Filamentous Pattern Research Articles

Intensity control of individual DBD plasma filament. II. Fundamental physical mechanism

Filamentary volume dielectric barrier discharge (DBD) produces patterned plasma structures that are currently being explored for reconfigurable metamaterial applications. Previous work has demonstrated control of the presence and intensity of a single DBD plasma filament (within an array of filaments) by biasing a low voltage needle electrode. The results were attributed to redistributed charge inside the DBD due to the modified electric field created by the needle electrode. In the present work, results from a 3D electrodynamic field simulation bolster this argument. Results show that increasing needle bias voltage causes changes in the transverse electric field structure, resulting in redistribution and build-up of surface charge at the needle location. This reduces the needle plasma filament intensity and eventually extinguishes the filament. Specifically, extinguishment of the filament corresponds with the following transitions in the field profile: (1) the applied longitudinal electric field profile along the needle lies below that of the adjacent mesh filament; (2) the surface charge on the dielectric at the needle and adjacent mesh locations is equal; and (3) the transverse electric field reverses direction and forces charge toward the needle location. The calculated surface charge on the dielectric barrier agrees with experimentally measured filament light intensity to within 8%, in agreement with theoretical predictions. Analysis of the data and trends suggests a method for predicting filament pattern formation and reducing the necessary voltage bias.

Growing actin networks regulated by obstacle size and shape

Growing actin networks provide the driving force for the motility of cells and intracellular pathogens. Based on the molecular-level processes of actin polymerization, branching, capping, and depolymerization, we have developed a modeling framework to simulate the stochastic and cooperative behaviors of growing actin networks in propelling obstacles, with an emphasis on the size and shape effects on work capacity and filament orientation in the growing process. Our results show that the characteristic size of obstacles changes the protrusion power per unit length, without influencing the orientation distribution of actin filaments in growing networks. In contrast, the geometry of obstacles has a profound effect on filament patterning, which influences the orientation of filaments differently when the drag coefficient of environment is small, intermediate, or large. We also discuss the role of various parameters, such as the aspect ratio of obstacles, branching rate, and capping rate, in affecting the protrusion power of network growth.

Controlling multiple filaments by relativistic optical vortex beams in plasmas.

Filamentation dynamics of relativistic optical vortex beams (OVBs) propagating in underdense plasma is investigated. It is shown that OVBs with finite orbital angular momentum (OAM) exhibit much more robust propagation behavior than the standard Gaussian beam. In fact, the growth rate of the azimuthal modulational instability decreases rapidly with increase of the OVB topological charge. Thus, relativistic OVBs can maintain their profiles for significantly longer distances in an underdense plasma before filamentation occurs. It is also found that an OVB would then break up into regular filament patterns due to conservation of the OAM, in contrast to a Gaussian laser beam, which in general experiences random filamentation.

Foveolar Müller Cells of the Pied Flycatcher: Morphology and Distribution of Intermediate Filaments Regarding Cell Transparency.

Specialized intermediate filaments (IFs) have critical importance for the clearness and uncommon transparency of vertebrate lens fiber cells, although the physical mechanisms involved are poorly understood. Recently, an unusual low-scattering light transport was also described in retinal Müller cells. Exploring the function of IFs in Müller cells, we have studied the morphology and distribution pattern of IFs and other cytoskeletal filaments inside the Müller cell main processes in the foveolar part of the avian (pied flycatcher) retina. We found that some IFs surrounded by globular nanoparticles (that we suggest are crystallines) are present in almost every part of the Müller cells that span the retina, including the microvilli. Unlike IFs implicated in the mechanical architecture of the cell, these IFs are not connected to any specific cellular membranes. Instead, they are organized into bundles, passing inside the cell from the endfeet to the photoreceptor, following the geometry of the processes, and repeatedly circumventing numerous obstacles. We believe that the presently reported data effectively confirm that the model of nanooptical channels built of the IFs may provide a viable explanation of Müller cell transparency.

Biopaintings Produced by Filamentous Fungi

The author explores the use of tridimensional filamentous fungi patterns to produce biopaintings. The painting process involves incorporation of food dyes into a fungi growth medium. Then, after some biochemical processes, the fungal forms are dehydrated and immobilized in polyester resin. Changes in colors and texture occur, resulting in lively images.

