Formation Of Dynamic Structures Research Articles

Escape motility of multicellular magnetotactic prokaryotes.

Microorganisms often actively respond to multiple external stimuli to navigate toward their preferred niches. For example, unicellular magnetotactic bacteria integrate both oxygen sensory information and the Earth's geomagnetic field to help them locate anoxic conditions in a process known as magneto-aerotaxis. However, for multicellular magnetotactic prokaryotes (MMPs), the colonial structure of 4-16 cells places fundamental constraints on collective sensing, colony motility and directed swimming. To investigate how colonies navigate environments with multiple stimuli, we performed microfluidic experiments of MMPs with opposing magnetic fields and oxygen gradients. These experiments reveal unusual back-and-forth excursions called 'escape motility', in which colonies shuttle along magnetic field lines, punctuated by abrupt-yet highly coordinated-changes in collective ciliary beating. Through cell tracking and numerical simulations, we demonstrate that escape motility can arise through a simple magneto-aerotaxis mechanism, which includes the effect of magnetic torques and chemical sensing. At sufficiently high densities of MMPs, we observe the formation of dynamic crystal structures, whose stability is governed by the magnetic field strength and near-field hydrodynamic interactions. The results shed light on how some of the earliest multicellular organisms navigate complex physico-chemical landscapes.

Spatio-temporal organization of the E. coli chromosome from base to cellular length scales.

Escherichia coli has been a vital model organism for studying chromosomal structure, thanks, in part, to its small and circular genome (4.6 million base pairs) and well-characterized biochemical pathways. Over the last several decades, we have made considerable progress in understanding the intricacies of the structure and subsequent function of the E. coli nucleoid. At the smallest scale, DNA, with no physical constraints, takes on a shape reminiscent of a randomly twisted cable, forming mostly random coils but partly affected by its stiffness. This ball-of-spaghetti-like shape forms a structure several times too large to fit into the cell. Once the physiological constraints of the cell are added, the DNA takes on overtwisted (negatively supercoiled) structures, which are shaped by an intricate interplay of many proteins carrying out essential biological processes. At shorter length scales (up to about 1 kb), nucleoid-associated proteins organize and condense the chromosome by inducing loops, bends, and forming bridges. Zooming out further and including cellular processes, topological domains are formed, which are flanked by supercoiling barriers. At the megabase-scale both large, highly self-interacting regions (macrodomains) and strong contacts between distant but co-regulated genes have been observed. At the largest scale, the nucleoid forms a helical ellipsoid. In this review, we will explore the history and recent advances that pave the way for a better understanding of E. coli chromosome organization and structure, discussing the cellular processes that drive changes in DNA shape, and what contributes to compaction and formation of dynamic structures, and in turn how bacterial chromatin affects key processes such as transcription and replication.

MIP-4 is Induced by Bleomycin and Stimulates Cell Migration Partially via Nir-1 Receptor.

CC-chemokine ligand 18 also known as MIP-4 is a chemokine with roles in inflammation and immune responses. It has been shown that MIP-4 is involved in the development of several diseases including lung fibrosis and cancer. How exactly MIP-4 is regulated and exerts its role in lung fibrosis remains unclear. Therefore, in the present study, we examined how MIP-4 is regulated and whether it acts via its potential receptor Nir-1. A549 cells were grown and maintained in DMEM : F12 (1 : 1) and supplemented with 10% FBS and 1000 U of penicillin/streptomycin and maintained as recommended by the manufacturer (ATCC). Cell migration and invasion, immunohistochemistry (IHC), Western blot, qPCR, and siRNA Nir-1 were used to determine MIP-4 regulation and its role in cell migration. Cell migration was increased following stimulation of cells with recombinant (r) MIP-4 and bleomycin (BLM), whereas quenching rMIP-4 with its antibody (Ab) or addition of the Ab to BLM or H2O2 diminished rMIP-4-induced cell migration. Along with cell migration, rMIP-4, BLM, and H2O2 induced the formation of actin filaments dynamic structures whereas costimulation with MIP-4 Ab limited BLM- and H2O2-induced effects. MIP-4 mRNA and protein were increased by BLM and H2O2, and the addition of its Ab significantly reduced treatments effect. Experiments with siRNA investigating whether Nir-1 is a potential MIR-4 receptor indicated that the inhibition of Nir-1 decreased cell migration/invasion but did not totally inhibit rMIP-4-induced cell migration. Therefore, our data indicate that MIP-4 is regulated by BLM and H2O2 and costimulation with its Ab limits the effects on MIP-4 and that the Nir-1 receptor partially mediates MIP-4's effects on increased cell migration. These data also evidenced that MIP-4 is regulated by fibrotic and oxidative stimuli and that quenching MIP-4 with its Ab or therapeutically targeting the Nir-1 receptor may partially limit MIP-4 effects under fibrotic or oxidative stimulation.

