Filament-like Structures Research Articles

Investigation of Droplet Deposition for Suspensions Usable for Thermoplastic 3D Printing (T3DP)

Thermoplastic 3D printing (T3DP) is an additive manufacturing (AM) technology, which can be used for the production of dense single- and especially multi-material components. This becomes possible because of the combination of the precise deposition of small droplets of molten thermoplastic suspensions containing ceramic or metal particles, and a curing mechanism caused on cool down increasing the viscosity. In this paper, the droplet formation behavior of zirconia suspensions for T3DP (82 and 84 wt.%) was investigated. The droplet fusion factor (dff) is introduced to calculate the necessary distance between two droplets to form filament-like structures by fusion of adjacent droplets. Filament-like structures with a smooth surface and a nearly homogeneous cross section were manufactured for both suspensions with a dff of 44% or higher.

Variety of shapes of solar wind ion flux spectra: Spektr-R measurements

The paper is devoted to the shapes of the solar wind ion flux fluctuation spectrum at the transition between the inertial and the kinetic range usingin situhigh-resolution measurements of the Russian mission Spektr-R. We analyse the variability of the transition region and select five typical types of spectral shapes: (i) spectra with two slopes and one break, (ii) spectra characterized by a nonlinear steepening in the kinetic range, (iii) spectra with flattening in the vicinity of the break, (iv) spectra with a bump in the vicinity of the break and (v) spectra without any steepening in the kinetic range. The most popular is the well-known type (i) observed in approximately half of the cases. The second most popular type of spectra is type (iii) occurring in approximately one third of the cases. The other three types are observed less often: type (ii) – in approximately 6 %; type (iv) in 3 % and type (v) in 6 % of cases. An analysis of typical plasma conditions for different types of spectra revealed that the last two type of spectra (iv) and (v) are generally observed in a very slow solar wind with a low proton density, (i) and (iii) are observed in the solar wind with rather typical conditions and (ii) is usually observed in high-speed streams. The effect of nonlinear steepening of the spectra in the kinetic range increases with the solar wind speed. We present also the analysis of statistical properties of the observed events and compare them with the predictions of several statistical turbulence models. We show that intermittency is always observed in the solar wind flow despite the presence of one or another shape of spectra. The log-Poisson model with a dominant contribution of filament-like structures shows the best parameterization of the experimentally observed scaling.

Filament-like DREP4 CIDE domain: characterization and preliminary X-ray crystallographic studies.

DREP4 is a nuclease from fruit fly that is involved in apoptotic DNA fragmentation. DREP4 contains a conserved CIDE domain that acts as a protein-interaction module and is critical for its function. In this study, it was found that DREP4 CIDE domains form filament-like structures in solution. The length of the highly ordered filament-like structure is dependent on the salt concentration. By adjusting the salt concentration the DREP4 CIDE domain could be crystallized, and X-ray diffraction data were collected to a resolution of 1.9 Å. The crystals were found to belong to the orthorhombic space group P212121, with unit-cell parameters a = 53.08, b = 76.58, c = 174.59 Å.

A closer look at the ‘characteristic’ width of molecular cloud filaments

Filaments in Herschel molecular cloud images are found to exhibit a "characteristic width". This finding is in tension with spatial power spectra of the data, which show no indication of this characteristic scale. We demonstrate that this discrepancy is a result of the methodology adopted for measuring filament widths. First, we perform the previously used analysis technique on artificial scale-free data, and obtain a peaked width distribution of filament-like structures. Next, we repeat the analysis on three Herschel maps and reproduce the narrow distribution of widths found in previous studies $-$ when considering the average width of each filament. However, the distribution of widths measured at all points along a filament spine is broader than the distribution of mean filament widths, indicating that the narrow spread (interpreted as a "characteristic" width) results from averaging. Furthermore, the width is found to vary significantly from one end of a filament to the other. Therefore, the previously identified peak at 0.1 pc cannot be understood as representing the typical width of filaments. We find an alternative explanation by modelling the observed width distribution as a truncated power-law distribution, sampled with uncertainties. The position of the peak is connected to the lower truncation scale and is likely set by the choice of parameters used in measuring filament widths. We conclude that a "characteristic" width of filaments is not supported by the available data.

