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At least 1,675 records · Page 93

Triggering typical nemaline myopathy with compound heterozygous nebulin mutations reveals myofilament structural changes as pathomechanism

Nebulin is a giant protein that winds around the actin filaments in the skeletal muscle sarcomere. Compound-heterozygous mutations in the nebulin gene (NEB) cause typical nemaline myopathy (NM), a muscle disorder characterized by muscle weakness with limited treatment options. We created a mouse model with a missense mutation p.Ser6366Ile and a deletion of NEB exon 55, the Compound-Het model that resembles typical NM. We show that Compound-Het mice are growth-retarded and have muscle weakness. Muscles have a reduced myofibrillar fractional-area and sarcomeres are disorganized, contain rod bodies, and have longer thin filaments. In contrast to nebulin-based severe NM where haplo-insufficiency is the disease driver, Compound-Het mice express normal amounts of nebulin. X-ray diffraction revealed that the actin filament is twisted with a larger radius, that tropomyosin and troponin behavior is altered, and that the myofilament spacing is increased. The unique disease mechanism of nebulin-based typical NM reveals novel therapeutic targets.

59 BASIC BIOLOGICAL SCIENCES↗

Vapor-induced phase-separation-enabled versatile direct ink writing

Abstract Versatile printing of polymers, metals, and composites always calls for simple, economic approaches. Here we present an approach to three-dimensional (3D) printing of polymeric, metallic, and composite materials at room conditions, based on the polymeric vapor-induced phase separation (VIPS) process. During VIPS 3D printing (VIPS-3DP), a dissolved polymer-based ink is deposited in an environment where nebulized non-solvent is present, inducing the low-volatility solvent to be extracted from the filament in a controllable manner due to its higher chemical affinity with the non-solvent used. The polymeric phase is hardened in situ as a result of the induced phase separation process. The low volatility of the solvent enables its reclamation after the printing process, significantly reducing its environmental footprint. We first demonstrate the use of VIPS-3DP for polymer printing, showcasing its potential in printing intricate structures. We further extend VIPS-3DP to the deposition of polymer-based metallic inks or composite powder-laden polymeric inks, which become metallic parts or composites after a thermal cycle is applied. Furthermore, spatially tunable porous structures and functionally graded parts are printed by using the printing path to set the inter-filament porosity as well as an inorganic space-holder as an intra-filament porogen.

42 ENGINEERING↗

Structural diversity and clustering of bacterial flagellar outer domains

Supercoiled flagellar filaments function as mechanical propellers within the bacterial flagellum complex, playing a crucial role in motility. Flagellin, the building block of the filament, features a conserved inner D0/D1 core domain across different bacterial species. In contrast, approximately half of the flagellins possess additional, highly divergent outer domain(s), suggesting varied functional potential. In this study, we report atomic structures of flagellar filaments from three distinct bacterial species: Cupriavidus gilardii , Stenotrophomonas maltophilia , and Geovibrio thiophilus . Our findings reveal that the flagella from the facultative anaerobic G. thiophilus possesses a significantly more negatively charged surface, potentially enabling adhesion to positively charged minerals. Furthermore, we analyze all AlphaFold predicted structures for annotated bacterial flagellins, categorizing the flagellin outer domains into 682 structural clusters. This classification provides insights into the prevalence and experimental verification of these outer domains. Remarkably, two of the flagellar structures reported herein belong to a distinct cluster, indicating additional opportunities on the study of the functional diversity of flagellar outer domains. Our findings underscore the complexity of bacterial flagellins and open up possibilities for future studies into their varied roles beyond motility.