Plasma membrane nanodeformations promote actin polymerization through CIP4/CDC42 recruitment and regulate type II IFN signaling

In their environment, cells must cope with mechanical stresses constantly. Among these, nanoscale deformations of plasma membrane induced by substrate nanotopography are now largely accepted as a biophysical stimulus influencing cell behavior and function. However, the mechanotransduction cascades involved and their precise molecular effects on cellular physiology are still poorly understood. Here, using homemade fluorescent nanostructured cell culture surfaces, we explored the role of Bin/Amphiphysin/Rvs (BAR) domain proteins as mechanosensors of plasma membrane geometry. Our data reveal that distinct subsets of BAR proteins bind to plasma membrane deformations in a membrane curvature radius–dependent manner. Furthermore, we show that membrane curvature promotes the formation of dynamic actin structures mediated by the Rho GTPase CDC42, the F-BAR protein CIP4, and the presence of PI(4,5)P 2 . In addition, these actin-enriched nanodomains can serve as platforms to regulate receptor signaling as they appear to contain interferon-γ receptor (IFNγ-R) and to lead to the partial inhibition of IFNγ-induced JAK/STAT signaling.

Dynamic evolution and morphological analysis of supersonic turbulence arising during the collision of prolate and spherical clouds

Our understanding of the formation and interaction processes of astronomical structures in the Universe and in galaxies has significantly expanded due to recent progress in improving the quality of observations, brought about by the emergence of new telescopes. Such processes are associated with the release of a significant amount of energy and may influence our vital activities. One example of energy flow release is magnetic storms, which are associated with processes occurring on the Sun. Such storms lead to disruptions of communication facilities, impact people, and can cause satellite and aircraft failures. There are objects in both near and deep space that are much more powerful than our star. In such objects, enormous energy flows are generated and released in the form of space jets. These energy flows occur in quasars, black holes, protostars, and during supernova explosions of types Ia, Ib, Ic, and II. During a supernova explosion, an immense amount of energy is released in the form of energy and high-energy particles. Such processes can have a significant impact on the safety of space flights. In this paper, the processes of formation of stellar systems within a turbulent interstellar medium are considered. This process is the result of complex processes that occur in the interstellar medium and denser gas formations – molecular clouds. At the same time, there are nonlinear interactions between turbulence and gravity, collisions between molecular clouds, interactions with shock waves, and so on. Supersonic turbulence is one of the main reasons for the formation of dynamic prestellar structures. The evolution of superdense substances formation begins when they gather in turbulent flows or are formed by supersonic collisions between molecular clouds. This process continues until these areas reach prestellar density. Depending on various factors, these superdense formations can either collapse and form new star systems or disintegrate, returning the substance to the interstellar medium. Until recently, the prevailing opinion was that a significant portions of molecular clouds were not gravitationally bound. Conclusions about this were made based on the virial theorem, which expresses the relationship between gravitational and kinetic energy. However, recent studies have refuted this. In this paper, the results of a simulation carried out to study the collision of large ellipsoidal and spherical molecular clouds in a three-dimensional setting. The simulation was conducted on high-resolution grids and utilized the adaptive mesh refinement (AMR) method.

