Individual Filaments Research Articles

Trace_y: Software algorithms for structural analysis of individual helical filaments by three-dimensional contact point reconstruction atomic force microscopy.

Atomic force microscopy (AFM) is a powerful and increasingly accessible technology that has a wide range of bio-imaging applications. AFM is capable of producing detailed three-dimensional topographical images with high signal-to-noise ratio, which enables the structural features of individual molecules to be studied without the need for ensemble averaging. Here, a software tool Trace_y, designed to reconstruct the three-dimensional surface envelopes of individual helical filament structures from topographical AFM images, is presented. Workflow using Trace_y is demonstrated on the structural analysis of individual helical amyloid protein fibrils where the assembly mechanism of heterogeneous, complex and diverse fibril populations due to structural polymorphism is not understood. The algorithms presented here allow structural information encoded in topographical AFM height images to be extracted and understood as three-dimensional (3D) contact point clouds. This approach will facilitate the use of AFM in structural biology to understand molecular structures and behaviors at individual molecule level.

On the diversity, phylogeny and biogeography of cable bacteria.

Cable bacteria have acquired a unique metabolism, which induces long-distance electron transport along their centimeter-long multicellular filaments. At present, cable bacteria are thought to form a monophyletic clade with two described genera. However, their diversity has not been systematically investigated. To investigate the phylogenetic relationships within the cable bacteria clade, 16S rRNA gene sequences were compiled from literature and public databases (SILVA 138 SSU and NCBI GenBank). These were complemented with novel sequences obtained from natural sediment enrichments across a wide range of salinities (2-34). To enable taxonomic resolution at the species level, we designed a procedure to attain full-length 16S rRNA gene sequences from individual cable bacterium filaments using an optimized nested PCR protocol and Sanger sequencing. The final database contained 1,876 long 16S rRNA gene sequences (≥800 bp) originating from 92 aquatic locations, ranging from polar to tropical regions and from intertidal to deep sea sediments. The resulting phylogenetic tree reveals 90 potential species-level clades (based on a delineation value of 98.7% 16S rRNA gene sequence identity) that reside within six genus-level clusters. Hence, the diversity of cable bacteria appears to be substantially larger than the two genera and 13 species that have been officially named up to now. Particularly brackish environments with strong salinity fluctuations, as well as sediments with low free sulfide concentrations and deep sea sediments harbor a large pool of novel and undescribed cable bacteria taxa.

Temperature-Dependent Characterization of Long-Range Conduction in Conductive Protein Fibers of Cable Bacteria.

Multicellular cable bacteria display an exceptional form of biological conduction, channeling electric currents across centimeter distances through a regular network of protein fibers embedded in the cell envelope. The fiber conductivity is among the highest recorded for biomaterials, but the underlying mechanism of electron transport remains elusive. Here, we performed detailed characterization of the conductance from room temperature down to liquid helium temperature to attain insight into the mechanism of long-range conduction. A consistent behavior is seen within and across individual filaments. The conductance near room temperature reveals thermally activated behavior, yet with a low activation energy. At cryogenic temperatures, the conductance at moderate electric fields becomes virtually independent of temperature, suggesting that quantum vibrations couple to the charge transport through nuclear tunneling. Our data support an incoherent multistep hopping model within parallel conduction channels with a low activation energy and high transfer efficiency between hopping sites. This model explains the capacity of cable bacteria to transport electrons across centimeter-scale distances, thus illustrating how electric currents can be guided through extremely long supramolecular protein structures.

