Filamentation Instability Research Articles

ROCK inhibition with Fasudil induces beta-catenin nuclear translocation and inhibits cell migration of MDA-MB 231 human breast cancer cells

Tumor aggressiveness is usually associated with metastasis. MDA-MB 231, a triple-negative breast cancer (TNBC), is an aggressive type of breast cancer and associated with early metastasis. The Rho/ROCK pathway is a key regulator of cell motility involving cytoskeleton regulation through stabilization of actin filaments and stress fiber formation. In this study we show that Fasudil, a ROCK inhibitor, inhibited the migration of MDA-MB 231 and A549 cells, without altering the viability of these cells at the concentration of 10 μM, modified tumor cell morphology, with disorganization of stress fibers and promotes activation of the canonical-Wnt/beta-catenin pathway. Therefore, Fasudil present a promising approach to the prevention of breast cancer metastasis through a different mechanism of action from the well-known one.

Wavelet Imaging on Multiple Scales (WIMS) reveals focal adhesion distributions, dynamics and coupling between actomyosin bundle stability.

We introduce and use Wavelet Imaging on Multiple Scales (WIMS) as an improvement to fluorescence correlation spectroscopy to measure physical processes and features that occur across multiple length scales. In this study, wavelet transforms of cell images are used to characterize molecular dynamics at the cellular and subcellular levels (i.e. focal adhesions). We show the usefulness of the technique by applying WIMS to an image time series of a migrating osteosarcoma cell expressing fluorescently labelled adhesion proteins, which allows us to characterize different components of the cell ranging from optical resolution scale through to focal adhesion and whole cell size scales. Using WIMS we measured focal adhesion numbers, orientation and cell boundary velocities for retraction and protrusion. We also determine the internal dynamics of individual focal adhesions undergoing assembly, disassembly or elongation. Thus confirming as previously shown, WIMS reveals that the number of adhesions and the area of the protruding region of the cell are strongly correlated, establishing a correlation between protrusion size and adhesion dynamics. We also apply this technique to characterize the behavior of adhesions, actin and myosin in Chinese hamster ovary cells expressing a mutant form of myosin IIB (1935D) that displays decreased filament stability and impairs front-back cell polarity. We find separate populations of actin and myosin at each adhesion pole for both the mutant and wild type form. However, we find these populations move rapidly inwards toward one another in the mutant case in contrast to the cells that express wild type myosin IIB where those populations remain stationary. Results obtained with these two systems demonstrate how WIMS has the potential to reveal novel correlations between chosen parameters that belong to different scales.

Theoretical insights and experimental characterization of $$\hbox {HfO}_2$$ HfO 2 -based OxRRAMs operation

The intensive research in resistive random access memories (RRAM) field has brought in significant improvements in the performance, optimization and reliability of the devices as well as more understanding on their operation. This was made possible through the combination of different tools starting from material engineering to device characterization, modeling and simulations. In this review, we bring an overview of our recent work on RRAM through experimental characterization and first-principles calculations. We explore the effects of metal electrodes on the switching performance and conductive filament (CF) stability of $$\hbox {HfO}_2$$ oxide-based RRAM (OxRRAM). With the insight gained from the experimental data, we employ first-principles calculations to have a better microscopic understanding on OxRRAM operation. We show that CF stability and device operating voltages strongly depend on the electrode material. Ti being an electrode material of high interest, we investigate the type of $$\hbox {Ti/HfO}_2$$ interface that may be formed and propose a probable composition. We also study the formation and migration of extended Frenkel-pair (EFP) defect in $$\hbox {HfO}_2$$ which we consider to be the prototype defect responsible for OxRRAM degradation leading to CF formation. This EFP emission occurs through a cascading migration of O atoms inside $$\hbox {HfO}_2$$ lattice. Based on EFP formation and diffusion, we present a simplified CF formation model. Finally, we study low resistance data retention failure in OxRRAM through $$\hbox {HfO}_2$$ , $$\hbox {Hf}_{1x}\hbox {Al}_{2x}\hbox {O}_{2+x}$$ (HfAlO) and $$\hbox {Hf}_{1-x}\hbox {Ti}_{x}\hbox {O}_{2}$$ (HfTiO) type of cells. We link its origin to the lateral diffusion of oxygen vacancies at the constriction/tip of the conductive filament in $$\hbox {HfO}_2$$ -based RRAM.