Thermal optimisation through the stratified bioconvective jetflow of nanofluid

Bioconvection is a fascinating phenomenon observed in various biological systems, where the motion of motile microorganisms generates fluid flow patterns. This article explores the occurrence and characteristics of bioconvection within the context of a jet flow. The study of bioconvection in jet flow involves the interaction between motile microorganisms and the fluid dynamics of the surrounding medium. Microorganisms such as bacteria and algae are known to exhibit directed swimming behavior, which can lead to the formation of dynamic flow structures. Investigating the mechanisms underlying bioconvection in jet flow requires a multidisciplinary approach encompassing fluid dynamics, microbial ecology, and mathematical modeling. Experimental techniques, such as microscopy and particle image velocimetry, along with computational simulations, are employed to analyze the complex interactions between microorganisms and the fluid flow. In this regard, a supportive mathematical model is designed using partial differential equations (PDEs) which are later transformed into ordinary differential equations using similarity transformations. The resulting system of equations is solved using the RKF-45 method and the outcomes are recorded in tables and graphs. The consideration of thermophoresis has shown a significant impact on the heat and mass transfer of the jet flow and both these profiles are observed to increase with thermophoresis. Meanwhile, the Schmidt number decrease their respective mass profiles. Furthermore, the porosity is found to create a drag force which tends to oppose the fluid flow.

Numerical Modelling of Myocardial Infarction. I. Analysis of Spatiotemporal Aspects of the Local Inflammatory Response

The results of numerical modelling of the necrotic death of myocardial cells and immune response dynamics in type II ischemic infarction are presented. The initial conditions were consistent with the experimental data. The adopted minimal mathematical model focused on the balance of pro- and anti-inflammatory factors of aseptic inflammation and their influence on the process of cardiomyocyte death. The issue of the formation of nonlinear dynamic structures in the adopted reaction-diffusion system of equations in the absence of convective terms has been examined. It is shown that a stable localization of the solution of the initial-boundary value problem within the spatial region of practically unchanged size is observed in a fairly wide range of parameters of the initial conditions set in the form of bell-shaped finite functions. Qualitative properties of solutions allow biological interpretation. Within the framework of the adopted model, we considered several important examples and, on this basis, described a typical scenario of a heart attack with a favorable outcome. We have studied the most general patterns of the formation of demarcation inflammation near a large necrosis focus in a typical acute infarction scenario, taking into account individual differences in the topology of the coronary vascular network and the topography of the infarction. The adequacy of the results is confirmed by quantitative and qualitative agreement with a fairly wide range of experimental data on the dynamics of infarction in the left ventricle of the mouse heart.

COMPARATIVE ANALYSIS 2: MULTISCALE MECHANISMS OF DEFORMATION AND FRACTURE UNDER HIGH-VELOCITY PENETRATION

Two kinds of aluminum alloy, 1561 and 1565 alloys, were tested in parallel within impact velocity range of 250–750 m/s in two schemes of shock loading: (i) under uniaxial strain conditions and (ii) in high velocity penetration. Combination of load regimes allows a formation of multiscale structure to be retraced. In both schemes of dynamic loading, the transition into structure-unstable state and change of scale level of dynamic deformation was found to occur under identical impact velocities. Formation of mesoscale-1 (1–10 µm) for both alloys is found to be identical – the mesoscale-1 structures are nucleated due to particle velocity fluctuations resulting from interaction of shock front with the structural hetero-geneities. The intensity of the velocity fluctuations is registered in real time in tests under uniaxial strain condition by using the interferometric technique. For the mesoscale-2 (50–150 µm), the formation of dynamic structures is studied by using microstructural data of post-shocked specimens. In 1561 alloy, the structural elements in the form of cell-structures of 50–150 µm are the result of collectivization of mesoscale-1 structures whereas in 1565 alloy the mesoscale-2 structures are the periodical fault-cellson the boundary of penetration cavern. The strength behavior of both kinds of aluminum alloys in different schemes of loading turns out to be opposite – where the resistance to penetration increases, the spall strength decreases.

