scholarly journals Sub-Diffusive Dynamics Lead to Depleted Particle Densities Near Cellular Borders

2018 ◽  
Author(s):  
William R. Holmes
Keyword(s):  
Particle Density ◽  
Specific Model ◽  
Transport Processes ◽  
Generalized Langevin Equation ◽  
Diffusive Motion ◽  
Protein Activation ◽  
Cellular Environment ◽  
Anomalous Particle ◽  
Canonical Type ◽  
Different Characteristics

AbstractIt has long been known that the complex cellular environment leads to anomalous motion of intracellular particles. At a gross level, this is characterized by mean squared displacements that deviate from the standard linear profile. Statistical analysis of particle trajectories has helped further elucidate how different characteristics of the cellular environment can introduce different types of anomalousness. A significant majority of this literature has however focused on characterizing the properties of trajectories that do not interact with cell borders (e.g. cell membrane or nucleus). Numerous biological processes ranging from protein activation to exocytosis however require particles to be near a membrane. This study investigates the consequences of a canonical type of sub-diffusive motion, Fractional Brownian Motion (FBM), and its physical analogue Generalized Langevin Equation (GLE) Dynamics, on the spatial localization of particles near reflecting boundaries. Results show that this type of sub-diffusive motion leads to the formation of significant zones of depleted particle density near boundaries, and that this effect is independent of the specific model details encoding those dynamics. Rather these depletion layers are a natural and robust consequence of the anti-correlated nature of motion increments that is at the core of FBM / GLE dynamics. If such depletion zones are present, it would be of profound importance given the wide array of signaling and transport processes that occur near membranes. If not, that would suggest our understanding of this type of anomalous motion may be flawed. Either way, this result points to the need to further investigate the consequences of anomalous particle motions near cell borders from both theoretical and experimental perspectives.

Role of G proteins in stimulation of Na-H exchange by cell shrinkage

1992 ◽  
Vol 262 (2) ◽  
pp. C533-C536 ◽  
Author(s):  
B. A. Davis ◽  
E. M. Hogan ◽  
W. F. Boron
Keyword(s):  
G Protein ◽  
G Proteins ◽  
Transport Processes ◽  
Cell Shrinkage ◽  
Protein Activation ◽  
Kinase C ◽  
G Protein Activation ◽  
Barnacle Muscle Fibers ◽  
Stimulation Of

Many cells respond to shrinkage by stimulating specific ion transport processes (e.g., Na-H exchange). However, it is not known how the cell senses this volume change, nor how this signal is transduced to an ion transporter. We have studied the activation of Na-H exchange in internally dialyzed barnacle muscle fibers, measuring intracellular pH (pHi) with glass microelectrodes. When cells are dialyzed to a pHi of approximately 7.2, Na-H exchange is active only in shrunken cells. We found that the shrinkage-induced stimulation of Na-H exchange, elicited by increasing medium osmolality from 975 to 1,600 mosmol/kgH2O, is inhibited approximately 72% by including in the dialysis fluid 1 mM guanosine 5'-O-(2-thiodiphosphate). The latter is an antagonist of G protein activation. Even in unshrunken cells, Na-H exchange is activated by dialyzing the cell with 1 mM guanosine 5'-O-(3-thiotriphosphate), which causes the prolonged activation of G proteins. Activation of Na-H exchange is also elicited in unshrunken cells by injecting cholera toxin, which activates certain G proteins. Neither exposing cells to 100 nM phorbol 12-myristate 13-acetate nor dialyzing them with a solution containing 20 microM adenosine 3',5'-cyclic monophosphate (cAMP) (or 50 microM dibutyryl cAMP) plus 0.5 mM 3-isobutyl-1-methylxanthine substantially stimulates the exchanger. Thus our data suggest that a G protein plays a key role in the transduction of the shrinkage signal to the Na-H exchanger via a pathway that involves neither protein kinase C nor cAMP.

Toward a more biologically accurate model of diffusion: adhesion and collisions

SIMULATION ◽  
2017 ◽  
Vol 93 (12) ◽  
pp. 1037-1044
Author(s):  
Ahmed M Fouad ◽  
John A Noel
Keyword(s):  
Large Scale ◽  
Particle Density ◽  
File Systems ◽  
Tracer Diffusion ◽  
Transport Processes ◽  
Average Particle ◽  
Diffusion Behavior ◽  
Single File ◽  
Tracer Particles ◽  
The One