A method for identifying and characterising particle clusters in a two-phase turbulent jet

A novel technique for identifying and characterising clusters of particles from measurements within a densely seeded two-phase flow is reported. This technique involves the smoothing of normalised instantaneous planar images of particle concentration followed by the application of a robust and unambiguous dynamic threshold to identify particle clusters. Also reported is a method to extract quantitative cluster data including cluster length, width and number of branches. The method employs an algorithm to morphologically skeletonize images of clusters, and subsequently, prune skeleton branches to select those which most strongly represent the shape of the cluster. Together, these techniques have been shown to identify and characterise two-dimensional slices of three-dimensional particle clusters of complex shapes, including those that are bent, wrinkled and branched, with an uncertainty of ≈4% relative to the manually determined values. This method was applied to planar measurements of particles in a heavily seeded turbulent jet with an exit Stokes number of SkD=1.4 and Reynolds number of ReD=10,000, based on the pipe diameter, D. The results show that particle clusters are already present at the exit plane and have a characteristic width that is narrowly distributed around an average value of ≈0.17D. This implies that particle clusters are generated inside the pipe at this preferred length scale. The results also show that the average cluster length at the pipe exit is ≈1.0D, which, together with the observation that the clusters are oriented at oblique angles to the axis of the jet, suggests that the length of these clusters within the pipe is limited by the pipe diameter. The aspect ratio of the cluster slices was found to be typically AR≈6−7, consistent with the observations that the clusters form long, thin, filament-like structures.

Independent multimerization of Latent TGFβ Binding Protein-1 stabilized by cross-linking and enhanced by heparan sulfate.

TGFβ plays key roles in fibrosis and cancer progression, and latency is conferred by covalent linkage to latent TGFβ binding proteins (LTBPs). LTBP1 is essential for TGFβ folding, secretion, matrix localization and activation but little is known about its structure due to its inherent size and flexibility. Here we show that LTBP1 adopts an extended conformation with stable matrix-binding N-terminus, extended central array of 11 calcium-binding EGF domains and flexible TGFβ-binding C-terminus. Moreover we demonstrate that LTBP1 forms short filament-like structures independent of other matrix components. The termini bind to each other to facilitate linear extension of the filament, while the N-terminal region can serve as a branch-point. Multimerization is enhanced in the presence of heparin and stabilized by the matrix cross-linking enzyme transglutaminase-2. These assemblies will extend the span of LTBP1 to potentially allow simultaneous N-terminal matrix and C-terminal fibrillin interactions providing tethering for TGFβ activation by mechanical force.

A 5′P degradation hot spot influences molecular farming of anticancerogenic nuclease TBN1 in tobacco cells

Tomato bifunctional nuclease 1 (TBN1) is a polyfunctional protein with anticancerogenic activity originally isolated as an overexpressed protein from viroid-infected tomato. Its molecular farming in plant cells could be a non-expensive source for its biotechnology preparation. So we analysed TBN1 expression in Agrobacterium-infiltrated leaf sectors of Nicotiana benthamiana and in transformed suspension culture of tobacco BY-2 cells. During its transient expression, TBN1 mRNA was strongly degraded within a hot spot localized in the 3′ region. This early degradation process was inhibited by PTGS suppressors p19 and p38 resulting in increased TBN1 mRNA and protein yield. In parallel to degradation of TBN1 mRNA, high mRNA levels of two RNA-dependent RNA polymerases were detected in infiltrated leaf sectors, as well as in the transformed tobacco suspension culture BY-2, where low expression of the nuclease was stably maintained. Higher TBN1 mRNA and nuclease activity levels were found during its molecular farming in RDR6-deficient N. benthamiana plants. By fluorescent microscopy of infiltrated and transformed plant cells, the nuclease-GFP fusion protein was shown to be organized in filament-like structures.