Left ventricular non-compaction with Ebstein anomaly attributed to a TPM1 mutation

Left ventricular non-compaction (cardiomyopathy) (LVN(C)) is a rare hereditary cardiac condition, resulting from abnormal embryonic myocardial development. While it mostly occurs as an isolated condition, association with other cardiovascular manifestations such as Ebstein anomaly (EA) has been reported. This congenital heart defect is characterized by downward displacement of the tricuspid valve and leads to diminished ventricular size and function. In an autosomal dominant LVN(C) family consisting of five affected individuals, of which two also presented with EA and three with mitral valve insufficiency, we pursued the genetic disease cause using whole exome sequencing (WES). WES revealed a missense variant (p.Leu113Val) in TPM1 segregating with the LVN(C) phenotype. TPM1 encodes α-tropomyosin, which is involved in myocardial contraction, as well as in stabilization of non-muscle cytoskeletal actin filaments. So far, LVN(C)-EA has predominantly been linked to pathogenic variants in MYH7. However, one sporadic LVN(C)-EA case with a de novo TPM1 variant has recently been described. We here report the first LVN(C)-EA family segregating a pathogenic TPM1 variant, further establishing the association between EA predisposition and TPM1-related LVN(C). Consequently, we recommend genetic testing for both MYH7 and TPM1 in patients or families in which LVN(C)/non-compaction and EA coincide.

Near-atomic structure of jasplakinolide-stabilized malaria parasite F-actin reveals the structural basis of filament instability

During their life cycle, apicomplexan parasites, such as the malaria parasite Plasmodium falciparum, use actomyosin-driven gliding motility to move and invade host cells. For this process, actin filament length and stability are temporally and spatially controlled. In contrast to canonical actin, P. falciparum actin 1 (PfAct1) does not readily polymerize into long, stable filaments. The structural basis of filament instability, which plays a pivotal role in host cell invasion, and thus infectivity, is poorly understood, largely because high-resolution structures of PfAct1 filaments were missing. Here, we report the near-atomic structure of jasplakinolide (JAS)-stabilized PfAct1 filaments determined by electron cryomicroscopy. The general filament architecture is similar to that of mammalian F-actin. The high resolution of the structure allowed us to identify small but important differences at inter- and intrastrand contact sites, explaining the inherent instability of apicomplexan actin filaments. JAS binds at regular intervals inside the filament to three adjacent actin subunits, reinforcing filament stability by hydrophobic interactions. Our study reveals the high-resolution structure of a small molecule bound to F-actin, highlighting the potential of electron cryomicroscopy for structure-based drug design. Furthermore, our work serves as a strong foundation for understanding the structural design and evolution of actin filaments and their function in motility and host cell invasion of apicomplexan parasites.

Electrostatic and magnetic instabilities in the transition layer of a collisionless weakly relativistic pair shock

Energetic electromagnetic emissions by astrophysical jets like those that are launched during the collapse of a massive star and trigger gamma-ray bursts (GRBs) are partially attributed to relativistic internal shocks. The shocks are mediated in the collisionless plasma of such jets by the filamentation instability of counterstreaming particle beams. The filamentation instability grows fastest only if the beams move at a relativistic relative speed. We model here with a particle-in-cell (PIC) simulation the collision of two cold pair clouds at the speed c/2 (c: speed of light). We demonstrate that the two-stream instability outgrows the filamentation instability for this speed and is thus responsible for the shock formation. The incomplete thermalization of the upstream plasma by its quasi-electrostatic waves allows other instabilities to grow. A shock transition layer forms, in which a filamentation instability modulates the plasma far upstream of the shock. The inflowing upstream plasma is progressively heated by a two-stream instability closer to the shock and compressed to the expected downstream density by the Weibel instability. The strong magnetic field due to the latter is confined to a layer 10 electron skin depths wide.