In single-file dynamics, Brownian particles (referred to as tracer or tagged particles) diffuse and collide with each other in one-dimensional domains. If the average particle density is kept fixed during the diffusion, the collisions between the tracer particles result in their famous anomalous sub-diffusion behavior with time to the one half dependence. Many systems in nature are found to obey single-file dynamics, such as ion transport processes, and inter-particle adhesion plays a crucial role, either structurally or functionally, in the diffusion of such systems; however, the exact effect of adhesion on the diffusion has not been studied so far. We have examined the effect of adhesion on the collective diffusion of single-file systems. Here, we extend previous work where we perform large-scale numerical simulations that utilize Monte Carlo techniques and high-performance computing resources to examine the effect of adhesion on the diffusion of the tracer particles in systems that obey single-file dynamics. We show that if all the tracer particles experience the same adhesion coefficient, adhesion only slows down the diffusion by reducing the magnitude of the tracer diffusion coefficient; however, both the anomalous sub-diffusion behavior and time to the one half dependence of the tracer particles remain almost intact, independent of the adhesion.

scholarly journals Dynamics of Synthesis of Large Carbon Structures in the Interstellar Medium

2013 ◽  
Vol 9 (S297) ◽  
pp. 353-355
Author(s):  
N. Patra ◽  
H. R. Sadeghpour
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Gas Phase ◽  
Particle Density ◽  
Hydrogen Atoms ◽  
Reactive Molecular Dynamics ◽  
Carbon Chains ◽  
Carbon Structures ◽  
Dynamics Simulations ◽  
Different Characteristics

AbstractWe investigate the nucleation of carbon and hydrogen atoms in the gas phase to form large carbon chains, clusters and cages by reactive molecular dynamics simulations. We study how temperature, particle density, presence of hydrogen, and carbon inflow affect the nucleation of molecular moieties with different characteristics.

scholarly journals Animal evolution coincides with a novel degree of freedom in exocytic transport processes

2019 ◽  
Author(s):  
Martin Kollmar ◽  
Tobias Welz ◽  
Felix Straub ◽  
Noura Alzahofi ◽  
Klas Hatje ◽  
...  
Keyword(s):  
Protein Function ◽  
Tissue Expression ◽  
Transport Processes ◽  
Degree Of Freedom ◽  
Rab Gtpase ◽  
Animal Evolution ◽  
Protein Activation ◽  
Vesicle Membranes ◽  
Genome Duplications ◽  
Membrane Tethering

AbstractExocytic transport of transmembrane receptors and secreted ligands provides the basis for cellular communication in animals. The RAB8/RAB3/RAB27 trafficking regulators function in transport processes towards the cell membrane. The small G-proteins recruit a diversity of effectors that mediate transport along microtubule and actin tracks, as well as membrane tethering and fusion. SPIRE actin nucleators organise local actin networks at exocytic vesicle membranes. By complex formation with class-5 myosins, vesicle transport track generation and motor protein activation are coordinated. Our phylogenetic analysis traced the onset of SPIRE function back to the origin of the Holozoa. We have identified SPIRE in the closest unicellular relatives of animals, the choanoflagellates, and the more distantly related ichthyosporeans. The discovery of a SPIRE-like protein encoding a KIND and tandem-WH2 domains in the amoebozoanPhysarum polycephalumsuggests that the SPIRE-type actin nucleation mechanism originated even earlier. Choanoflagellate SPIRE interacts with RAB8, the sole choanoflagellate representative of the metazoan RAB8/RAB3/RAB27 family. Major interactions including MYO5, FMN-subgroup formins and vesicle membranes are conserved between the choanoflagellate and mammalian SPIRE proteins and the choanoflagellateMonosiga brevicollisSPIRE protein can rescue mouse SPIRE1/2 function in melanosome transport. Genome duplications generated two mammalianSPIREgenes (SPIRE1andSPIRE2) and allowed for the separation of SPIRE protein function in terms of tissue expression and RAB GTPase binding. SPIRE1 is highest expressed in the nervous system and interacts with RAB27 and RAB8. SPIRE2 shows high expression in the digestive tract and specifically interacts with RAB8. We propose that at the dawn of the animal kingdom a new transport mechanism came into existence, which bridges microtubule tracks, detached vesicles and the cellular actin cytoskeleton by organising actin/myosin forces directly at exocytic vesicle membranes. The new degree of freedom in transport may reflect the increased demands of the sophisticated cellular communications in animals.

scholarly journals Effect of Physical Characteristics and Hydrodynamic Conditions on Transport and Deposition of Microplastics in Riverine Ecosystem

