Intersection Of Filaments Research Articles

Bisous model—Detecting filamentary patterns in point processes

The cosmic web is a highly complex geometrical pattern, with galaxy clusters at the intersection of filaments and filaments at the intersection of walls. Identifying and describing the filamentary network is not a trivial task due to the overwhelming complexity of the structure, its connectivity and the intrinsic hierarchical nature. To detect and quantify galactic filaments we use the Bisous model, which is a marked point process built to model multi-dimensional patterns. The Bisous filament finder works directly with the galaxy distribution data and the model intrinsically takes into account the connectivity of the filamentary network. The Bisous model generates the visit map (the probability to find a filament at a given point) together with the filament orientation field. Using these two fields, we can extract filament spines from the data. Together with this paper we publish the computer code for the Bisous model that is made available in GitHub. The Bisous filament finder has been successfully used in several cosmological applications and further development of the model will allow to detect the filamentary network also in photometric redshift surveys, using the full redshift posterior. We also want to encourage the astro-statistical community to use the model and to connect it with all other existing methods for filamentary pattern detection and characterisation.

Cycling State that Can Lead to Glassy Dynamics in Intracellular Transport

Studies of molecular motors and their cargo moving within cells have revealed that they can be trapped for long periods of times. Researchers show that this trapping can occur when the motors encounter intersections of cytoskeletal filaments within cells.

Searching for filaments and large-scale structure around DAFT/FADA clusters

Clusters of galaxies are at the intersection of cosmic filaments and are still accreting galaxies and groups along these preferential directions, but, because of their relatively low contrast on the sky, they are difficult to detect (unless a large amount of spectroscopic data are available), and unambiguous detections have been limited until now to relatively low redshifts (z<0.3). We searched for extensions and filaments around the thirty clusters of the DAFT/FADA survey (redshift range 0.4<z<0.9) with deep wide field photometric data. For each cluster, based on a colour-magnitude diagram, we selected galaxies that were likely to belong to the red sequence, and hence to be at the cluster redshift, and built density maps. By computing the background for each map and drawing 3sigma contours, we estimated the elongations of the structures detected in this way. Whenever possible, we identified the other structures detected on the density maps with clusters listed in NED. We found clear elongations in twelve clusters, with sizes reaching up to 7.6 Mpc. Eleven other clusters have neighbouring structures, but the zones linking them are not detected in the density maps at a 3sigma level. Three clusters show no extended structure and no neighbours, and four clusters are of too low contrast to be clearly visible on our density maps. The simple method we have applied appears to work well to show the existence of filaments and/or extensions around a number of clusters in the redshift range 0.4<z<0.9. We plan to apply it to other large cluster samples such as the clusters detected in the CFHTLS and SDSS-Stripe 82 surveys in the near future.

Myosin Va Motor Teams Navigate Vesicle Cargos through 3D Actin Filament Intersections

Myosin Va (MyoVa) motor teams collectively move intracellular cargo through a complex, three dimensional (3D), actin meshwork. To address how MyoVa motors navigate this physical challenge, we imaged fluorescently labeled 350nm synthetic lipid vesicles, bound with ∼10 MyoVa HMM motors, moving through 3D actin filament intersections strung between 3µm beads. Intersections were formed by filaments being ∼90 degrees to one another and separated by 30-250nm. As the vesicle surface contacted the intersecting actin filaments, two regions of potential motor engagement were created on the vesicle surface. Geometric constraints limited the engaged motor number at each contact point to no more than 3, as confirmed by laser trap stall force measurements. These points of vesicle-actin filament contact resulted in an effective tug of war between two motor teams that were physically separated on the vesicle surface. The vesicle's directional outcome at an intersection was visualized using high spatial and temporal 3D super resolution imaging. For vesicles that physically contacted both actin filaments at the intersection, 55% of vesicles continued straight through the intersection, 35% switched filaments, while only 10% terminated. These outcomes were successfully simulated by a model in which the directional outcome was dependent on the interfilament gap, the vesicle's azimuthal approach angle to the intersection, the stochastic attachment and detachment of motors within a team (i.e. a team's force generation), and the Brownian motion of the vesicle while attached to the actin filaments. All of these physical factors contributed to which motor ensemble won the tug of war at the intersection and thus the vesicle's directional outcome. This simplified biomimetic system and resultant data provide an experimental framework for understanding how MyoVa motor teams navigate their cargo through evermore complex 3D actin networks that exist within cells.