Myosin storage myopathy mutations yield defective myosin filament assembly in vitro and disrupted myofibrillar structure and function in vivo.

Myosin storage myopathy (MSM) is a congenital skeletal muscle disorder caused by missense mutations in the β-cardiac/slow skeletal muscle myosin heavy chain rod. It is characterized by subsarcolemmal accumulations of myosin that have a hyaline appearance. MSM mutations map near or within the assembly competence domain known to be crucial for thick filament formation. Drosophila MSM models were generated for comprehensive physiological, structural, and biochemical assessment of the mutations' consequences on muscle and myosin structure and function. L1793P, R1845W, and E1883K MSM mutant myosins were expressed in an indirect flight (IFM) and jump muscle myosin null background to study the effects of these variants without confounding influences from wild-type myosin. Mutant animals displayed highly compromised jump and flight ability, disrupted muscle proteostasis, and severely perturbed IFM structure. Electron microscopy revealed myofibrillar disarray and degeneration with hyaline-like inclusions. In vitro assembly assays demonstrated a decreased ability of mutant myosin to polymerize, with L1793P filaments exhibiting shorter lengths. In addition, limited proteolysis experiments showed a reduced stability of L1793P and E1883K filaments. We conclude that the disrupted hydropathy or charge of residues in the heptad repeat of the mutant myosin rods likely alters interactions that stabilize coiled-coil dimers and thick filaments, causing disruption in ordered myofibrillogenesis and/or myofibrillar integrity, and the consequent myosin aggregation. Our Drosophila models are the first to recapitulate the human MSM phenotype with ultrastructural inclusions, suggesting that the diminished ability of the mutant myosin to form stable thick filaments contributes to the dystrophic phenotype observed in afflicted subjects.

Filamentation Instability of Electromagnetic Beams in Nonlinear Media: A Tutorial Review

Filamentation Instability of Electromagnetic Beams in Nonlinear Media: A Tutorial Review

Exploiting the Marangoni Effect To Initiate Instabilities and Direct the Assembly of Liquid Metal Filaments.

Utilization of the Marangoni effect in a liquid metal is investigated, focusing on initiating instabilities to direct material assembly via the Rayleigh-Plateau instability. Thin (2 nm) copper (Cu) films are lithographically patterned onto thick (12 nm) nickel (Ni) strips to induce a surface energy gradient at the maximum wavelength of the filament instability predicted by Rayleigh-Plateau instability analysis. The pattern is irradiated with an 18 ns pulsed laser such that the pattern melts and the resultant Ni-Cu surface tension gradient induces Marangoni flows due to the difference in surface energies. The experimental results, supported by extensive direct numerical simulations, demonstrate that the Marangoni flow exceeds the capillary flow induced by the initial geometry, guiding instabilities such that final nanoparticle location is directed toward the regions of higher surface energy (Ni regions). Our work shows a route for manipulation, by means of the Marangoni effect, to direct the evolution of the surface instabilities and the resulting pattern formation.

Self-compression of soliton-like laser pulses in the process of self-focusing

We study the possibility of efficient self-compression of femtosecond laser pulses in nonlinear media with anomalous dispersion of group velocity during the self-focusing of wave packets with a power several times greater than the critical self-focusing power. The results of qualitative analysis of the evolution of three-dimensional wave packets with the quasi-soliton field distribution are confirmed by the computer simulation. The simulation proves that the considered regime of compression of high-power laser pulses with initial durations of about ten optical cycles is stable relative to filamentation instability, due to the influence of the nonlinear dispersion. We demonstrate the possibility of self-compression of laser pulses at a multi-millijoule energy level and up to one optical cycle with an energy efficiency of more than 50%.