Isolation and Functional Characterization of SOC1-like Genes in Prunus mume

The MADS-box gene SOC1/TM3 (suppressor of overexpression of constans 1/tomato MADS-box gene 3) integrates multiple flowering signals to regulate the transition from vegetative to reproductive development in arabidopsis (Arabidopsis thaliana). Although SOC1-like genes have been isolated from a wide range of plant species, their orthologs are not well characterized in mei (Prunus mume), an important ornamental and fruit plant in east Asia. To better understand the molecular regulation of flower development in mei, we isolated and characterized three putative orthologs of arabidopsis SOC1, including PmSOC1-1, PmSOC1-2, and PmSOC1-3. The phylogenetic tree revealed that these genes fall into different subgroups within the SOC1-like gene group, suggesting distinct functions. PmSOC1-1 and PmSOC1-3 were mainly expressed in vegetative organs and at low expression levels in floral parts of the plants, whereas PmSOC1-2 was expressed only in vegetative organs. Furthermore, the expression level decreased significantly during flower bud differentiation development, suggesting a role for these genes in the transition from the vegetative to the reproductive phase. Overexpression of PmSOC1-1, PmSOC1-2, and PmSOC1-3 in arabidopsis caused early flowering. Early flowering also increased expression levels of four other flowering promoters, agamous-like 24 (AGL24), leafy (LFY), apetala 1 (AP1), and fruitfull (FUL). Moreover, the overexpression of PmSOC1-1 and PmSOC1-2 resulted in a range of floral phenotype changes such as sepals into leaf-like structures, petal color into green, and petal into filament-like structures. These results suggested that the genes PmSOC1-1, PmSOC1-2, and PmSOC1-3 play an evolutionarily conserved role in promoting flowering in mei, and may have distinct roles during flower development. Our findings will help elucidate the molecular mechanisms involved in the transition from vegetative to reproductive development in mei.

Dust dynamics in 2D gravito-turbulent discs

The dynamics of solid bodies in protoplanetary disks are subject to the properties of any underlying gas turbulence. Turbulence driven by disk self-gravity shows features distinct from those driven by the magnetorotational instability (MRI). We study the dynamics of solids in gravito-turbulent disks with two-dimensional (in the disk plane), hybrid (particle and gas) simulations. Gravito-turbulent disks can exhibit stronger gravitational stirring than MRI-active disks, resulting in greater radial diffusion and larger eccentricities and relative speeds for large particles (those with dimensionless stopping times $t_{stop} \Omega > 1$, where $\Omega$ is the orbital frequency). The agglomeration of large particles into planetesimals by pairwise collisions is therefore disfavored in gravito-turbulent disks. However, the relative speeds of intermediate-size particles $t_{stop} \Omega \sim 1$ are significantly reduced as such particles are collected by gas drag and gas gravity into coherent filament-like structures with densities high enough to trigger gravitational collapse. First-generation planetesimals may form via gravitational instability of dust in marginally gravitationally unstable gas disks.

The structure and poloidal dynamics of blob filaments in TJ-K

Relatively dense, field-aligned, filament-like structures (blobs) have been observed to propagate radially and poloidally through the scrape-off layer (SOL) in magnetically confined fusion plasmas, and contribute significantly to SOL transport. A detailed understanding of blob structure and dynamics, and their dependence on magnetic field geometry, is important in magnetic confinement physics for the prediction of heat loads on reactor wall facing components, as well as for understanding plasma confinement and neutral particle recycling. Experimentally deduced centre of mass poloidal blob velocity components, obtained using the conditional averaging technique, have been compared to an analytical blob model which has been simplified to express blob velocity in terms of the magnetic field curvature vector. Background flows are not incorporated into the analytical model, and must be added in to obtain good agreement with the experimental data. In addition, the 3D structure of blobs in TJ-K has been investigated using the conditional average of density fluctuations in two toroidally separated poloidal planes. Blobs are observed to be aligned to a flux tube near to the last closed flux surface, in the blob birth region. However at positions further along the blob trajectory, the structures do not deform according to the magnetic shear, rather they remain rigid, and retain their original form.