Water ◽  
2021 ◽  
Vol 13 (19) ◽  
pp. 2710
Author(s):  
Rakesh Kumar ◽  
Prabhakar Sharma ◽  
Anurag Verma ◽  
Prakash Kumar Jha ◽  
Prabhakar Singh ◽  
...  
Keyword(s):  
Particle Density ◽  
Biodiversity Loss ◽  
Horizontal Distribution ◽  
Physical Characteristics ◽  
Transport Processes ◽  
Limited Information ◽  
Riverine Ecosystems ◽  
Laminar And Turbulent Flow ◽  
Vertical And Horizontal Distribution ◽  
Gravity Driven

Microplastic disposal into riverine ecosystems is an emergent ecological hazard that mainly originated from land-based sources. This paper presents a comprehensive review on physical processes involved in microplastics transport in riverine ecosystems. Microplastic transport is governed by physical characteristics (e.g., plastic particle density, shape, and size) and hydrodynamics (e.g., laminar and turbulent flow conditions). High-density microplastics are likely to prevail near riverbeds, whereas low-density particles float over river surfaces. Microplastic transport occurs either due to gravity-driven (vertical transport) or settling (horizontal transport) in river ecosystems. Microplastics are subjected to various natural phenomena such as suspension, deposition, detachment, resuspension, and translocation during transport processes. Limited information is available on settling and rising velocities for various polymeric plastic particles. Therefore, this paper highlights how appropriately empirical transport models explain vertical and horizontal distribution of microplastic in riverine ecosystems. Microplastics interact, and thus feedback loops within the environment govern their fate, particularly as these ecosystems are under increasing biodiversity loss and climate change threat. This review provides outlines for fate and transport of microplastics in riverine ecosystems, which will help scientists, policymakers, and stakeholders in better monitoring and mitigating microplastics pollution.

Computer Simulation of Kinetics Relationship between Gymnast and Mat

2014 ◽  
Vol 1044-1045 ◽  
pp. 1693-1696
Author(s):  
Xiao Fei Xiao ◽  
Wei Ya Hao
Keyword(s):  
Computer Simulation ◽  
Ground Reaction Force ◽  
Reaction Force ◽  
Specific Model ◽  
Vertical Ground Reaction Force ◽  
Time To Peak ◽  
Landing Impact ◽  
Reaction Forces ◽  
Different Characteristics ◽  
Landing Mat

Landing mats are essential for the safe completion of landing impact in gymnastics. Shock absorption and stability during landing impact is provided by both gymnasts’ ability and mat properties. The aim is to determine the influence of different characteristics of mat on mat-ground reaction forces. A subject-specific model with 12 segments rigid body and a model about landing mat in floor exercise were developed by computer simulation. The stiffness and dampness of landing mat influenced the peak of vertical ground reaction force and time to peak, but there were significant correlations between the friction of landing mat and the peak of horizontal ground reaction force and time to peak.

scholarly journals Re-evaluating how low intrinsic efficacy and apparent bias for G protein activation relates to the improved side effect profiles of new opioid agonists

2020 ◽  
Author(s):  
Edward L. Stahl ◽  
Laura M. Bohn
Keyword(s):  
G Protein ◽  
Therapeutic Window ◽  
G Protein Signaling ◽  
Protein Signaling ◽  
Protein Activation ◽  
Biased Agonism ◽  
Intrinsic Efficacy ◽  
Cellular Environment ◽  
G Protein Activation ◽  
G Protein Coupled

AbstractIn a recent report by Gillis et al., 2020 (1), it was suggested that low intrinsic agonism, and not biased agonism, leads to an improvement in the separation of potency in opioid-induced respiratory suppression versus antinociception. Although the compounds that were tested have been shown to display G protein signaling bias in prior publications, the authors conclude that since they cannot detect biased agonism in their cellular signaling studies the compounds are therefore not biased agonists. Rather, they conclude that it is low intrinsic efficacy that leads to the therapeutic window improvement. Intrinsic efficacy is the extent to which an agonist can stimulate a G protein-coupled receptor (GPCR) response in a system. The designation of full agonist is made to compounds that produce the highest observable activation in a system (maximum intrinsic efficacy); agonists producing some fraction of that response are considered partial agonists. The maximum response window is determined by the cellular environment, receptor and effector expression levels, and the amplification readout of the system. Biased agonism takes into consideration not only intrinsic efficacy, but also potency (concentration required to reach half maximal efficacy) of an agonist in an assay. Herein, the data published in the aforementioned manuscript was used to rederive the intrinsic efficacy and bias factors as ΔΔlog(τ/KA) and ΔΔlog(Emax/EC50). Based on this reanalysis, the data does not support the conclusion that biased agonism, favoring G protein signaling, was not present. Further, these observations agree with prior studies wherein oliceridine, PZM21 and SR-17018 were first described as biased agonists with improvement in antinociception over respiratory suppression in mice. Therefore, introducing G protein signaling bias may be a means to improve opioid analgesia while avoiding certain undesirable side effects.