Yesterday, Today and Tomorrow of Mycology

Fungi are a part of environmental life. The use of yeasts dates back to Sumeria 7000 B.C for beer. Fungi essentially produce beer, wine, citric acid, single cell protein, fodder yeast, and baker’s yeast. Fungi had become objects of interest with a growing awareness as a material for botanical investigation at the beginning of 1900s. It had contributed to development of Biology, and Botany in the first fifty years of the 20th century. Fungi are suitable material for investigation, as they can be cultured under controlled conditions within a short time and remain stable for long-term investigations as well. Diversity of physiological activity, eighty to ninety thousand species within their versatility according to taxonomic prejudice, from singlecelled forms and simple aggregates to branching filamentous pattern, sexual and asexual reproduction, and fusion between filaments had made them study subject for scientists. Progress in mycological work contributed to Botany and increased the interest in this area [1]. However, fundamental of mycology was laid before. Dr. John Gill was firstly reported Mycetoma as Madura foot by in a dispensary report of the Madras Medical Service of British Army in India in 1842. Nevertheless, French missionaries defined a disease similar to mycetoma in Pondicherry in 1714. Godfrey, a surgeon, described mycetoma in 1846 as Morbus tuberculosis paddies. Carter published the monograph in 1874 as ‘‘on mycetoma or the fungus disease of India’’ [1]. Rhinosporidiosis, Tinea capitis, Chromoblastomycosis, pulmonary mycoses, and animal to man dermatomycoses were presented as published studies in India as well [2-6].

Studying Nestin and its Interrelationship with Cdk5.

Current research utilizes the specific expression pattern of intermediate filaments (IF) for identifying cellular state and origin, as well as for the purpose of disease diagnosis. Nestin is commonly utilized as a specific marker and driver for CNS progenitor cell types, but in addition, nestin can be found in several mesenchymal progenitor cells, and it is constitutively expressed in a few restricted locations, such as muscle neuromuscular junctions and kidney podocytes. Alike most other members of the IF protein family, nestin filaments are dynamic, constantly being remodeled through posttranslational modifications, which alter the solubility, protein levels, and signaling capacity of the nestin filaments. Through its interactions with kinases and other signaling executors, resulting in a complex and bidirectional regulation of cell signaling events, nestin has the potential to determine whether cells divide, differentiate, migrate, or stay in place. In this review, the broad and similar roles of IFs as dynamic signaling scaffolds, is exemplified by observations of nestin functions and its interaction with the cyclin- dependent kinase 5, the atypical kinase in the family of cyclin-dependent kinases.

Colocalization properties of elementary Ca(2+) release signals with structures specific to the contractile filaments and the tubular system of intact mouse skeletal muscle fibers.

Ca(2+) regulates several important intracellular processes. We combined second harmonic generation (SHG) and two photon excited fluorescence microscopy (2PFM) to simultaneously record the SHG signal of the myosin filaments and localized elementary Ca(2+) release signals (LCSs). We found LCSs associated with Y-shaped structures of the myosin filament pattern (YMs), so called verniers, in intact mouse skeletal muscle fibers under hypertonic treatment. Ion channels crucial for the Ca(2+) regulation are located in the tubular system, a system that is important for Ca(2+) regulation and excitation-contraction coupling. We investigated the tubular system of intact, living mouse skeletal muscle fibers using 2PFM and the fluorescent Ca(2+) indicator Fluo-4 dissolved in the external solution or the membrane dye di-8-ANEPPS. We simultaneously measured the SHG signal from the myosin filaments of the skeletal muscle fibers. We found that at least a subset of the YMs observed in SHG images are closely juxtaposed with Y-shaped structures of the transverse tubules (YTs). The distances of corresponding YMs and YTs yield values between 1.3 μm and 4.1 μm including pixel uncertainty with a mean distance of 2.52±0.10 μm (S.E.M., n=41). Additionally, we observed that some of the linear-shaped areas in the tubular system are colocalized with linear-shaped areas in the SHG images.

Dicalcin, a zona pellucida protein that regulates fertilization competence of the egg coat in Xenopus laevis.