The properties of magnetised cold filaments in a cool-core galaxy cluster

Filaments of cold gas ($T $ K) are found in the inner regions of many cool-core clusters. These structures are thought to play a major role in the regulation of feedback from active galactic nuclei (AGNs). We study the morphology of the filaments, their formation, and their impact on the propagation of the outflowing AGN jets. We present a set of GPU-accelerated 3D magnetohydrodynamic simulations of an idealised Perseus-like cluster using the performance portable code AthenaPK . We include radiative cooling and a self-regulated AGN feedback model that redistributes accreted material through kinetic, thermal, and magnetic feedback. We confirm that magnetic fields play an important role in both the formation and evolution of the cold material. These suppress the formation of massive cold discs and favour magnetically supported filaments over clumpy structures. Achieving resolutions of $25-50$ pc, we find that filaments are not monolithic as they contain numerous and complex magnetically supported sub-structures. We find that the mass distribution of these clumps follows a power law of slope of $ for all investigated filaments. Studying the evolution of individual filaments, we find that their formation pathways can be diverse. We find examples of filaments forming through a combination of gas uplifting and condensation, as well as systems of purely infalling clumps condensing out of the intracluster medium. The density contrast between the cold gas and the outflowing hot material leads to recurring deflections of the jets, favouring inflation of bubbles. Filaments in cool-core clusters are clumpy and contain numerous sub-structures, resulting from a complex interplay between magnetic fields, thermal instability, and jet-cloud interaction. Frequent deflections of the AGN outflows suppress jet collimation and favour the formation of large X-ray bubbles, and smaller off-axis cavities.

Small organic osmolytes accelerate actin filament assembly and stiffen filaments.

Actin filament assembly and mechanics are crucial for maintenance of cell structure, motility, and division. Actin filament assembly occurs in a crowded intracellular environment consisting of various types of molecules, including small organic molecules known as osmolytes. Ample evidence highlights the protective functions of osmolytes such as trimethylamine-N-oxide (TMAO), including their effects on protein stability and their ability to counteract cellular osmotic stress. Yet, how TMAO affects individual actin filament assembly dynamics and mechanics is not well understood. We hypothesize that, owing to its protective nature, TMAO will enhance filament dynamics and stiffen actin filaments due to increased stability. In this study, we investigate osmolyte-dependent actin filament assembly and bending mechanics by measuring filament elongation rates, steady-state filament lengths, and bending persistence lengths in the presence of TMAO using total internal reflection fluorescence microscopy and pyrene assays. Our results demonstrate that TMAO increases filament elongation rates as well as steady-state average filament lengths, and enhances filament bending stiffness. Together, these results will help us understand how small organic osmolytes modulate cytoskeletal protein assembly and mechanics in living cells.

Towards unbiased recovery of cosmic filament properties: the role of spine curvature and optimized smoothing

Cosmic filaments, the most prominent features of the cosmic web, possibly hold untapped potential for cosmological inference. While it is natural to expect the structure of filaments to show universality similar to that seen in dark matter halos, the lack of agreement between different filament finders on what constitutes a filament has hampered progress on this topic. We initiate a programme to systematically investigate and uncover possible universal features in the phase space structure of cosmic filaments, by generating particle realizations of mock filaments with a priori known properties. Using these, we identify an important source of bias in the extraction of radial density profiles, which occurs when the local curvature κ of the spine exceeds a threshold determined by the filament thickness. This bias exists even for perfectly determined spines, thus affecting all filament finders. We show that this bias can be nearly eliminated by simply discarding the regions with the highest κ, with little loss of precision. An additional source of bias is the noise generated by the filament finder when identifying the spine, which depends on both the finder algorithm as well as intrinsic properties of the individual filament. We find that to mitigate this bias, it is essential not only to smooth the estimated spine, but to optimize this smoothing separately for each filament. We propose a novel optimization based on minimizing the estimated filament thickness, along with Fourier space smoothing. We implement these techniques using two tools, FilGen which generates mock filaments and FilAPT which analyses and processes them. We expect these tools to be useful in calibrating the performance of filament finders, thereby enabling searches for filament universality.

In situ X-ray diffraction and thermal simulation of material extrusion additive manufacturing of polymer

Material extrusion additive manufacturing (AM) has gradually become a dominant technology for the fabrication of complex-designed thermoplastic polymers that require a higher level of control over the morphological and mechanical properties. The polymer internal crystal structure formed during the AM process can present significant impacts on the mechanical properties of the individual filaments, as well as the whole structure. Currently, limited details are known about the crystal structure evolution during the material extrusion AM processes of polymers. A novel in situ synchrotron X-ray diffraction (XRD) experimental configuration was developed enabling us to capture the material evolution data throughout the extrusion AM process. The in situ time-resolved data was analysed to reveal nucleation and crystallization sequences during the continuous deposition, with the aid of both complimentary numerical simulations and post-process (ex situ) characterisations. The thermal simulations supported the prediction of the filament temperature profile over time and location during the AM process, while ex situ characterisations validated the correlation between polymer crystallinity (resulting from printing parameters) and corresponding mechanical properties. The results obtained from varied process parameters suggest that the processing temperature has a dominant influence on the crystal microstructure evolution compared to the deposition velocity. A lower processing temperature just above the melting temperature permitted favourable crystallization conditions. The overall analysis demonstrated prospects for enhancing polymer AM, to engineering mechanically hierarchical structures through correlative investigations.