PML-Bodies as Open Dynamic System

According to modern concepts, the formation of functional dynamic structures in a cell that do not have a membrane (membrane-less organelles) is based on reversible phase transitions of the “liquid - liquid” type of biopolymers. The properties of such systems significantly depend on the changes in external conditions and the action of various stimuli. One of the best studied membrane-less organelles are PML bodies. These polyfunctional protein organelles are present in most cell types and are involved in the regulation of transcription, cell differentiation, stress response, etc. It is known that all PML are involved in the formation of PML bodies. PML bodies are sensors of the cell stress response to an increase in reactive oxygen species. Therefore, it can be assumed that such stressful conditions will cause significant changes in the structure and properties of PML bodies. We examined the effect of acute oxidative stress caused by cells treatment with hydrogen peroxide (H2O2) on the localization, morphology, and dynamics of the exchange of isoforms of the scaffold PML protein of these structures with nucleoplasm. Stressful conditions led to a significant decrease in the proportion of the mobile fraction during the restoration of fluorescence after photobleaching of the fusion proteins EGFP-PML-I, EGFP-PML-II, and EGFP-PML-V involved in PML bodies. At the same time cells treatmened with H2O2 does not change the dynamics of the exchange of isoforms EGFP-PML-III, EGFP-PML-IV, EGFP-PML-VI with nucleoplasm. Thus, oxidative stress causes a redistribution of scaffold proteins within PML bodies. The obtained data proved the dynamic nature of membrane-less organelles as an open dynamic systems existing at the edge of chaos, whose evolution essentially depends on the changes in external conditions. This work was supported by the Russian Science Foundation (RSF No 19-15-00107) and the RF President Fellowship SP-259.2019.4.

In cultured cells the baculovirus P10 protein forms two independent intracellular structures that play separate roles in occlusion body maturation and their release by nuclear disintegration.

P10 is a small, abundant baculovirus protein that accumulates to high levels in the very late stages of the infection cycle. It is associated with a number of intracellular structures and implicated in diverse processes from occlusion body maturation to nuclear stability and lysis. However, studies have also shown that it is non-essential for virus replication, at least in cell culture. Here, we describe the use of serial block-face scanning electron microscopy to achieve high-resolution 3D characterisation of P10 structures within Trichoplusia ni TN-368 cells infected with Autographa californica multiple nucleopolyhedrovirus. This has enabled unparalleled visualisation of P10 and determined the independent formation of dynamic perinuclear and nuclear vermiform fibrous structures. Our 3D data confirm the sequence of ultrastructural changes that create a perinuclear cage from thin angular fibrils within the cytoplasm. Over the course of infection in cultured cells, the cage remodels to form a large polarised P10 mass and we suggest that these changes are critical for nuclear lysis to release occlusion bodies. In contrast, nuclear P10 forms a discrete vermiform structure that was observed in close spatial association with both electron dense spacers and occlusion bodies; supporting a previously suggested role for P10 and electron dense spacers in the maturation of occlusion bodies. We also demonstrate that P10 hyper-expression is critical for function. Decreasing levels of p10 expression, achieved by manipulation of promoter length, correlated with reduced P10 production, a lack of formation of P10 structures and a concomitant decrease in nuclear lysis.

Identification and Space-Time Evolution of Vortex-Like Motion of Atoms in a Loaded Solid

The paper studies the redistribution of internal stresses and atomic displacements in a preloaded copper crystallite using the molecular dynamics method. It is shown that relaxation within the crystallite volume is accompanied by the formation of dynamic structures in which atomic displacements produce a coherent system of vortex lines. In so doing, the displacement of atoms in neighboring vortex structures has the opposite sign of the angular velocities. The evolution of the dynamic vortex structures is analyzed using an original technique for identifying the vortex motion in the space of a vector variable with a discrete step. It is shown that a system of dynamic vortices and antivortices can propagate inside the crystallite, ensuring the transfer of stresses from the bulk of the loaded material to its unloaded periphery in order to preserve continuity. The developed technique has revealed that the lifetime of such defects depends on their size and ranges from fractions to tens of picoseconds. The simulation results correlate well with the experimental electron microscopy data on the estimation of spatial parameters and lattice curvature during strain localization in the region of elastic distortions.

Dynamic Macromolecular Material Design-The Versatility of Cyclodextrin-Based Host-Guest Chemistry.