Fertilization is a highly coordinated process whereby sperm interact with the egg-coating envelope (called the zona pellucida, ZP) in a taxon-restricted manner, Fertilization triggers the resumption of the cell cycle of the egg, ultimately leading to generation of a new organism that contains hereditary information of the parents. The complete sperm-ZP interaction comprises sperm recognition of the ZP, the acrosome reaction, penetration of the ZP, and fusion with the egg. Recent evidence suggests that these processes involve oligosaccharides associated with a ZP constituent (termed ZP protein), the polypeptide backbone of a ZP protein, and/or the proper three-dimensional filamentous structure of the ZP. However, a detailed description of the molecular mechanisms involved in sperm-ZP interaction remains elusive. Recently, I found that dicalcin, a novel ZP protein-associated protein, suppresses fertilization through its association with gp41, the frog counterpart of the mammalian ZPC protein. This review focuses on molecular aspects of sperm-ZP interaction and describes the fertilization-suppressive function of dicalcin and associated molecular mechanisms. The amount of dicalcin in the ZP significantly correlates with alteration of the lectin-staining pattern within the ZP and the orientation pattern of ZP filaments, which may assist in elucidating the complex molecular mechanisms that underlie sperm-ZP interaction.

Star formation triggered by cloud–cloud collisions

We present the results of SPH simulations in which two clouds, each having mass $M_{_{\rm{o}}}\!=\!500\,{\rm M}_{_\odot}$ and radius $R_{_{\rm{o}}}\!=\!2\,{\rm pc}$, collide head-on at relative velocities of $\Delta v_{_{\rm{o}}} =2.4,\;2.8,\;3.2,\;3.6\;{\rm and}\;4.0\,{\rm km}\,{\rm s}^{-1}$. There is a clear trend with increasing $\Delta v_{_{\rm{o}}}$. At low $\Delta v_{_{\rm{o}}}$, star formation starts later, and the shock-compressed layer breaks up into an array of predominantly radial filaments; stars condense out of these filaments and fall, together with residual gas, towards the centre of the layer, to form a single large-$N$ cluster, which then evolves by competitive accretion, producing one or two very massive protostars and a diaspora of ejected (mainly low-mass) protostars; the pattern of filaments is reminiscent of the hub and spokes systems identified recently by observers. At high $\Delta v_{_{\rm{o}}}$, star formation occurs sooner and the shock-compressed layer breaks up into a network of filaments; the pattern of filaments here is more like a spider's web, with several small-$N$ clusters forming independently of one another, in cores at the intersections of filaments, and since each core only spawns a small number of protostars, there are fewer ejections of protostars. As the relative velocity is increased, the {\it mean} protostellar mass increases, but the {\it maximum} protostellar mass and the width of the mass function both decrease. We use a Minimal Spanning Tree to analyse the spatial distributions of protostars formed at different relative velocities.

Filaments on the Western Iberian Margin: A modeling study

AbstractCoastal upwelling filaments off the Western Iberian Margin, detected in AVHRR satellite imagery and in a realistic ROMS simulation of sea surface temperature, were studied in the upwelling seasons (May–October) of 2001–2010. Sea surface temperature data were retrieved from AVHRR satellite imagery and from a realistic ROMS numerical simulation. The development and variability of the observed filaments were characterized and analyzed during each upwelling season of the 10 year period. Filaments were generally found anchored to the main bathymetric and coastal features but off the more regular northern coast of the Western Iberian Margin their locations were more variable. The results from the modeling analysis reproduced well the general features of filament development. Moreover results of model and observation showed very similar characteristics as those found in the earlier study of Haynes et al. (1993). The model output was used to relate filament patterns, eddy activity, and wind forcing. There was a clear relation between upwelling‐favorable wind strength and number and length of filaments, although the relation was weaker in the north of the region. Model filaments were clearly related to eddies only during periods of weak winds. The filament detection method was also applied to a climatologically forced ROMS simulation, which reproduced only gross features of the observed and interannually forced model filament development. This suggests that direct wind forcing and its spatial structure are highly important.

Spin-Glass Model Governs Laser Multiple Filamentation.

