of microns and lasting for seconds. To elucidate the mechanism(s) behind these motions, we develop a novel coarse-grained active-polymer model where chromatin is represented as a confined flexible chain acted upon by molecular motors, which perform work by exerting dipolar forces on the system. Numerical simulations of this model account for steric and hydrodynamic interactions as well as internal chain mechanics. These demonstrate that coherent motions emerge in systems involving extensile dipoles and are accompanied by large-scale chain reconfigurations and nematic ordering. Comparisons with experiments show good qualitative agreement and support the hypothesis that self-organizing long-ranged hydrodynamic couplings between chromatin-associated active motor proteins are responsible for the observed coherent dynamics.

scholarly journals Self-organization of an acentrosomal microtubule network at the basal cortex of polarized epithelial cells

2005 ◽  
Vol 171 (5) ◽  
pp. 845-855 ◽  
Author(s):  
Amy Reilein ◽  
Soichiro Yamada ◽  
W. James Nelson
Keyword(s):  
Steady State ◽  
Epithelial Cells ◽  
Dynamic Instability ◽  
Self Organization ◽  
Microtubule Network ◽  
Microtubule Stabilization ◽  
Microtubule Stability ◽  
Mixed Polarity ◽  
Polarized Epithelial Cells ◽  
Microtubule Networks

Mechanisms underlying the organization of centrosome-derived microtubule arrays are well understood, but less is known about how acentrosomal microtubule networks are formed. The basal cortex of polarized epithelial cells contains a microtubule network of mixed polarity. We examined how this network is organized by imaging microtubule dynamics in acentrosomal basal cytoplasts derived from these cells. We show that the steady-state microtubule network appears to form by a combination of microtubule–microtubule and microtubule–cortex interactions, both of which increase microtubule stability. We used computational modeling to determine whether these microtubule parameters are sufficient to generate a steady-state acentrosomal microtubule network. Microtubules undergoing dynamic instability without any stabilization points continuously remodel their organization without reaching a steady-state network. However, the addition of increased microtubule stabilization at microtubule–microtubule and microtubule–cortex interactions results in the rapid assembly of a steady-state microtubule network in silico that is remarkably similar to networks formed in situ. These results define minimal parameters for the self-organization of an acentrosomal microtubule network.

Solving the mechanisms responsible for organelle behavior in vivo by same-cell correlative light and electron microscopy

1992 ◽  
Vol 50 (1) ◽  
pp. 14-15
Author(s):  
Conly L. Rieder
Keyword(s):  
Electron Microscopy ◽  
Quantitative Analysis ◽  
Light Microscopy ◽  
Living Cell ◽  
Light And Electron Microscopy ◽  
Time Behavior ◽  
Dynamic Interactions ◽  
Positive Identification ◽  
Cellular Components

The behavior of many cellular components, and their dynamic interactions, can be characterized in the living cell with considerable spatial and temporal resolution by video-enhanced light microscopy (video-LM). Indeed, under the appropriate conditions video-LM can be used to determine the real-time behavior of organelles ≤ 25-nm in diameter (e.g., individual microtubules—see). However, when pushed to its limit the structures and components observed within the cell by video-LM cannot be resolved nor necessarily even identified, only detected. Positive identification and a quantitative analysis often requires the corresponding electron microcopy (EM).

Purification of the Antihemophilic Factor by Gel Filtration on Agarose

1969 ◽  
Vol 22 (03) ◽  
pp. 577-583 ◽  
Author(s):  
M.M.P Paulssen ◽  
A.C.M.G.B Wouterlood ◽  
H.L.M.A Scheffers
Keyword(s):  
Factor Viii ◽  
Plasma Proteins ◽  
Large Scale ◽  
Gel Filtration ◽  
Large Scale Preparation ◽  
Scale Preparation ◽  
Antihemophilic Factor

SummaryFactor VIII can be isolated from plasma proteins, including fibrinogen by chromatography on agarose. The best results were obtained with Sepharose 6B. Large scale preparation is also possible when cryoprecipitate is separated by chromatography. In most fractions containing factor VIII a turbidity is observed which may be due to the presence of chylomicrons.The purified factor VIII was active in vivo as well as in vitro.

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