Both monovalent cations and plectin are potent modulators of mechanical properties of keratin K8/K18 networks.

Intermediate filament (IF) networks are a major contributor to cell rigidity and thus serve as vital elements to preserve the integrity of entire cell layers. Keratin K8 and K18 IFs are the basic constituents of the cytoskeleton of epithelial cells. The mechanical properties of K8/K18 networks depend on the structural arrangements of individual filaments within the network. This paper investigates the architecture of these networks in vitro under the influence of the monovalent cation potassium and that of the cytolinker protein plectin. Whereas increasing amounts of potassium ions lead to filament bundling, plectin interlinks filaments at filament intersection points but does not lead to bundle formation. The mechanics of the resulting networks are investigated by microrheology with assembled K8/K18 networks. It is shown that bundling induced by potassium ions significantly stiffens the network. Furthermore, our measurements reveal an increase in plectin-mediated keratin network rigidity as soon as an amount corresponding to more than 20% of the plectin present in cells is added to the keratin IF networks. In parallel, we investigated the influence of plectin on cell rigidity in detergent-extracted epithelial vulva carcinoma derived A431 cells in situ. These cytoskeletons, containing mostly IFs, actin filaments and associated proteins, exhibit a significantly decreased stiffness, when plectin is downregulated to ≈10% of the normal value. Therefore, we assume that plectin, via the formation of IF-IF connections and crosslinking of IFs to actin filaments, is an important contributor to cell stiffness.

Quantitative Analysis of Filament Branch Orientation in Listeria Actin Comet Tails

Several bacterial and viral pathogens hijack the host actin cytoskeleton machinery to facilitate spread and infection. In particular, Listeria uses Arp2/3-mediated actin filament nucleation at the bacterial surface to generate a branched network that will help propel the bacteria. However, the mechanism of force generation remains elusive due to the lack of high-resolution three-dimensional structural data on the spatial organization of the actin mother and daughter (i.e., branch) filaments within this network. Here, we have explored the three-dimensional structure of Listeria actin tails in Xenopus laevis egg extracts using cryo-electron tomography. We found that the architecture of Listeria actin tails is shared between those formed in cells and in cell extracts. Both contained nanoscopic bundles along the plane of the substrate, where the bacterium lies, and upright filaments (also called Z filaments), both oriented tangentially to the bacterial cell wall. Here, we were able to identify actin filament intersections, which likely correspond to branches, within the tails. A quantitative analysis of putative Arp2/3-mediated branches in the actin network showed that mother filaments lie on the plane of the substrate, whereas daughter filaments have random deviations out of this plane. Moreover, the analysis revealed that branches are randomly oriented with respect to the bacterial surface. Therefore, the actin filament network does not push directly toward the surface but rather accumulates, building up stress around the Listeria surface. Our results favor a mechanism of force generation for Listeria movement where the stress is released into propulsive motion.

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.

Extraction of Individual Filaments from 2D Confocal Microscopy Images of Flat Cells.