Science & Technology - Other Topics↗

The case for electron re-acceleration at galaxy cluster shocks

On the largest scales, the Universe consists of voids and filaments making up the cosmic web. Galaxy clusters are located at the knots in this web, at the intersection of filaments. Clusters grow through accretion from these large-scale filaments and by mergers with other clusters and groups. In a growing number of galaxy clusters, elongated Mpc-sized radio sources have been found. Also known as radio relics, these regions of diffuse radio emission are thought to trace relativistic electrons in the intracluster plasma accelerated by low-Mach-number shocks generated by cluster–cluster merger events. A long-standing problem is how low-Mach-number shocks can accelerate electrons so efficiently to explain the observed radio relics. Here, we report the discovery of a direct connection between a radio relic and a radio galaxy in the merging galaxy cluster Abell 3411–3412 by combining radio, X-ray and optical observations. This discovery indicates that fossil relativistic electrons from active galactic nuclei are re-accelerated at cluster shocks. Lastly, it also implies that radio galaxies play an important role in governing the non-thermal component of the intracluster medium in merging clusters.

79 ASTRONOMY AND ASTROPHYSICS↗

Kinesin motor density and dynamics in gliding microtubule motility

Abstract Kinesin motors and their associated filaments, microtubules, are essential to many biological processes. The motor and filament system can be reconstituted in vitro with the surface-adhered motors transporting the filaments along the surface. In this format, the system has been used to study active self-assembly and to power microdevices or perform analyte detection. However, fundamental properties of the system, such as the spacing of the kinesin motors bound to the microtubule and the dynamics of binding, remain poorly understood. We show that Fluorescence Interference Contrast (FLIC) microscopy can illuminate the exact height of the microtubule, which for a sufficiently low surface density of kinesin, reveals the locations of the bound motors. We examine the spacing of the kinesin motors on the microtubules at various kinesin surface densities and compare the results with theory. FLIC reveals that the system is highly dynamic, with kinesin binding and unbinding along the length of the microtubule as it is transported along the surface.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Fast myosin binding protein C knockout in skeletal muscle alters length-dependent activation and myofilament structure

In striated muscle, the sarcomeric protein myosin-binding protein-C (MyBP-C) is bound to the myosin thick filament and is predicted to stabilize myosin heads in a docked position against the thick filament, which limits crossbridge formation. Here, we use the homozygous Mybpc2 knockout (C2 -/- ) mouse line to remove the fast-isoform MyBP-C from fast skeletal muscle and then conduct mechanical functional studies in parallel with small-angle X-ray diffraction to evaluate the myofilament structure. We report that C2 -/- fibers present deficits in force production and calcium sensitivity. Structurally, passive C2 -/- fibers present altered sarcomere length-independent and -dependent regulation of myosin head conformations, with a shift of myosin heads towards actin. At shorter sarcomere lengths, the thin filament is axially extended in C2 -/- , which we hypothesize is due to increased numbers of low-level crossbridges. These findings provide testable mechanisms to explain the etiology of debilitating diseases associated with MyBP-C.

59 BASIC BIOLOGICAL SCIENCES↗

Visualizing diverse lithium growth and stripping behaviors in anode-free solid-state batteries with operando X-ray tomography

Anode-free solid-state batteries (SSBs), which eliminate the need for lithium metal use during cell assembly, have the potential to enable high energy densities and simplified manufacturing. However, the factors that control lithium growth/stripping at the anode current collector are not well understood. Here, we use operando X-ray microcomputed tomography to comprehensively image and quantify lithium deposition and stripping under various conditions in three different Li|Li 6 PS 5 Cl|current collector cells, revealing diverse behavior that depends on interface morphology, cell resistance, and solid-state electrolyte (SSE) microstructure. A cell with high resistance exhibits extensive lithium filament growth across the entire current collector interface, with filaments that grow around pre-existing pores in the SSE rather than lithium filling these pores. Lithium filament formation is partially reversible, with the cracks shrinking as lithium metal is stripped. Uniform lithium deposition is achievable at low current densities in low-resistance cells, whereas higher current densities in these cells cause an increase in interfacial roughness, which is correlated with subsequent filamentary growth at the edges of the cell. These results provide insight into filamentary vs. planar lithium growth and highlight that the evolution of lithium is sensitively dependent on SSE microstructure and electrochemical processes.