Two microtubule-plus-end binding proteins LIS1-1 and LIS1-2, homologues of human LIS1 in Neurospora crassa

LIS1 is a microtubule (Mt) plus-end binding protein that interacts with the dynein/dynactin complex. In humans, LIS1 is required for proper nuclear and organelle migration during cell growth. Although gene duplication is absent from Neurospora crassa, we found two paralogues of human LIS1. We named them LIS1-1 and LIS1-2 and studied their dynamics and function by fluorescent tagging. At the protein level, LIS1-1 and LIS1-2 were very similar. Although, the characteristic coiled-coil motif was not present in LIS1-2. LIS1-1-GFP and LIS1-2-GFP showed the same cellular distribution and dynamics, but LIS1-2-GFP was less abundant. Both LIS1 proteins were found in the subapical region as single fluorescent particles traveling toward the cell apex, they accumulated in the apical dome forming prominent short filament-like structures, some of which traversed the Spitzenkörper (Spk). The fluorescent structures moved exclusively in anterograde fashion along straight paths suggesting they traveled on Mts. There was no effect in the filament behavior of LIS1-1-GFP in the Δlis1-2 mutant but the dynamics of LIS1-2-GFP was affected in the Δlis1-1 mutant. Microtubular integrity and the dynein–dynactin complex were necessary for the formation of filament-like structures of LIS1-1-GFP in the subapical and apical regions; however, conventional kinesin (KIN-1) was not. Deletion mutants showed that the lack of lis1-1 decreased cell growth by ∼75%; however, the lack of lis1-2 had no effect on growth. A Δlis1-1;Δlis1-2 double mutant showed slower growth than either single mutant. Conidia production was reduced but branching rate increased in Δlis1-1 and the Δlis1-1;Δlis1-2 double mutants. The absence of LIS1-1 had a strong effect on Mt organization and dynamics and indirectly affected nuclear and mitochondrial distribution. The absence of LIS1-1 filaments in dynein mutants (ropy mutants) or in benomyl treated hyphae indicates the strong association between this protein and the regulation of the dynein–dynactin complex and Mt organization. LIS1-1 and LIS1-2 had a high amino acid homology, nevertheless, the absence of the coiled-coil motif in LIS1-2 suggests that its function or regulation may be distinct from that of LIS1-1.

Dynamic properties of small-scale solar wind plasma fluctuations.

The paper presents the latest results of the studies of small-scale fluctuations in a turbulent flow of solar wind (SW) using measurements with extremely high temporal resolution (up to 0.03 s) of the bright monitor of SW (BMSW) plasma spectrometer operating on astrophysical SPECTR-R spacecraft at distances up to 350,000 km from the Earth. The spectra of SW ion flux fluctuations in the range of scales between 0.03 and 100 s are systematically analysed. The difference of slopes in low- and high-frequency parts of spectra and the frequency of the break point between these two characteristic slopes was analysed for different conditions in the SW. The statistical properties of the SW ion flux fluctuations were thoroughly analysed on scales less than 10 s. A high level of intermittency is demonstrated. The extended self-similarity of SW ion flux turbulent flow is constantly observed. The approximation of non-Gaussian probability distribution function of ion flux fluctuations by the Tsallis statistics shows the non-extensive character of SW fluctuations. Statistical characteristics of ion flux fluctuations are compared with the predictions of a log-Poisson model. The log-Poisson parametrization of the structure function scaling has shown that well-defined filament-like plasma structures are, as a rule, observed in the turbulent SW flows.

Formation of filament-like structures in the pulsar magnetosphere and the short-term variability of pulsar emission

Magnetohydrodynamic (MHD) instabilities can play an important role in the dynamics of the pulsar magnetosphere and can be responsible for the formation of various structures. We consider the instability caused by a gradient of the magnetic pressure which can occur in a non-neutral magnetospheric plasma. We arguethat the pulsar magnetospheres are always unstable. The unstable disturbances have a form of filaments directed along the magnetic field lines with plasma motions being almost parallel (or anti-parallel) to the magnetic field. The growth rate of instability is high and can reach a fraction of $ck$, where $k$ is the wavevector of unstable disturbances. The instability can be responsible for fluctuations of plasma and the short-term variability of pulsar emission.