A crucial step in understanding the architecture of cells and tissues from microscopy images, and consequently explain important biological events such as wound healing and cancer metastases, is the complete extraction and enumeration of individual filaments from the cellular cytoskeletal network. Current efforts at quantitative estimation of filament length distribution, architecture and orientation from microscopy images are predominantly limited to visual estimation and indirect experimental inference. Here we demonstrate the application of a new algorithm to reliably estimate centerlines of biological filament bundles and extract individual filaments from the centerlines by systematically disambiguating filament intersections. We utilize a filament enhancement step followed by reverse diffusion based filament localization and an integer programming based set combination to systematically extract accurate filaments automatically from microscopy images. Experiments on simulated and real confocal microscope images of flat cells (2D images) show efficacy of the new method.

Cargo Transport at Microtubule Crossings: Evidence for Prolonged Tug-of-War between Kinesin Motors

Intracellular transport of cargos along microtubules is often complicated by the topology of the underlying filament network. The fundamental building blocks for this complex arrangement are filament intersections. The navigation of cargos across microtubule intersections remains poorly understood. Here, we demonstrate that kinesin-driven cargos are engaged in a tug-of-war at microtubule intersections. Tug-of-war events result in long pauses that can last from a few seconds to several minutes. We demonstrate that the extent of the tug-of-war and the duration of pauses change with the number of motors on the cargo and can be regulated by ionic strength. We also show that dwell times at intersections depend on the angle between crossing microtubules. Our data suggest that local microtubule geometry can regulate microtubule-based transport.

Probing Lipid Vesicle Transport in 3D by Teams of Myosin Va Motors at Suspended Actin Intersections in vitro

In cells, myosin Va motor teams are forced to transport vesicles through a complex three-dimensional (3D) actin meshwork. To characterize how these motors navigate this physically challenging meshwork, we created actin filament intersections adhered to a coverslip surface and confronted a team of ∼10 myosin Va HMM motors carrying a 350nm synthetic lipid vesicle. When approaching the intersection on the lower filament, the motor-vesicle complex (MVC) switched to the upper intersecting filament with a 51% probability while crossing over the intersection with only a 33% probability. If approaching the intersection on the upper filament, the MVC preferred staying on the upper filament through the intersection and only switched to the lower filament with a 31% probability. These data suggest that the extent of MVC surface contact with the target binding zone of the intersecting actin filaments dictates the directional outcome. To build complexity, actin filaments were strung between 3μm beads, creating suspended filament intersections. The 3D spatial relations between the MVC and the individual filaments were determined by super-resolution STORM imaging. As the MVC approached the intersection, the complex spiraled around the actin filament with a pitch of ∼1.3µm. If the MVC was forced to navigate through the intersection and the separation between actin filaments (<100nm) was less than the vesicle diameter, the MVC initially paused and then switched to the intersecting filament. For this to occur, motors must be free to diffuse on the fluid lipid (DOPC) vesicle surface and engage an actin filament anywhere that the vesicle surface contacts an actin filament. This 3D model system with added complexity will provide an experimental platform to understand how myosin Va motor ensembles maneuver their cargo through the complex actin cytoskeletal network.

Reactive fluxes delivered by dielectric barrier discharge filaments to slightly wounded skin

The application of atmospheric-pressure plasmas to human tissue has been shown to have therapeutic effects for wound healing and in treatment of skin diseases. In this paper, we report on a computational study of the intersection of plasma filaments in a dielectric barrier discharge (DBD) with a small wound in human skin in the context of plasma medicine. The wound is represented as a small cut in the epidermal layer of cells. Intracellular structures and their electrical properties were incorporated into the two-dimensional computational mesh in order to self-consistently couple gas phase plasma transport with the charging of the surface of the wound. We quantify the fluxes of reactive oxygen and nitrogen species, ions and photons produced in or diffusing into the wound as might occur during the first few discharge pulses of treatment. Comparison is made to fluxes predicted by global modelling. We show that the relative location of the plasma filament with respect to the wound is important on plasma time scales (ns) for ions and photons, and for radicals directly produced by electron impact processes. On the longer-term diffusion time scales (ms) the position of the plasma filament relative to the wound is not so critical. For typical DBD conditions, the magnitude of these fluxes to the cellular surfaces corresponds to fluences of radicals nearly equal to the surface site density. These results imply that the biological reactivity is limited by reaction probabilities and not the availability of radical fluxes.