Testing Munk's hypothesis for submesoscale eddy generation using observations in the North Atlantic

AbstractA high‐resolution satellite image that reveals a train of coherent, submesoscale (6 km) vortices along the edge of an ocean front is examined in concert with hydrographic measurements in an effort to understand formation mechanisms of the submesoscale eddies. The infrared satellite image consists of ocean surface temperatures at m resolution over the midlatitude North Atlantic (48.69°N, 16.19°W). Concomitant altimetric observations coupled with regular spacing of the eddies suggest the eddies result from mesoscale stirring, filamentation, and subsequent frontal instability. While horizontal shear or barotropic instability (BTI) is one mechanism for generating such eddies (Munk's hypothesis), we conclude from linear theory coupled with the in situ data that mixed layer or submesoscale baroclinic instability (BCI) is a more plausible explanation for the observed submesoscale vortices. Here we assume that the frontal disturbance remains in its linear growth stage and is accurately described by linear dynamics. This result likely has greater applicability to the open ocean, i.e., regions where the gradient Rossby number is reduced relative to its value along coasts and within strong current systems. Given that such waters comprise an appreciable percentage of the ocean surface and that energy and buoyancy fluxes differ under BTI and BCI, this result has wider implications for open‐ocean energy/buoyancy budgets and parameterizations within ocean general circulation models. In summary, this work provides rare observational evidence of submesoscale eddy generation by BCI in the open ocean.

Mesh-free Hamiltonian implementation of two dimensional Darwin model

A new approach to Darwin or magnetoinductive plasma simulation is presented, which combines a mesh-free field solver with a robust time-integration scheme avoiding numerical divergence errors in the solenoidal field components. The mesh-free formulation employs an efficient parallel Barnes-Hut tree algorithm to speed up the computation of fields summed directly from the particles, avoiding the necessity of divergence cleaning procedures typically required by particle-in-cell methods. The time-integration scheme employs a Hamiltonian formulation of the Lorentz force, circumventing the development of violent numerical instabilities associated with time differentiation of the vector potential. It is shown that a semi-implicit scheme converges rapidly and is robust to further numerical instabilities which can develop from a dominant contribution of the vector potential to the canonical momenta. The model is validated by various static and dynamic benchmark tests, including a simulation of the Weibel-like filamentation instability in beam-plasma interactions.

Role of cytoskeletal mechanics and cell membrane fluidity in the intracellular delivery of molecules mediated by laser-activated carbon nanoparticles.

Exposure of cells and nanoparticles to near-infrared nanosecond pulsed laser light can lead to efficient intracellular delivery of molecules while maintaining high cell viability by a photoacoustic phenomenon known as transient nanoparticle energy transduction (TNET). Here, we examined the influence of cytoskeletal mechanics and plasma membrane fluidity on intracellular uptake of molecules and loss of cell viability due to TNET. We found that destabilization of actin filaments using latrunculin A led to greater uptake of molecules and less viability loss caused by TNET. Stabilization of actin filaments using jasplakinolide had no significant effect on uptake or viability loss caused by TNET. To study the role of plasma membrane fluidity, we increased fluidity by depletion of membrane cholesterol using methyl-β-cyclodextrin and decreased fluidity by enrichment of the membrane with cholesterol using water-soluble cholesterol. Neither of these membrane fluidity changes significantly altered cellular uptake or viability loss caused by TNET. We conclude that weakening mechanical integrity of the cytoskeleton can increase intracellular uptake and decrease loss of cell viability, while plasma membrane fluidity does not appear to play a significant role in uptake or viability loss caused by TNET. The positive effects of cytoskeletal weakening may be due to an enhanced ability of the cell to recover from the effects of TNET and maintain viability. Biotechnol. Bioeng. 2017;114: 2390-2399. © 2017 Wiley Periodicals, Inc.