Dynamic and adaptive materials are powerful constructs in macromolecular and polymer chemistry with a wide array of applications in drug delivery, bioactive systems, and self-healing materials. Very often, dynamic materials are based on carefully tailored cyclodextrin host-guest interactions. The precise incorporation of these host and guest moieties into macromolecular building blocks allows the formation of complex macromolecular structures with predefined functions. Thus, dynamic materials with extraordinary adaptive property profiles-responsive to thermal, chemical, and photonic fields-become accessible. This Review explores the hierarchical formation of dynamic materials and complex macromolecular structures from the molecular via the macromolecular to the colloidal and macroscopic level, with a specific emphasis on the functionality and responsiveness of the assemblies, specifically in biological contexts.

Impact of cordon‐bleu expression on actin cytoskeleton architecture and dynamics

Cordon‐bleu (COBL) is a multifunctional WASP‐Homology 2 (WH2) domain‐containing protein implicated in a wide variety of cellular functions ranging from dendritic arborization in neurons to the assembly of microvilli on the surface of transporting epithelial cells. In vitro biochemical studies suggest that COBL is capable of nucleating and severing actin filaments, among other activities. How the multiple activities of COBL observed in vitro contribute to its function in cells remains unclear. Here, we used live imaging to evaluate the impact of COBL expression on the actin cytoskeleton in cultured cells. We found that COBL induces the formation of dynamic linear actin structures throughout the cytosol. We also found that stabilizing these dynamic structures with the parallel actin‐bundling protein espin slows down their turnover and enables the robust formation of self‐supported protrusions on the dorsal cell surface. Super‐resolution imaging revealed a global remodeling of the actin cytoskeleton in cells expressing these two factors. Taken together, these results provide insight as to how COBL contributes to the assembly of actin‐based structures such as epithelial microvilli. © 2016 Wiley Periodicals, Inc.

Dynamics of light structures during filamentation of femtosecond laser pulses in air

A model of single filamentation of a high-power ultrashort light pulse has been developed on the basis of evolutionary dependencies of phase and amplitude parameters of the light field found from the numerical solution of a nonlinear Schrodinger equation for air. A key role of aberration and diffraction effects during the formation of localized stable dynamic light structures near the propagation axis is shown. It is found that the angular divergence of the postfilamentation light channel decreases with an increase in the laser beam radius at a fixed peak pulse power and is saturated when the radius is greater than 1 mm.

Impact of cordon-bleu expression on actin cytoskeleton architecture and dynamics.

Cordon-bleu (COBL) is a multifunctional WASP-Homology 2 (WH2) domain-containing protein implicated in a wide variety of cellular functions ranging from dendritic arborization in neurons to the assembly of microvilli on the surface of transporting epithelial cells. In vitro biochemical studies suggest that COBL is capable of nucleating and severing actin filaments, among other activities. How the multiple activities of COBL observed in vitro contribute to its function in cells remains unclear. Here, we used live imaging to evaluate the impact of COBL expression on the actin cytoskeleton in cultured cells. We found that COBL induces the formation of dynamic linear actin structures throughout the cytosol. We also found that stabilizing these dynamic structures with the parallel actin-bundling protein espin slows down their turnover and enables the robust formation of self-supported protrusions on the dorsal cell surface. Super-resolution imaging revealed a global remodeling of the actin cytoskeleton in cells expressing these two factors. Taken together, these results provide insight as to how COBL contributes to the assembly of actin-based structures such as epithelial microvilli. © 2016 Wiley Periodicals, Inc.

A model of a human-dominated urban ecosystem as an active medium

The concept of active medium is used as a biophysical basis for modeling spatial and temporal self-organization in anthropogenic ecosystems that results in formation of regular dynamic structures with stable or unstable modes of development. Urban ecosystem is represented as a hierarchy of interacting active media, and their non-linearity is the result of extreme anthropogenic load and mismatch between characteristic times and scales in evolution of the natural and anthropogenic components together with the complex set of positive and negative feedbacks between the subsystems. Description of the presented model is deliberately simplified so as to use a modified Fitz-Hugh-Nagumo equation. The approach developed here is quite general and allows for systematic description of urban ecosystems as distributed dissipative systems.

ARF6 promotes the formation of Rac1 and WAVE-dependent ventral F-actin rosettes in breast cancer cells in response to epidermal growth factor.