Star-forming Substructure within Molecular Clouds

AbstractWide-field far-infrared/submillimeter continuum maps of molecular clouds by the Herschel Space Observatory GBS and HOBYS surveys are revealing the star-forming substructures that lead to star formation in dense gas. In particular, these maps have revealed the central role in clouds of filaments, likely formed through turbulent motions. These filaments appear to be non-isothermal and fragment into cores only when their column densities exceed a stability threshold. Organizations of filament networks suggest the relative role of turbulence and gravity can be traced in different parts of a cloud, and filament intersections may lead to larger amounts of mass flow that form the precursors of high-mass stars or clusters.

Force-Dependent Detachment of Kinesin-2 Biases Track Switching at Cytoskeletal Filament Intersections

Intracellular trafficking of organelles often involves cytoskeletal track switching. Organelles such as melanosomes are transported by multiple motors including kinesin-2, dynein, and myosin-V, which drive switching between microtubules and actin filaments during dispersion and aggregation. Here, we used optical trapping to determine the unitary and ensemble forces of kinesin-2, and to reconstitute cargo switching at cytoskeletal intersections in a minimal system with kinesin-2 and myosin-V motors bound to beads. Single kinesin-2 motors exerted forces up to ∼5 pN, similar to kinesin-1. However, kinesin-2 motors were more likely to detach at submaximal forces, and the duration of force maintenance was short as compared to kinesin-1. In multimotor assays, force increased with kinesin-2 density but was not affected by the presence of myosin-V. In crossed filament assays, switching frequencies of motor-bound beads were dependent on the starting track. At equal average forces, beads tended to switch from microtubules onto overlying actin filaments consistent with the relatively faster detachment of kinesin-2 at near-maximal forces. Thus, in addition to relative force, switching probability at filament intersections is determined by the dynamics of motor-filament interaction, such as the quick detachment of kinesin-2 under load. This may enable fine-tuning of filament switching in the cell.

Coordination of Multiple Motors Bound to Intracellular Cargos

The movement of organelles and vesicles along the cellular cytoskeleton is often driven by multiple motor types, including kinesins, dynein, and myosins. Both in vitro and cellular studies suggest that multiple motors are bound simultaneously to intracellular cargos. For some cargos, such as late endosomes/lysosomes, we find that opposing motors may be active simultaneously, leading to stochastic directional switching best characterized as a tug-of-war. Run lengths are generally short and apparent diffusive movement predominates. For other cargos, such as autophagosomes, both kinesin and dynein motors remain stably bound but motility is highly processive in a single direction, suggesting motor activities are regulated. Intracellular transport is also regulated at the level of the track, as dictated by the complex organization of the intracellular cytoskeleton, characterized by microtubule-microtubule and microtubule-actin filament intersections as well as filament dynamics and filament-binding proteins. By analyzing motility at multiple levels, including: (1) in vitro with purified motors bound to beads at filament intersections; (2) in vitro with motors that co-purify with isolated organelles; (3) in the cell using high resolution tracking of endocytosed quantum dots; and (4) intracellular manipulation of phagocytosed beads using an optical trap, we can investigate the mechanisms that coordinate the interactions of multiple motors in intracellular organelle transport. Supported by NIH GM087253.

Dynamics of Dielectric Barrier Discharges Over Wounded Skin

The intersection of plasma filaments in a dielectric barrier discharge with a small wound in the human skin in the context of plasma medicine is investigated with results from a computer model. The relative location of the filament with respect to the wound determines the symmetry of treatment.