Modeling resistive switching materials and devices across scales

Resistance switching devices based on electrochemical processes have attractive significant attention in the field of nanoelectronics due to the possibility of switching in nanosecond timescales, miniaturization to tens of nanometer and multi-bit storage. Their deceptively simple structures (metal-insulator-metal stack) hide a set of complex, coupled, processes that govern their operation, from electrochemical reactions at interfaces, diffusion and aggregation of ionic species, to electron and hole trapping and Joule heating. A combination of experiments and modeling efforts are contributing to a fundamental understanding of these devices, and progress towards a predictive understanding of their operation is opening the possibility for the rational optimization. In this paper we review recent progress in modeling resistive switching devices at multiple scales; we briefly describe simulation tools appropriate at each scale and the key insight that has been derived from them. Starting with ab initio electronic structure simulations that provide an understanding of the mechanisms of operation of valence change devices pointing to the importance of the aggregation of oxygen vacancies in resistance switching and how dopants affect performance. At slightly larger scales we describe reactive molecular dynamics simulations of the operation of electrochemical metallization cells. Here the dynamical simulations provide an atomic picture of the mechanisms behind the electrochemical formation and stabilization of conductive metallic filaments that provide a low-resistance path for electronic conduction. Kinetic Monte Carlo simulations are one step higher in the multiscale ladder and enable larger scale simulations and longer times, enabling, for example, the study of variability in switching speed and resistance. Finally, we discuss physics-based simulations that accurately capture subtleties of device behavior and that can be incorporated in circuit simulations.

Actin Filament Strain Promotes Severing and Cofilin Dissociation

Computational and structural studies have been indispensable in investigating the molecular origins of actin filament mechanical properties and modulation by the regulatory severing protein cofilin. All-atom molecular dynamics simulations of cofilactin filament structures determined by electron cryomicroscopy reveal how cofilin enhances the bending and twisting compliance of actin filaments. Continuum mechanics models suggest that buckled cofilactin filaments localize elastic energy at boundaries between bare and cofilin-decorated segments because of their nonuniform elasticity, thereby accelerating filament severing. Here, we develop mesoscopic length-scale (cofil)actin filament models and evaluate the effects of compressive and twisting loads on strain energy distribution at specific interprotein interfaces. The models reliably capture the filament bending and torsional rigidities and intersubunit torsional flexibility measured experimentally with purified protein components. Buckling is predicted to enhance cofilactin filament severing with minimal effects on cofilin occupancy, whereas filament twisting enhances cofilin dissociation without compromising filament integrity. Preferential severing at actin-cofilactin boundaries of buckled filaments is more prominent than predicted by continuum models because of the enhanced spatial resolution. The models developed here will be valuable for evaluating the effects of filament shape deformations on filament stability and interactions with regulatory proteins, and analysis of single filament manipulation assays.

Development of transcripts regulating dendritic spines in layer 3 pyramidal cells of the monkey prefrontal cortex: Implications for the pathogenesis of schizophrenia

Certain cognitive deficits in schizophrenia appear to emerge from altered postnatal development of the dorsolateral prefrontal cortex (DLPFC). Dendritic spines on DLPFC layer 3 pyramidal cells are essential for certain cognitive functions, change in density over development, and are reduced in number in schizophrenia. Altered expression of molecular regulators of actin filament assembly and stability, which are essential for spine formation and maintenance, is thought to contribute to the pathogenesis of spine deficits in the disease. However, the normal developmental expression patterns of these molecular regulators of dendritic spines, which might provide insight into the timing of spine deficits in schizophrenia, are unknown. Therefore, we quantified the expression from birth to adulthood of key transcripts regulating dendritic spine density in monkey DLPFC. Layer 3 pyramidal cells, and tissue samples containing layers 3 or 6, were captured by laser microdissection and selected transcripts were quantified using PCR. In layer 3 pyramidal cells, the expression levels of most of the transcripts studied changed early, and not late, in postnatal development. These developmental shifts in expression were generally not detected in tissue homogenates of layers 3 or 6, suggesting that the changes may be enriched in layer 3 pyramidal cells. The timing of these shifts in expression suggests that early, rather than later, postnatal development may be a vulnerable period for layer 3 pyramidal neurons. Disruption of the normal developmental trajectories of these transcripts may contribute to layer 3 pyramidal neuron spine deficits in individuals who are later diagnosed with schizophrenia.