Length control emerges from cytoskeletal network geometry

Many cytoskeletal networks consist of individual filaments that are organized into elaborate higher-order structures. While it is appreciated that the size and architecture of these networks are critical for their biological functions, much of the work investigating control over their assembly has focused on mechanisms that regulate the turnover of individual filaments through size-dependent feedback. Here, we propose a very different, feedback-independent mechanism to explain how yeast cells control the length of their actin cables. Our findings, supported by quantitative cell imaging and mathematical modeling, indicate that actin cable length control is an emergent property that arises from the cross-linked and bundled organization of the filaments within the cable. Using this model, we further dissect the mechanisms that allow cables to grow longer in larger cells and propose that cell length-dependent tuning of formin activity allows cells to scale cable length with cell length. This mechanism is a significant departure from prior models of cytoskeletal filament length control and presents a different paradigm to consider how cells control the size, shape, and dynamics of higher-order cytoskeletal structures.

Investigation of Gamma-Induced Changes to Screening Currents and AC Losses in Mono- Versus Multi-filamentary REBCO Coated Conductors Using DC and AC Magnetometry

REBCO (rare-earth barium copper oxide) coated conductor tapes are a highly attractive option for magnet materials in future tokamak fusion power plants. However, the threat of intense neutron and gamma radiation, together with AC losses during magnet coil ramping, has raised concerns around magnet coil lifetimes. Irradiation-induced changes to flux creep rate has been identified as a key performance-limiting factor in REBCO tapes at low temperatures and high fields post-irradiation with gamma rays; spontaneous flux creep contributes to hysteretic AC loss in REBCO cables under applied AC fields. Knowing that multi-filamentary tapes are under consideration for tokamaks as an AC loss mitigation, magnetic measurements and gamma irradiation experiments are presented here on striated and mono-filamentary YBCO tapes to investigate the differences in post-irradiation screening currents and AC losses. Reduction in AC losses improved magnetisation critical current density (Jc) retention after 1 MGy in the multi- relative to the mono-filamentary samples. After the 5 MGy dose, striations then made the multi-filamentary tape more susceptible to Jc degradation because of the thinner individual filament width. Scanning transmission electron microscopy analysis on an analogous GdYBCO mono-filamentary tape did not indicate the introduction of nm-scale amorphisation to the active GdYBCO layer after gamma irradiation. A potential theoretical explanation for the underlying mechanism altering the flux-pinning landscape across the REBCO layer surface in gamma-irradiated tapes is discussed. This work concluded that gamma effects on screening current capability should be considered in future tokamak REBCO tape qualification studies.

Abstract Tu092: Role of Z-disc as a Driver of Hypertrophy and Sarcomere Assembly in Hypertrophic Cardiomyopathy

The Z-disc is an electron-dense structure demarcating the lateral boundaries of the sarcomere and postulated to play a key role in both cell signaling and sarcomere assembly. We performed EM on both HCM patient septal myectomies and human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) with 3 different HCM MYH7 mutations, finding marked Z-disc widening along with a hallmark feature of HCM, myofibrillar disarray. Mutations in MYH7 that cause HCM do so by increasing force at the sarcomere level, leading to the proposal that the Z-disc may act as a mechanosensor that converts myosin-generated force into the intracellular signaling that drives hypertrophy. We focused on understanding the mechanisms of Z-disc mechanotransduction of both hypertrophy and sarcomere disarray. RNA-seq from HCM myectomies demonstrated 52 Z-disc differentially expressed genes (DEGs). scRNA-seq from HCM hiPSC-CMs identified 24 Z-disc DEGs. 14 Z-disc DEGs were shared across both datasets, most notably 5 upstream regulators of calcineurin signalling. To correlate changes in gene expression with altered force we transfected hiPSC-CMs with a FRET-based tension sensor in the Z-disc protein vinculin allowing the direct measurement of force experienced by the Z-disc. Live-cell confocal imaging of hiPSC-CMs expressing EGFP-α-actinin-2 showed that indistinct α-actinin-2 foci coalesced into sarcomeres over the course of 24-48 h after replating. Imaging at nm scale using cryo-electron tomography revealed marked disorder in individual thick filaments in HCM hiPSC-CMs, distinct from the classical disarray at the level of whole myofibrils and which would not be visible on conventional EM. Our data suggest that early alterations in sarcomeric micro-structure and signaling induced by altered myosin force may precede hypertrophy and could occur decades before clinical signs (hypertrophy on ECG or echo) are present, with potential implications for early preventive intervention.