Ion energy and angular distributions onto polymer surfaces delivered by dielectric barrier discharge filaments in air: I. Flat surfaces

In atmospheric pressure discharges, ion energies are typically thought to be thermal with values dominantly <1 eV. In the heads of filaments in dielectric barrier discharges (DBDs), electric fields can exceed 200 kV cm−1 when the filament is far from a surface. As the filament approaches and intersects a dielectric surface, much of the applied potential is compressed into the voltage drop across the head of the filament due to the high conductivity of the trailing plasma channel. When the filament strikes the surface, this voltage is transferred to the resulting sheath and into the material of the surface. The degree of electric field compression depends on the dielectric constant ε/ε0 of the surface. Upon intersection of the filament with the surface, the electric fields in the resulting sheath can exceed 400–800 kV cm−1, with larger values corresponding to larger ε/ε0. When accelerated in these fields, ions can gain energies across their mean free path (0.5–1 µm) up to 20 eV for dielectrics with low ε/ε0 and up to 150 eV for dielectrics with high ε/ε0, albeit only for the duration of the intersection of the streamer with the surface of a few ns. In this paper we report on results from a computational investigation of the ion energy and angular distributions (IEADs) incident on dielectric flat surfaces resulting from the intersection of DBD filaments sustained in atmospheric pressure air. We describe the transient and spatially dependent IEADs as the filament spreads across the polymer.

The persistent cosmic web and its filamentary structure - II. Illustrations

The recently introduced discrete persistent structure extractor (DisPerSE, Soubie 2010, paper I) is implemented on realistic 3D cosmological simulations and observed redshift catalogues (SDSS); it is found that DisPerSE traces equally well the observed filaments, walls, and voids in both cases. In either setting, filaments are shown to connect onto halos, outskirt walls, which circumvent voids. Indeed this algorithm operates directly on the particles without assuming anything about the distribution, and yields a natural (topologically motivated) self-consistent criterion for selecting the significance level of the identified structures. It is shown that this extraction is possible even for very sparsely sampled point processes, as a function of the persistence ratio. Hence astrophysicists should be in a position to trace and measure precisely the filaments, walls and voids from such samples and assess the confidence of the post-processed sets as a function of this threshold, which can be expressed relative to the expected amplitude of shot noise. In a cosmic framework, this criterion is comparable to friend of friend for the identifications of peaks, while it also identifies the connected filaments and walls, and quantitatively recovers the full set of topological invariants (Betti numbers) {\sl directly from the particles} as a function of the persistence threshold. This criterion is found to be sufficient even if one particle out of two is noise, when the persistence ratio is set to 3-sigma or more. The algorithm is also implemented on the SDSS catalogue and used to locat interesting configurations of the filamentary structure. In this context we carried the identification of an ``optically faint'' cluster at the intersection of filaments through the recent observation of its X-ray counterpart by SUZAKU. The corresponding filament catalogue will be made available online.

How Varying the Processivity of Myosin V Affects its Motion in Cos-7 Cells

The processive, hand-over-hand mechanism of myosin Va (myoVa) walking on actin has been intensively studied in vitro, but less is known about its behavior within cells. We previously showed that myoVa undergoes a random walk in COS-7 cells as it processively steps along actin tracks within the dense and randomly oriented cortical actin network (Nelson et al. BJ 97:509, 2009). Here we test how the processivity of myoV impacts on the observed cellular motion. A mutant construct with 3-fold shorter run lengths than wild-type myoVa (WT), and one with ∼1.5-fold longer run lengths, were introduced into cultured COS-7 cells by pinocytosis. The motion of Quantum dot (Qdot)-labeled single motors within the cultured cells was analyzed through high resolution TIRF microscopy and single particle tracking. Mean Squared Displacement (MSD) analysis of the motor:Qdot trajectories appear to be diffusive over short time scale (∼1s), and sub-diffusive over longer time scales (∼10s). Strikingly, the diffusion coefficients for the short time scales strictly correlate with the processivity of the motor, and range from 0.06μm2/s for the least processive motor, to 0.15μm2/s for the more processive variant. The non-processive and very slow myoVc, had the lowest diffusion coefficient of any of the constructs tested (0.019μm2/s). The observed diffusion coefficients and the sub-diffusive motion for longer time scales was successfully modeled through Monte Carlo simulations assuming that a processive myoVa motor will either cross over, turn or terminate at actin filament intersections within the randomly oriented actin meshwork. Once the motor terminates its run it undergoes restricted diffusion, being potentially confined within domains that are bounded by cytoskeletal or organellar structures. The motor-dependent cellular behavior supports the idea that the apparently wandering trajectories are random walks by active motors.