Structure of crenactin, an archaeal actin homologue active at 90°C

The crystal structure of the archaeal actin, crenactin, from the rod-shaped hyperthermophilic (optimal growth at 90°C) crenarchaeon Pyrobaculum calidifontis is reported at 3.35 Å resolution. Despite low amino-acid sequence identity, the three-dimensional structure of the protein monomer is highly similar to those of eukaryotic actin and the bacterial MreB protein. Crenactin-specific features are also evident, as well as elements that are shared between crenactin and eukaryotic actin but are not found in MreB. In the crystal, crenactin monomers form right-handed helices, demonstrating that the protein is capable of forming filament-like structures. Monomer interactions in the helix, as well as interactions between crenactin and ADP in the nucleotide-binding pocket, are resolved at the atomic level and compared with those of actin and MreB. The results provide insights into the structural and functional properties of a heat-stable archaeal actin and contribute to the understanding of the evolution of actin-family proteins in the three domains of life.

Comparative proteomics reveals key proteins recruited at the nucleoid of Deinococcus after irradiation‐induced DNA damage

The nucleoids of radiation-resistant Deinococcus species show a high degree of compaction maintained after ionizing irradiation. We identified proteins recruited after irradiation in nucleoids of Deinococcus radiodurans and Deinococcus deserti by means of comparative proteomics. Proteins in nucleoid-enriched fractions from unirradiated and irradiated Deinococcus were identified and semiquantified by shotgun proteomics. The ssDNA-binding protein SSB, DNA gyrase subunits GyrA and GyrB, DNA topoisomerase I, RecA recombinase, UvrA excinuclease, RecQ helicase, DdrA, DdrB, and DdrD proteins were found in significantly higher amounts in irradiated nucleoids of both Deinococcus species. We observed, by immunofluorescence microscopy, the subcellular localization of these proteins in D. radiodurans, showing for the first time the recruitment of the DdrD protein into the D. radiodurans nucleoid. We specifically followed the kinetics of recruitment of RecA, DdrA, and DdrD to the nucleoid after irradiation. Remarkably, RecA proteins formed irregular filament-like structures 1 h after irradiation, before being redistributed throughout the cells by 3 h post-irradiation. Comparable dynamics of DdrD localization were observed, suggesting a possible functional interaction between RecA and DdrD. Several proteins involved in nucleotide synthesis were also seen in higher quantities in the nucleoids of irradiated cells, indicative of the existence of a mechanism for orchestrating the presence of proteins involved in DNA metabolism in nucleoids in response to massive DNA damage. All MS data have been deposited in the ProteomeXchange with identifier PXD00196 (http://proteomecentral.proteomexchange.org/dataset/PXD000196).

The Bacterial Effector VopL Organizes Actin into Filament-like Structures

VopL is an effector protein from Vibrio parahaemolyticus that nucleates actin filaments. VopL consists of a VopL C-terminal domain (VCD) and an array of three WASP homology 2 (WH2) motifs. Here, we report the crystal structure of the VCD dimer bound to actin. The VCD organizes three actin monomers in a spatial arrangement close to that found in the canonical actin filament. In this arrangement, WH2 motifs can be modeled into the binding site of each actin without steric clashes. The data suggest a mechanism of nucleation wherein VopL creates filament-like structures, organized by the VCD with monomers delivered by the WH2 array, that can template addition of new subunits. Similarities with Arp2/3 complex and formin proteins suggest that organization of monomers into filament-like structures is a general and central feature of actin nucleation.