A memristive-photoconductive transduction methodology for accurately nondestructive memory readout

Crossbar resistive memory architectures enable high-capacity storage and neuromorphic computing, accurate retrieval of the stored information is a prerequisite during read operation. However, conventional electrical readout normally suffer from complicated process, inaccurate and destructive reading due to crosstalk effect from sneak path current. Here we report a memristive-photoconductive transduction (MPT) methodology for precise and nondestructive readout in a memristive crossbar array. The individual devices present dynamic filament form/fuse for resistance modulation under electric stimulation, which leads to photogenerated carrier transport for tunable photoconductive response under subsequently light pulse stimuli. This coherent signal transduction can be used to directly detect the memorized on/off states stored in each cell, and a prototype 4 * 4 crossbar memories has been constructed and validated for the fidelity of crosstalk-free readout in recall process.

Formation mechanism of bright and dark concentric-ring pattern in dielectric barrier discharge

In this work, a bright and dark concentric-ring pattern is reported in a dielectric barrier discharge for the first time. The spatiotemporal dynamics of the bright and dark concentric-ring pattern are investigated with an intensified charge-coupled device and photomultiplier tubes. The results indicate that the bright and dark concentric-ring pattern is composed of three concentric-ring sublattices. These are bright concentric-ring structures, dark concentric-ring structures and wider concentric-ring structures, respectively. The bright concentric-ring structures and dark concentric-ring structures are alternately distributed. The bright concentric-ring structures are located at the centre of the wider concentric-ring structures. The wider concentric-ring structures first form from the outer edge and gradually develop to the centre. The essence of all three concentric-ring structures is the individual discharge filaments. The optical emission spectra of different sublattices are acquired and analysed. It is found that the plasma parameters of the three concentric-ring sublattices are different. Finally, the formation mechanism of the bright and dark concentric-ring pattern is discussed.

Multiscale periodic homogenization for additive manufacturing of honeycomb lattices

Additive manufacturing (AM) is revolutionizing how we create things, offering innovative solutions that rival traditional manufacturing methods. In Fused Filament Fabrication (FFF), incorporating continuous fiber-reinforced filaments has significantly enhanced mechanical properties, making them valuable across diverse sectors like aerospace, automotive, and robotics. However, before printing a part, numerical simulation for design verification is essential. Yet, there’s a lack of suitable tools for modeling the complex material properties, particularly for composite lattice structures. To address this, we propose a three-level periodic homogenization method. The first level focuses on modeling individual filaments, followed by characterizing inter-bead voids at the second level, and finally, modeling collective lattice behavior at the third level. Hexagonal cellular lattice composite structures were modeled and tested to confirm the method’s accuracy and its value in supporting simulation and modular design for the composite FFF process.

Knitting Elastic Conductive Fibers of MXene/Natural Rubber for Multifunctional Wearable Sensors.

Wearable electronic sensors have recently attracted tremendous attention in applications such as personal health monitoring, human movement detection, and sensory skins as they offer a promising alternative to counterparts made from traditional metallic conductors and bulky metallic conductors. However, the real-world use of most wearable sensors is often hindered by their limited stretchability and sensitivity, and ultimately, their difficulty to integrate into textiles. To overcome these limitations, wearable sensors can incorporate flexible conductive fibers as electrically active components. In this study, we adopt a scalable wet-spinning approach to directly produce flexible and conductive fibers from aqueous mixtures of Ti3C2Tx MXene and natural rubber (NR). The electrical conductivity and stretchability of these fibers were tuned by varying their MXene loading, enabling knittability into textiles for wearable sensors. As individual filaments, these MXene/NR fibers exhibit suitable conductivity dependence on strain variations, making them ideal for motivating sensors. Meanwhile, textiles from knitted MXene/NR fibers demonstrate great stability as capacitive touch sensors. Collectively, we believe that these elastic and conductive MXene/NR-based fibers and textiles are promising candidates for wearable sensors and smart textiles.