Myosin Va Cargo Transport on Actin Bundles

Myosin Va (myoVa) walks processively while carrying cargo towards the plus end of actin filaments. In cells, parallel actin filament bundles (e.g. stress fibers and filopodia) present a directional challenge to myoVa cargo transport. Therefore, we formed unipolar (fascin) and mixed polarity (alpha-actinin) actin bundles as tracks for expressed myoVa-HMM with a C-terminal biotin tag. In this assay, a single streptavidin-Qdot served as cargo for one or many (∼ 5) myoVa motors. Qdots transported by one or many myoVa molecules traveled in the same direction on unipolar bundles, while moving in either direction on mixed polarity bundles. Qdot speeds were the same regardless of bundle type or number of motors (400nm/s), and similar to that for one or many motors on a single actin filament (Nelson et al., 2009). However, run lengths for single motors were 2-3 times longer on bundles than previously observed on single actin filaments. This suggests that on parallel tracks the leading head has a greater number of actins within its reach, thus decreasing the probability of run termination. Interestingly, on mixed polarity bundles, we observed individual Qdots changing directions in the middle of a run, the frequency of which increases in the multiple motor case. It was not surprising that a Qdot with a single motor can switch directions on a mixed polarity bundle, given myoVa's inherent flexibility that allows it to turn up to 150o at actin filament intersections (Ali et al., 2007). These data also suggest that one or many myoVa molecules bound to a single cargo have the ability to jump tracks to neighboring actin filaments. With Qdot-labeling of the individual heads, high spatial resolution studies will confirm this on mixed polarity bundles, and determine whether the motors also wander on unipolar bundles.

How Do Myosin VI and Myosin Va Navigate Intersections And Cooperate On Actin Tracks While Transporting Cargo In Vitro?

Myosin Va (myoVa) and myosin VI (myoVI) are processive molecular motors that transport cargo on actin tracks in opposite directions. We have shown that myoVa can effectively maneuver through an in vitro cytoskeletal model system composed of actin filament intersections and Arp2/3 branches (Ali et al. 2007). Here we challenge Quantum dot (Qdot)-labeled expressed myoVI with actin filament intersections and observed that myoVI maneuvers through intersections with the following statistics: 38% turned left or right with equal probability; 28% crossed over the intersecting actin filament; 34% terminated their run. The myoVI cross over probability is twice that of myoVa suggesting that the range of the myoVI leading head's diffusional search may be longer than myoVa. Similar to myoVa, myoVI has significant flexibility allowing it to turn at intersection angles up to 155°. When multiple myoVI were attached a Qdot, the turning probability increased to 53% whereas the cross over probability decreased to 15%. MyoVa and myoVI may be colocalized to the same cargo in vivo and to determine how these oppositely directed motors might interact during cargo transport, we attached both motors in a 1:1 ratio to a Qdot. We observed two types of movement associated with these myoVa/myoVI-labeled Qdots. A given Qdot would move in both the plus- or minus-end direction for periods of time at velocities appropriate for the specific motor, suggesting that myoVa and myoVI take turns transporting the Qdot. Other Qdots moved continuously but at velocities suggesting that both motors are simultaneous interacting with actin and undergoing an effective “tug of war.” These studies may help characterize how actin-based motors deliver their cargo through the complex actin network.