Surface Reconstruction by a “Grafting Through” Approach: Polyacrylamide Grafted onto Chitosan Film

Grafted polymers and polymer brushes in particular have attracted significant attention in the last 2 decades as a way to alter and control interfacial properties. In the case of polymer brushes on solid substrates, a high grafting density of polymer chains results in stretching of the polymer coils normal to the substrate surface due to the effect of excluded volume. In this study, polyacrylamide is grafted to the surface of relatively soft thin films of chitosan. The "grafting through" approach is used by introducing double C═C bonds to amino groups of chitosan. The acquired kinetic data of grafting along with AFM and ellipsometry characterization suggest that the chitosan substrate undergoes surface reconstruction during the grafting of PAAm and simultaneously induces PAAm growth inside the soft substrate. As a result, much higher amounts of grafted polymer are achieved in comparison to traditional hard substrates like silicon or glass. Additionally, selective plasma etching of PAAm reveals filament-like structures oriented normal to the surface.

Nucleotide‐independent cytoskeletal scaffolds in bacteria

Bacteria possess a diverse set of cytoskeletal proteins that mediate key cellular processes such as morphogenesis, cell division, DNA segregation, and motility. Similar to eukaryotic actin or tubulin, many of them require nucleotide binding and hydrolysis for proper polymerization and function. However, there is also a growing number of bacterial cytoskeletal elements that assemble in a nucleotide-independent manner, including intermediate filament-like structures as well several classes of bacteria-specific polymers. The members of this group form stable scaffolds that have architectural roles or act as localization factors recruiting other proteins to distinct positions within the cell. Here, we highlight the elements that constitute the nucleotide-independent cytoskeleton of bacteria and discuss their biological functions in different species.

Attachment and Biofilm Forming Capabilities of Staphylococcus epidermidis Strains Isolated from Preterm Infants

Staphylococcus epidermidis, a human commensal, is an important opportunistic, biofilm-forming pathogen and the main cause of late onset sepsis in preterm infants, worldwide. In this study we describe the characteristics of S. epidermidis strains causing late onset (>72 h) bloodstream infection in preterm infants and skin isolates from healthy newborns. Attachment and biofilm formation capability were analyzed in microtiter plates and with transmission electron microscopy (TEM). Clonal relationship among strains was studied with pulsed-field gel electrophoresis. Antimicrobial susceptibility testing was performed, as well as the detection of biofilm-associated genes and of the invasiveness marker IS256 with polymerase chain reaction. Blood and skin isolates had similar attachment and biofilm-forming capabilities and biofilm formation was not related to the presence of specific genes. Filament-like membrane structures were seen by TEM early in the attachment close to the device surface, both in blood and skin strains. Nine of the ten blood isolates contained the IS256 and were also resistant to methicillin and gentamicin in contrast to skin strains. S. epidermidis strains causing bloodstream infection in preterm infants exhibit higher antibiotic resistance and are provided with an invasive genetic equipment compared to skin commensal strains. Adhesion capability to a device surface seems to involve bacterial membrane filaments.

Interactions of Actinomyces-Like Organisms with Host Cells: Light Microscopic Examination

Objective: To determine the interactions of Actinomyces-like organisms (ALOs) with host cells, including vaginal epithelial cells, polymorphonuclear leukocytes (PMNLs) and erythrocytes, using Pap smear microscopy and based on their light microscopic appearances. Study Design: Cervicovaginal samples obtained from 200 patients were examined by both Pap smear microscopy and anaerobic culturing. Since the results obtained by these methods were not concordant for diagnosis of genital Actinomyces, the results of Pap smear microscopy were used as a reference, and the smears with ALOs were carefully screened with regard to interactions of ALOs with host cells. Results: ALOs were detected as attached to vaginal epithelial cells, PMNLs and erythrocytes via their filament-like structures. At some attachment sites, the epithelial cell membrane and filaments of ALOs were almost fused with each other. A group of PMNLs surrounded the ALOs. However, ALOs were observed to form colonies to evade phagocytosis by PMNLs. At the connection points between erythrocytes and ALOs, the findings of interest were the changes in the shapes of the erythrocytes and filament-like structures of the ALOs on the erythrocyte membrane. Conclusions: The adhesiveness of ALOs can be observed in routine Papanicolaou-stained cervicovaginal smears at light microscopic level.