Shockingly Bright Warm Carbon Monoxide Molecular Features in the Supernova Remnant Cassiopeia A Revealed by JWST

We present JWST NIRCam (F356W and F444W filters) and MIRI (F770W) images and NIRSpec Integral Field Unit (IFU) spectroscopy of the young Galactic supernova remnant Cassiopeia A (Cas A) to probe the physical conditions for molecular CO formation and destruction in supernova ejecta. We obtained the data as part of a JWST survey of Cas A. The NIRCam and MIRI images map the spatial distributions of synchrotron radiation, Ar-rich ejecta, and CO on both large and small scales, revealing remarkably complex structures. The CO emission is stronger at the outer layers than the Ar ejecta, which indicates the re-formation of CO molecules behind the reverse shock. NIRSpec-IFU spectra (3–5.5 μm) were obtained toward two representative knots in the NE and S fields that show very different nucleosynthesis characteristics. Both regions are dominated by the bright fundamental rovibrational band of CO in the two R and P branches, with strong [Ar vi] and relatively weaker, variable strength ejecta lines of [Si ix], [Ca iv], [Ca v], and [Mg iv]. The NIRSpec-IFU data resolve individual ejecta knots and filaments spatially and in velocity space. The fundamental CO band in the JWST spectra reveals unique shapes of CO, showing a few tens of sinusoidal patterns of rovibrational lines with pseudocontinuum underneath, which is attributed to the high-velocity widths of CO lines. Our results with LTE modeling of CO emission indicate a temperature of ∼1080 K and provide unique insight into the correlations between dust, molecules, and highly ionized ejecta in supernovae and have strong ramifications for modeling dust formation that is led by CO cooling in the early Universe.

Transport and Organization of Individual Vimentin Filaments Within Dense Networks Revealed by Single Particle Tracking and 3D FIB-SEM.

Single-particle tracking demonstrates that individual filaments in bundles of vimentin intermediate filaments are transported in the cytoplasm by motor proteins along microtubules. Furthermore, using 3D FIB-SEM the authors showed that vimentin filament bundles are loosely packed and coaligned with microtubules. Vimentin intermediate filaments (VIFs) form complex, tight-packed networks; due to this density, traditional ensemble labeling and imaging approaches cannot accurately discern single filament behavior. To address this, we introduce a sparse vimentin-SunTag labeling strategy to unambiguously visualize individual filament dynamics. This technique confirmed known long-range dynein and kinesin transport of peripheral VIFs and uncovered extensive bidirectional VIF motion within the perinuclear vimentin network, a region we had thought too densely bundled to permit such motility. To examine the nanoscale organization of perinuclear vimentin, we acquired high-resolution electron microscopy volumes of a vitreously frozen cell and reconstructed VIFs and microtubules within a ~50 μm3 window. Of 583 VIFs identified, most were integrated into long, semi-coherent bundles that fluctuated in width and filament packing density. Unexpectedly, VIFs displayed minimal local co-alignment with microtubules, save for sporadic cross-over sites that we predict facilitate cytoskeletal crosstalk. Overall, this work demonstrates single VIF dynamics and organization in the cellular milieu for the first time.

Thermosensory Spiking Activity of Proteinoid Microspheres Cross-Linked by Actin Filaments.

Actin, found in all eukaryotic cells as globular (G) or filamentous (F) actin, undergoes polymerization, with G-actin units changing shape to become F-actin. Thermal proteins, or proteinoids, are created by heating amino acids (160-200 °C), forming polymeric chains. These proteinoids can swell in an aqueous solution at around 50 °C, producing hollow microspheres filled with a solution, exhibiting voltage spikes. Our research explores the signaling properties of proteinoids, actin filaments, and hybrid networks combining actin and proteinoids. Proteinoids replicate brain excitation dynamics despite lacking specific membranes or ion channels. We investigate enhancing conductivity and spiking by using pure actin, yielding improved coordination in networks compared with individual filaments or proteinoids. Temperature changes (20 short-peptide supramolecular C to 80 °C) regulate conduction states, demonstrating external control over emergent excitability in protobrain systems. Adding actin to proteinoids reduces spike timing variability, providing a more uniform feature distribution. These findings support theoretical models proposing cytoskeletal matrices for functional specification in synthetic protocell brains, promoting stable interaction complexity. The study concludes that life-like signal encoding can emerge spontaneously within biological polymer scaffolds, incorporating abiotic chemistry.