25 ENERGY STORAGE↗

Fossil group origins

Aims: We analyse the large-scale structure out to 100 Mpc around a sample of 16 confirmed fossil systems using spectroscopic information from the Sloan Digital Sky Survey Data Release 16. Methods: We computed the distance between our fossil groups (FGs) and the centres of filaments and nodes from the literature. We also studied the density of bright galaxies, since this parameter is thought to be a good mass tracers, as well as the projected over-densities of galaxies. Finally, we applied a friends-of-friends (FoF) algorithm to detect virialised structures around our FGs and obtain an estimate of the mass available in their surroundings. Results: We find that FGs are mainly located close to filaments, with a mean distance of 3.7 ± 1.1 R 200 and a minimum distance of 0.05 R 200 . On the other hand, none of our FGs were found close to intersections, with a mean and minimum distance of 19.3 ± 3.6 and 6.1 R 200 , respectively. There is a correlation that indicates FGs at higher redshifts are found in denser regions, when we use bright galaxies as tracers of the mass. At the same time, FGs with the largest magnitude gaps (Δm 12 > 2.5) are found in less dense environments and tend to host (on average) smaller central galaxies. Conclusions: Our results suggest that FGs formed in a peculiar position within the cosmic web, close to filaments and far from nodes, whereby their interaction with the cosmic web itself may be limited. We deduce that FGs with brightest central galaxies (BCGs) that are relatively faint, high values of Δm 12 , and low redshifts could, in fact, be systems that are at the very last stage of their evolution. Moreover, we confirm theoretical predictions that systems with the largest magnitude gap are not massive.

79 ASTRONOMY AND ASTROPHYSICS↗

Buckling transition in long α-helices

The treatment of bending and buckling of stiff biopolymer filaments by the popular worm-like chain model does not provide adequate understanding of these processes at the microscopic level. Thus, we have used the atomistic molecular-dynamic simulations and the Amber03 force field to examine the compression buckling of α-helix (AH) filaments at room temperature. It was found that the buckling instability occurs in AHs at the critical force f{sub c} in the range of tens of pN depending on the AH length. The decrease of the force f{sub c} with the contour length follows the prediction of the classic thin rod theory. At the force f{sub c} the helical filament undergoes the swift and irreversible transition from the smoothly bent structure to the buckled one. A sharp kink in the AH contour arises at the transition, accompanied by the disruption of the hydrogen bonds in its vicinity. The kink defect brings in an effective softening of the AH molecule at buckling. Nonbonded interactions between helical branches drive the rearrangement of a kinked AH into the ultimate buckled structure of a compact helical hairpin described earlier in the literature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dielectric permittivity tensor and low frequency instabilities of a magnetoactive current-driven plasma with nonextensive distribution

The dielectric permittivity tensor of a magnetoactive current-driven plasma is obtained by employing the kinetic theory based on the Vlasov equation and Lorentz transformation formulas with an emphasize on the q-nonextensive statistics. By deriving the q-generalized dispersion relation of the low frequency modes in this plasma system, the possibility and properties of filamentation and ion acoustic instabilities are then studied. It is shown that the occurrence and the growth rate of these instabilities depend strongly on the nonextensive parameters, external magnetic field strength, and drift velocity. It is observed that the growth rate of ion acoustic instability is affected by the magnetic field strength much more than that of the filamentation instability in the low frequency range. The external magnetic field facilitates the development of the ion-acoustic instability. It is also shown that the filamentation is the dominant instability only for the high value of drift velocity.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Growth and propagation of self-generated magnetic dipole vortices in collisionless shocks produced by interpenetrating plasmas

Collisionless shocks generated by colliding relativistic plasmas are studied using particle-in-cell (PIC) simulations. The shock is produced due to the Weibel instabilities that generate current and density filaments and small-scale magnetic fields that are amplified from initial fluctuations. Localized regions of the strong magnetic field in the form of magnetic dipole vortices upstream of the shock are observed in the simulation developed during the nonlinear evolution of the electron and ion filaments. The vortices developing from the merger and subsequent pinching of the small-scale filaments are shown to be moving in the direction opposite to that of the shock. Lastly, we also found an analytical estimate of the drift velocity of the vortices that are confirmed by the PIC simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Electrostatic solitary waves in ion beam neutralization