We show that multiple filamentation patterns in high-power laser beams can be described by means of two statistical physics concepts, namely, self-similarity of the patterns over two nested scales and nearest-neighbor interactions of classical rotators. The resulting lattice spin model perfectly reproduces the evolution of intense laser pulses as simulated by the nonlinear Schrödinger equation, shedding new light on multiple filamentation. As a side benefit, this approach drastically reduces the computing time by 2 orders of magnitude as compared to the standard simulation methods of laser filamentation.

Lagrangian coherent structures along atmospheric rivers.

We show that filamentous Atmospheric Rivers (ARs) over the Northern Atlantic Ocean are closely linked to attracting Lagrangian Coherent Structures (LCSs) in the large scale wind field. The detected LCSs represent lines of attraction in the evolving flow with a significant impact on all passive tracers. Using Finite-Time Lyapunov Exponents, we extract LCSs from a two-dimensional flow derived from water vapor flux of atmospheric reanalysis data and compare them to the three-dimensional LCS obtained from the wind flow. We correlate the typical filamentous water vapor patterns of ARs with LCSs and find that LCSs bound the filaments on the back side. Passive advective transport of water vapor in the AR from tropical latitudes is potentially possible.

Expression of Intermediate Filaments and Germ Cell Markers in the Developing Bovine Ovary: An Immunohistochemical and Laser-Assisted Microdissection Study

In the present investigation, bovine ovary prenatal development was studied using immunohistochemistry and laser-assisted microdissection (LAM). A major aim of this study was to evaluate the protein expression pattern of intermediate filaments (IF) and distinguish S100 protein (S100 alpha and S100 beta protein) isoforms during prenatal follicle differentiation, subsequently correlating them with germ cell marker expression. A development-specific expression pattern of different keratins as well as vimentin was detected in the prenatal bovine ovary; K18-specific expression was found during all developmental stages (i.e. in surface epithelium, germ cell cord somatic cells, and follicle cells), and keratins 5, 7, 8, 14, and 19 and vimentin had a stage-specific expression pattern in the different cell populations of the prenatal ovaries. Additionally, our results represent new data on the expression pattern of germ cell markers during bovine ovary prenatal development. S100 alpha and beta protein was localized to oocyte cytoplasm of different follicle stages, and S100 alpha staining could be observed in granulosa cells. Furthermore, through isolation of characteristic ovary cell populations using LAM, specific confirmation of some genes of interest (KRT8, KRT18, S100 alpha, S100 beta, and OCT4, DDX4) could be obtained by RT-PCR in single cell groups of the developing bovine ovary.

Multi variable control of filamentation of femtosecond laser pulses propagating in air

A comprehensive approach for control of filamentation and generation of a high density conductive channel during femtosecond intense laser pulse propagation in air is being reviewed. Imposing astigmatism on the beam with a tilted lens allows obtaining a single stable filament out of a high power pulse (orders of magnitude higher than the critical power), which would otherwise generate random multiple filamentation pattern. The collapse distance of filaments is controlled with a double lens setup. Once the filament is stabilized, a substantially extended lifetime of the high density plasma channel generated in its wake is experimentally demonstrated using combination of femtosecond and nanosecond laser pulses. Free electron density above 1015 cm−3 in the formed plasma filament is measured to sustain for over 30 ns. This high density plasma lifetime prolongation of more than one order of magnitude is achieved by properly timed irradiation of the filament with a relatively low intensity nanosecond laser pulse, in comparison to a filament without such irradiation. The experimental results are in good agreement with our theoretical model that follows the evolution of the temperature and density of various molecules, atoms and ion species. The results point to the possibility of generating substantially long time duration, stable high density plasma filaments in air.

Carbonate fabrics in the modern microbialites of Pavilion Lake: two suites of microfabrics that reflect variation in microbial community morphology, growth habit, and lithification.