Coordination between actin cytoskeleton assembly and localized polarization of intracellular trafficking routes is crucial for cancer cell migration. ARF6 has been implicated in the endocytic recycling of surface receptors and membrane components and in actin cytoskeleton remodeling. Here we show that overexpression of an ARF6 fast-cycling mutant in MDA-MB-231 breast cancer-derived cells to mimick ARF6 hyperactivation observed in invasive breast tumors induced a striking rearrangement of the actin cytoskeleton at the ventral cell surface. This phenotype consisted in the formation of dynamic actin-based podosome rosette-like structures expanding outward as wave positive for F-actin and actin cytoskeleton regulatory components including cortactin, Arp2/3 and SCAR/WAVE complexes and upstream Rac1 regulator. Ventral rosette-like structures were similarly induced in MDA-MB-231 cells in response to epidermal growth factor (EGF) stimulation and to Rac1 hyperactivation. In addition, interference with ARF6 expression attenuated activation and plasma membrane targeting of Rac1 in response to EGF treatment. Our data suggest a role for ARF6 in linking EGF-receptor signaling to Rac1 recruitment and activation at the plasma membrane to promote breast cancer cell directed migration.

Deep Holes in Free-Standing Smectic C Films

Free-standing smectic films consist of smectic layers stacked in the film plane. In equilibrium, the discrete number of layers usually guarantees a uniform film thickness over large areas. Regions with differing numbers of layers are separated by dislocation lines. Their dynamics can be studied when the surface area is rapidly reduced, whereby excess material accumulates in islands (regions with increased thickness). Alternatively, holes (regions with reduced thickness) can be created by expanding the film surface, e. g. by means of a moveable film holder barrier. We study the growth of deep holes, i. e. regions which are up to several micrometers thinner than the surrounding film, using polarizing microscopy. The formation of regular dynamic stripe structures is observed.

Hydrophobicity of counterions as a driving force in the self-assembly process: Dodecyltrimethylammonium chloride and parabens

The micelle formation of dodecyltrimethylammonium chloride (DTAC) in 0.01M methyl- and ethyl-4-hydroxybenzoate (MeP and EtP, respectively) sodium salt aqueous solutions has been investigated at several temperatures in the range from 278.15 to 328.15K by isothermal titration calorimetry, viscosity, electrical conductivity measurements, and NMR spectroscopy. It was found out, that hydrophobic counterion not only lowers the solubility of ionic amphiphile and thus its critical micelle concentration in aqueous solution, but interacts favorably with the surfactant molecules and enables the formation of higher organized structures also. Densely packed elongated micelles of higher aggregation number were found in the EtP sodium salt solution at low temperature, with their highest fraction in the solution at DTAC to EtP concentration ratio of approximately 1:1. The most negative heat capacity change determined for DTAC in presence of EtP can be related to the most pronounced hydrophobic effect due to the additional hydrophobic surface included into the dehydration process upon micellization and closed micelle formation with water molecules mostly excluded from their hydrophobic core. The slightly less hydrophobic MeP did not show such a behavior, although the formation of dynamic mixed micelle structures cannot be excluded for this system also. The role of counterion hydrophobicity as the main driving force for diverse rearrangements in the ionic amphiphile aqueous solutions is discussed.

Promiscuity as a functional trait: intrinsically disordered regions as central players of interactomes

Because of their pervasiveness in eukaryotic genomes and their unique properties, understanding the role that ID (intrinsically disordered) regions in proteins play in the interactome is essential for gaining a better understanding of the network. Especially critical in determining this role is their ability to bind more than one partner using the same region. Studies have revealed that proteins containing ID regions tend to take a central role in protein interaction networks; specifically, they act as hubs, interacting with multiple different partners across time and space, allowing for the co-ordination of many cellular activities. There appear to be three different modules within ID regions responsible for their functionally promiscuous behaviour: MoRFs (molecular recognition features), SLiMs (small linear motifs) and LCRs (low complexity regions). These regions allow for functionality such as engaging in the formation of dynamic heteromeric structures which can serve to increase local activity of an enzyme or store a collection of functionally related molecules for later use. However, the use of promiscuity does not come without a cost: a number of diseases that have been associated with ID-containing proteins seem to be caused by undesirable interactions occurring upon altered expression of the ID-containing protein.