Indirect Na+ dependency of urate and p-aminohippurate transport in pig basolateral membrane vesicles

1991 ◽  
Vol 261 (2) ◽  
pp. F265-F272 ◽  
Author(s):  
D. Werner ◽  
F. Roch-Ramel
Keyword(s):  
Proximal Tubule ◽  
Basolateral Membrane ◽  
Membrane Vesicles ◽  
Organic Anions ◽  
Transport Processes ◽  
Basolateral Membrane Vesicles ◽  
Pig Kidney ◽  
Different Characteristics ◽  
Stimulation Of

Membrane vesicles were used to study the basolateral transport of urate and p-aminohippurate (PAH) in the proximal tubule of the pig kidney. Consistent with a cooperation between a Na(+)-2-oxoglutarate cotransporter and a 2-oxoglutarate-urate or a 2-oxoglutarate-PAH exchanger, urate and PAH uptakes were stimulated in presence of extravesicular 2-oxoglutarate when an inwardly directed Na+ gradient was applied. Both transports exhibited, however, different characteristics. The optimal 2-oxoglutarate concentration for stimulating uptakes was 10 microM for PAH and 150 microM for urate. Extravesicular chloride was required to observe a stimulation of PAH uptake but not of urate uptake. Transports of both PAH and urate exhibited different affinity sequences for various organic anions. Stimulated PAH uptake was inhibited by probenecid greater than cold PAH greater than urate = pyrazinoate greater than lactate, whereas stimulated urate uptake was inhibited by probenecid greater than cold urate greater than PAH and not by pyrazinoate or lactate. These results are consistent with independent transport processes for urate and PAH in pig basolateral membrane vesicles, both being indirectly driven by an inwardly directed Na+ gradient.

scholarly journals NECESSARY CONDITIONS FOR THE ADEQUACY OF ECONOMIC AND MATHEMATICAL MODELS ON RIVER TRANSPORT

2020 ◽  
pp. 171-179
Author(s):  
Alexander Y. Platov ◽  
Yury I. Platov
Keyword(s):  
Mathematical Models ◽  
Transport Process ◽  
Necessary Conditions ◽  
Specific Model ◽  
Transport Processes ◽  
Fleet Planning ◽  
River Transport ◽  
Building Models ◽  
Traditional Approaches

One of the obvious conditions for the applicability of economic and mathematical models is their adequate reflection of transport processes. The issue of adequacy should be decided separately for each specific model. However, in the case of modeling for the river fleet, we can talk about the existence of traditional approaches to building models that are outdated and lead to inadequacy of all such models. It is shown that the proposed models do not fully reflect the properties of the transport process, and, therefore, their use in practice can lead to significant errors in the planning of the fleet. The analysis of typical errors in the models construction for the fleet planning is given.

scholarly journals Quantitative immunoferritin localization of [Na+,K+]ATPase on canine hepatocyte cell surface.

1984 ◽  
Vol 99 (4) ◽  
pp. 1502-1510 ◽  
Author(s):  
S Takemura ◽  
K Omori ◽  
K Tanaka ◽  
K Omori ◽  
S Matsuura ◽  
...  
Keyword(s):  
Cell Surface ◽  
Active Transport ◽  
Lateral Surface ◽  
Bile Flow ◽  
Particle Density ◽  
Transport Processes ◽  
Total Cell ◽  
Secondary Active Transport ◽  
Antibody Conjugates ◽  
Canine Kidney

Distribution of [Na+,K+]ATPase on the cell surface of canine hepatocytes was investigated quantitatively by incubating prefixed and dissociated liver cells with ferritin antibody conjugates against canine kidney holo[Na+,K+]ATPase. We found that [Na+,K+]-ATPase exists bilaterally both on the bile canalicular and sinusoid-lateral surfaces. The particle density on the bile canalicular surface was much higher (approximately 2.5 times) than that on the sinusoid-lateral surface. In the latter region, the enzyme was detected almost equally both on the sinusoidal and lateral surfaces. On all the surfaces, the distribution of the enzyme was homogeneous and no clustering of the enzyme was detected. Total number of the enzyme on the sinusoid-lateral surface was, however, approximately three times higher than that on the bile canalicular region, because the sinusoid-lateral surface represents approximately 87% of the total cell surface of a hepatocyte. We suggest that the [Na+, K+]ATPase on the bile canalicular surface is responsible for the bile acid-independent bile flow and the other transport processes on the bile canalicular cell surface, while that on the sinusoid-lateral surface is responsible not only for the active transport of Na+ but also for the secondary active transport of various substances in this region.

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