Modern microbialites in Pavilion Lake, BC, provide an analog for ancient non-stromatolitic microbialites that formed from insitu mineralization. Because Pavilion microbialites are mineralizing under the influence of microbial communities, they provide insights into how biological processes influence microbialite microfabrics and mesostructures. Hemispherical nodules and micrite-microbial crusts are two mesostructures within Pavilion microbialites that are directly associated with photosynthetic communities. Both filamentous cyanobacteria in hemispherical nodules and branching filamentous green algae in micrite-microbial crusts were associated with calcite precipitation at microbialite surfaces and with characteristic microfabrics in the lithified microbialite. Hemispherical nodules formed at microbialite surfaces when calcite precipitated around filamentous cyanobacteria with a radial growth habit. The radial filament pattern was preserved within the microbialite to varying degrees. Some subsurface nodules contained well-defined filaments, whereas others contained only dispersed organic inclusions. Variation in filament preservation is interpreted to reflect differences in timing and amount of carbonate precipitation relative to heterotrophic decay, with more defined filaments reflecting greater lithification prior to degradation than more diffuse filaments. Micrite-microbial crusts produce the second suite of microfabrics and form in association with filamentous green algae oriented perpendicular to the microbialite surface. Some crusts include calcified filaments, whereas others contained voids that reflect the filamentous community in shape, size, and distribution. Pavilion microbialites demonstrate that microfabric variation can reflect differences in lithification processes and microbial metabolisms as well as microbial community morphology and organization. Even when the morphology of individual filaments or cells is not well preserved, the microbial growth habit can be captured in mesoscale microbialite structures. These results suggest that when petrographic preservation is extremely good, ancient microbialite growth structures and microfabrics can be interpreted in the context of variation in community organization, community composition, and lithification history. Even in the absence of distinct microbial microfabrics, mesostructures can capture microbial community morphology.

Oligomerized, filamentous surface presentation of RANTES/CCL5 on vascular endothelial cells.

Vascular endothelial cells present luminal chemokines that arrest rolling leukocytes by activating integrins. It appears that several chemokines must form higher-order oligomers to elicit proper in vivo effects, as mutants restricted to forming dimers have lost the ability to recruit leukocytes to sites of inflammation. Here, we show for the first time that the chemokine RANTES/CCL5 binds to the surface of human endothelial cells in a regular filamentous pattern. Furthermore, the filaments bound to the surface in a heparan sulfate-dependent manner. By electron microscopy we observed labeling for RANTES on membrane projections as well as on the remaining plasma membrane. Mutant constructs of RANTES restricted either in binding to heparin, or in forming dimers or tetramers, appeared either in a granular, non-filamentous pattern or were not detectable on the cell surface. The RANTES filaments were also present after exposure to flow, suggesting that they can be present in vivo. Taken together with the lacking in vivo or in vitro effects of RANTES mutants, we suggest that the filamentous structures of RANTES may be of physiological importance in leukocyte recruitment.

Multiple filamentation of supercritical UV laser beam in atmospheric air

Multiple filamentation of subpicosecond UV pulses with peak power up to 0.2TW was investigated at the Ti:Sapphire/KrF GARPUN-MTW laser facility in the direct amplification scheme. Filamentation arose in the initial preamplifier stage when peak power exceeded the critical value of 0.1GW. The filamentation pattern was well reproducible for repetitive pulses in time scales from nanoseconds to several minutes.

Evaluating yeast filamentous growth at the single-cell level.

Budding yeast can undergo filamentous growth in response to nutrient limitation. Filament formation can be examined under glucose-limiting conditions by the single-cell invasive growth assay, or under nitrogen-limiting conditions with the pseudohyphal growth assay, both described here. The single-cell assay allows robust quantitation of changes in budding pattern and cell length, and most cells in the population show the response. The pseudohyphal growth assay reveals filamentous patterns in larger microcolonies and adjoining subpopulations of cells. Historically, the single-cell assay has been used to study filamentous growth in haploid cells and the pseudohyphal growth assay in diploid cells. However, both assays can be used in either cell type.

Quantifying two-dimensional filamentous and invasive growth spatial patterns in yeast colonies.

The top-view, two-dimensional spatial patterning of non-uniform growth in a Saccharomyces cerevisiae yeast colony is considered. Experimental images are processed to obtain data sets that provide spatial information on the cell-area that is occupied by the colony. A method is developed that allows for the analysis of the spatial distribution with three metrics. The growth of the colony is quantified in both the radial direction from the centre of the colony and in the angular direction in a prescribed outer region of the colony. It is shown that during the period of 100–200 hours from the start of the growth of the colony there is an increasing amount of non-uniform growth. The statistical framework outlined in this work provides a platform for comparative quantitative assays of strain-specific mechanisms, with potential implementation in inferencing algorithms used for parameter-rate estimation.