The excitation and propagation of electrostatic solitary waves (ESWs) are observed in two-dimensional particle-in-cell simulations of ion beam neutralization by electron injection by a filament. Electrons from the filament are attracted by positive ions and bounce inside the ion beam pulse. Bouncing back and forth electron streams start to mix, creating two-stream instability. The instability saturates with the formation of ESWs. These ESWs reach several centimeters in longitudinal size and are stable for a long time (>>τ b , the duration of the ion beam pulse). The excitation of large-amplitude ESWs reduces the degree of neutralization of the ion beam pulse. In addition, the dissipation of ESWs causes heating of neutralizing electrons and their escape from the ion beam, leading to a further reduction of neutralization degree. Here, the appearance of these waves can explain the results of previous experimental studies, which showed poor ion beam neutralization by electro-emitting filaments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Similarity parameter for the process of mid-IR light bullet formation

We study the influence of the ratio of diffraction and dispersion lengths of a femtosecond mid-IR wave packet on the filamentation threshold power and the light bullet (LB) formation upon nonlinear optical interaction with solid-state dielectrics under the conditions of anomalous group velocity dispersion. It is found that the ratio of the threshold power of filamentation and LB formation to the critical power of stationary self-focusing is independent of the radiation wavelength and the medium characteristics and is determined by the similarity parameter, equal to the ratio of the diffraction length to the dispersion one. With an increase in the similarity parameter, the threshold power of filamentation and light bullet formation increases. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Interference effects in the formation of the light bullet spectrum under axicon focusing

Specific features of the anti-Stokes band of the light bullet supercontinuum spectrum under filamentation of 1900-nm femtosecond pulses, focused by an axicon in fused silica and calcium fluoride, have been experimentally, numerically, and analytically investigated. It is found that the formation of two or more light bullets in a filament leads to modulation of spectral components’ intensity. The oscillation period of spectral components, defined as the wavelength interval between adjacent intensity minima, decreases with decreasing their wavelength. On a logarithmic scale, the relative change in the oscillation period in the spectrum is proportional to the spectral component wavelength and is independent of the pulse energy and the position of the light bullet formation region in the filament. It is established that the modulation in the spectrum is due to the interference of the broadband supercontinuum emitted by light bullets, and its period decreases with increasing interval between them. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Phytophthora palmivora establishes tissue-specific intracellular infection structures in the earliest divergent land plant lineage

The expansion of plants onto land was a formative event that brought forth profound changes to the earth’s geochemistry and biota. Filamentous eukaryotic microbes developed the ability to colonize plant tissues early during the evolution of land plants, as demonstrated by intimate, symbiosis-like associations in >400 million-year-old fossils. However, the degree to which filamentous microbes establish pathogenic interactions with early divergent land plants is unclear. Here, we demonstrate that the broad host-range oomycete pathogen Phytophthora palmivora colonizes liverworts, the earliest divergent land plant lineage. We show that P. palmivora establishes a complex tissue-specific interaction with Marchantia polymorpha , where it completes a full infection cycle within air chambers of the dorsal photosynthetic layer. Remarkably, P. palmivora invaginates M. polymorpha cells with haustoria-like structures that accumulate host cellular trafficking machinery and the membrane syntaxin MpSYP13B, but not the related MpSYP13A. Furthermore, our results indicate that the intracellular accommodation of filamentous microbes is an ancient plant trait that is successfully exploited by pathogens like P. palmivora .