Monoallelic Large Intragenic KRT5 Deletions Account for Genetically Unsolved Cases of Epidermolysis Bullosa Simplex

Monoallelic Large Intragenic KRT5 Deletions Account for Genetically Unsolved Cases of Epidermolysis Bullosa Simplex

Spray stability of self-assembled filaments for delivery

Filamentous viruses are common in nature and efficiently deliver – sometimes via aerosol – genetic material, viral proteins, and other factors to animals and plants. Aerosolization can be a severe physicochemical test of the stability of any filamentous assembly whether it is made from natural polymers such as viral proteins or synthetic polymers. Here, worm-like “filomicelles” that self-assemble in water from amphiphilic block copolymers were investigated as aerosolized delivery vehicles. After spraying and drying, fluorophore-loaded filomicelles that were originally ~10–20μm long could be imaged as 2–5μm long fragments that survived rehydration on natural and artificial surfaces (i.e. plant leaves and glass). As a functional test of delivery, the hydrophobic pesticide bifenthrin was loaded into filomicelles (up to 25% w/w) and sprayed onto plants infested with two agricultural pests, beet army worm or two-spotted spider mites; pesticidal efficacy exceeded that of commercial formulations. Persistent delivery by the filomicelle formulation was especially notable and broadly consistent with previous intravenous delivery of other drugs and dyes with the highly elongated filomicelles.

Impact of ultra-thin Al2O3–y layers on TiO2–x ReRAM switching characteristics

Transition metal-oxide resistive random access memory devices have demonstrated excellent performance in switching speed, versatility of switching and low-power operation. However, this technology still faces challenges like poor cycling endurance, degradation due to high electroforming (EF) switching voltages and low yields. Approaches such as engineering of the active layer by doping or addition of thin oxide buffer layers have been often adopted to tackle these problems. Here, we have followed a strategy that combines the two; we have used ultra-thin Al2O3–y buffer layers incorporated between TiO2–x thin films taking into account both 3+/4+ oxidation states of Al/Ti cations. Our devices were tested by DC and pulsed voltage sweeping and in both cases demonstrated improved switching voltages. We believe that the Al2O3–y layers act as reservoirs of oxygen vacancies which are injected during EF, facilitate a filamentary switching mechanism and provide enhanced filament stability, as shown by the cycling endurance measurements.

Transition from Collisional to Collisionless Regimes in Interpenetrating Plasma Flows on the National Ignition Facility.

A study of the transition from collisional to collisionless plasma flows has been carried out at the National Ignition Facility using high Mach number (M>4) counterstreaming plasmas. In these experiments, CD-CD and CD-CH planar foils separated by 6-10mm are irradiated with laser energies of 250kJ per foil, generating ∼1000 km/s plasma flows. Varying the foil separation distance scales the ion density and average bulk velocity and, therefore, the ion-ion Coulomb mean free path, at the interaction region at the midplane. The characteristics of the flow interaction have been inferred from the neutrons and protons generated by deuteron-deuteron interactions and by x-ray emission from the hot, interpenetrating, and interacting plasmas. A localized burst of neutrons and bright x-ray emission near the midpoint of the counterstreaming flows was observed, suggesting strong heating and the initial stages of shock formation. As the separation of the CD-CH foils increases we observe enhanced neutron production compared to particle-in-cell simulations that include Coulomb collisions, but do not include collective collisionless plasma instabilities. The observed plasma heating and enhanced neutron production is consistent with the initial stages of collisionless shock formation, mediated by the Weibel filamentation instability.