Surface Topography Induces and Orients Nematic Swarms of Active Filaments: Considerations for Lab-On-A-Chip Devices.

Surface-bound molecular motors can drive the collective motion of cytoskeletal filaments in the form of nematic bands and polar flocks in reconstituted gliding assays. Although these "swarming transitions" are an emergent property of active filament collisions, they can be controlled and guided by tuning the surface chemistry or topography of the substrate. To date, the impact of surface topography on collective motion in active nematics is only partially understood, with most experimental studies focusing on the escape of a single filament from etched channels. Since the late 1990s, significant progress has been made to utilize the nonequilibrium properties of active filaments and create a range of functional nanodevices relevant to biosensing and parallel computation; however, the complexity of these swarming transitions presents a challenge when attempting to increase filament surface concentrations. In this work, we etch shallow, linear trenches into glass substrates to induce the formation of swarming nematic bands and investigate the mechanisms by which surface topography regulates the two-dimensional (2D) collective motion of driven filamentous actin (F-actin). We demonstrate that nematic swarms only appear at intermediate trench spacings and vanish if the trenches are made too narrow, wide, or tortuous. To rationalize these results, we simulate the F-actin as self-propelled, semiflexible chains subject to a soft, spatially modulated potential that encodes the energetic cost of bending a filament along the edge of a trench. In our model, we hypothesize that an individual filament experiences a penalty when its projected end-to-end distance is smaller than the trench spacing ("bending and turning"). However, chains that span the channel width glide above the trenches in a force- and torque-free manner ("crowd-surfing"). Our simulations demonstrate that collections of filaments form nematic bands only at intermediate trench spacings, consistent with our experimental findings.

Atomic force microscopy 3D structural reconstruction of individual particles in the study of amyloid protein assemblies.

Recent developments in atomic force microscopy (AFM) image analysis have made three-dimensional (3D) structural reconstruction of individual particles observed on 2D AFM height images a reality. Here, we review the emerging contact point reconstruction AFM (CPR-AFM) methodology and its application in 3D reconstruction of individual helical amyloid filaments in the context of the challenges presented by the structural analysis of highly polymorphous and heterogeneous amyloid protein structures. How individual particle-level structural analysis can contribute to resolving the amyloid polymorph structure-function relationships, the environmental triggers leading to protein misfolding and aggregation into amyloid species, the influences by the conditions or minor fluctuations in the initial monomeric protein structure on the speed of amyloid fibril formation, and the extent of the different types of amyloid species that can be formed, are discussed. Future perspectives in the capabilities of AFM-based 3D structural reconstruction methodology exploiting synergies with other recent AFM technology advances are also discussed to highlight the potential of AFM as an emergent general, accessible and multimodal structural biology tool for the analysis of individual biomolecules.

Did the first two Argentine flags of Macha and Ayohuma wave together?

Historical sources claim that the Argentine ensigns commonly referred to as Macha and Ayohuma flags have the same origin. The difference in their designs is remarkable, with the former being white, blue, and white in horizontal bands, while the latter has the coloured stripes at its ends. According to a historical account, these two flags were used by the patriot and creator of the Argentine flag, one of the parents of the homeland, Manuel Belgrano, when he first raised them on the banks of the Paraná River on February 27, 1812. Both flags were found by Father Martín Castro in 1883 behind a painting of Santa Cecilia in the church of Titiri near the town of Macha in Bolivia at an altitude of 4350 m above sea level. The composition of the Ayohuma flag was analysed in this paper, and the results were compared with those obtained and already published for the study conducted on the flag of Macha. It was determined by ATR-FTIR spectroscopy that the Ayohuma flag is made of silk, with the diameter of the individual silk filament of 12.5 μm, the dye used to colour the silk is indigotin, according to its resonance Raman spectrum, and methylene blue was detected by Surface-Enhanced Resonance Raman Spectroscopy, presumably utilized for the restoration of the coloured part of the flag.