59 BASIC BIOLOGICAL SCIENCES↗

Molecular mechanism for NLRP6 inflammasome assembly and activation

Inflammasomes are large protein complexes that trigger host defense in cells by activating inflammatory caspases for cytokine maturation and pyroptosis. NLRP6 is a sensor protein in the nucleotide-binding domain (NBD) and leucine-rich repeat (LRR)-containing (NLR) inflammasome family that has been shown to play multiple roles in regulating inflammation and host defenses. Despite the significance of the NLRP6 inflammasome, little is known about the molecular mechanism behind its assembly and activation. Here we present cryo-EM and crystal structures of NLRP6 pyrin domain (PYD). We show that NLRP6 PYD alone is able to self-assemble into filamentous structures accompanied by large conformational changes and can recruit the ASC adaptor using PYD–PYD interactions. Additionally, using molecular dynamics simulations, we identify the surface that the NLRP6 PYD filament uses to recruit ASC PYD. We further find that full-length NLRP6 assembles in a concentration-dependent manner into wider filaments with a PYD core surrounded by the NBD and the LRR domain. These findings provide a structural understanding of inflammasome assembly by NLRP6 and other members of the NLR family.

59 BASIC BIOLOGICAL SCIENCES↗

Cyanobacteria and Chloroflexota cooperate to structure light-responsive biofilms

Microbial mats are stratified communities often dominated by unicellular and filamentous phototrophs within an exopolymer matrix. It is challenging to quantify the dynamic responses of community members in situ as they experience steep gradients and rapid fluctuations of light. To address this, we developed a binary consortium using two representative isolates from hot spring mats: the unicellular oxygenic phototrophic cyanobacterium Synechococcus OS-B′ (Syn OS-B′) and the filamentous anoxygenic phototroph Chloroflexus MS-CIW-1 (Chfl MS-1). We quantified the motility of individual cells and entire colonies and demonstrated that Chfl MS-1 formed bundles of filaments that moved in all directions with no directional bias to light. Syn OS-B′ was slightly less motile but exhibited positive phototaxis. This binary consortium displayed cooperative behavior by moving further than either species alone and formed ordered arrays where both species aligned with the light source. No cooperative motility was observed when a nonmotile pilB mutant of Syn OS-B′ was used instead of Syn OS-B′. The binary consortium also produced more adherent biofilm than individual species, consistent with the close interspecies association revealed by electron microscopy. We propose that cyanobacteria and Chloroflexota cooperate in forming natural microbial mats by colonizing new niches and building robust biofilms.

Functional and Systems Biology↗

Three-dimensional stochastic model of actin–myosin binding in the sarcomere lattice

The effect of molecule tethering in three-dimensional (3-D) space on bimolecular binding kinetics is rarely addressed and only occasionally incorporated into models of cell motility. The simplest system that can quantitatively determine this effect is the 3-D sarcomere lattice of the striated muscle, where tethered myosin in thick filaments can only bind to a relatively small number of available sites on the actin filament, positioned within a limited range of thermal movement of the myosin head. Here we implement spatially explicit actomyosin interactions into the multiscale Monte Carlo platform MUSICO, specifically defining how geometrical constraints on tethered myosins can modulate state transition rates in the actomyosin cycle. The simulations provide the distribution of myosin bound to sites on actin, ensure conservation of the number of interacting myosins and actin monomers, and most importantly, the departure in behavior of tethered myosin molecules from unconstrained myosin interactions with actin. In addition, MUSICO determines the number of cross-bridges in each actomyosin cycle state, the force and number of attached cross-bridges per myosin filament, the range of cross-bridge forces and accounts for energy consumption. At the macroscopic scale, MUSICO simulations show large differences in predicted force-velocity curves and in the response during early force recovery phase after a step change in length comparing to the two simplest mass action kinetic models. The origin of these differences is rooted in the different fluxes of myosin binding and corresponding instantaneous cross-bridge distributions and quantitatively reflects a major flaw of the mathematical description in all mass action kinetic models. Consequently, this new approach shows that accurate recapitulation of experimental data requires significantly different binding rates, number of actomyosin states, and cross-bridge elasticity than typically used in mass action kinetic models to correctly describe the biochemical reactions of tethered molecules and their interaction energetics.

60 APPLIED LIFE SCIENCES↗