Mushroom-shaped Structures Research Articles

DNS of bypass transition in entrance channel flow induced by boundary layer interaction

Developing entrance flows are of interest in a large number of application areas. They have been widely studied in the past, but many aspects of these flows are not yet fully understood. One of the questions concerns the stability and turbulent transition in the entrance region of a channel. The present study investigates by direct numerical simulation (DNS) the laminar–turbulent transition induced by boundary layer interaction in a spatially developing flow near the entrance of a channel, where the laminar flow is linearly stable. For uniform inlet flow conditions and at sufficiently high Reynolds number, the turbulent transition actually takes place inside the boundary layers and well before the fully developed regime. The transition of one of the two boundary layers is triggered near the entry section by small amplitude perturbations, such as the ones created by small isolated obstacles distributed on the wall. These generate elongated streaks, and their transient growth and breakdown lead to the turbulent transition of the boundary layer near the entrance region. The transition of the second boundary layer is induced by the interaction with the first further downstream. After the transition of the second boundary layer, turbulence occupies the whole channel width and a turbulent channel flow develops. The transition is analyzed with the help of an orthogonal decomposition of the solenoidal velocity field. The observed transition scenario differs from existing simulations of streak breakdown where the perturbation is optimized for a transition to occur in a region far away from the entry section. In our simulations, the perturbation setup generates a significant nonlinear growth of the streaks that are pushed away from the wall. Transient varicose instabilities, followed by sinuous instabilities induce the development of mushroom-shaped transitional structures in the outer region of the laminar boundary layer, that further break down downstream. The second boundary-layer transition resembles the one occurring under free-stream turbulence, with the generation of finite-length streaks and turbulent spots.

The hairpin vortex illusion

It has long been customary to assume that vortical structures in turbulent flows are synonymous with regions of rotational motion. Mathematical implementations of this idea using numerical and experimental velocity data from turbulent boundary layers reveal the presence of hairpin vortices, both singly and in groups called packets. However, vorticity may be present that does not directly cause rotation, and by failing to take this into account it is possible to be misled as to the true nature of the vortical structures. In this work a vortex filament scheme is applied to boundary layer flow that allows for a view of structures unrestrained by the requirement that they be regions of rotational motion. It is found that furrow-like streamwise aligned eruptions of the nominally spanwise near-wall vorticity overlying low-speed streaks are the primary structural feature of the transitioning boundary layer. These progress from an arch-like form at their upstream end to either one or two-lobed mushroom-shapes at their downstream end. The rotational motion associated with the furrows has the appearance of hairpins. Mushroom-shaped structures rapidly breakdown into complex forms in the post-transitional region that may have rotational signatures similar to that of packets.

Mnemonic microRNAs help make memories

Researchers find that two microRNAs prime the brain to learn.

Extracellular DNA in Biofilms

Extracellular DNA (eDNA) is an important biofilm component that was recently discovered. Its presence has been initially observed in biofilms of Pseudomonas aeruginosa, Streptococcus intermedius, Streptococcus mutans, then Enterococcus faecalis and staphylococci. Autolysis is the common mechanism by which eDNA is released. In P. aeruginosa eDNA is generated by lysis of a bacterial subpopulation, under control of quorum sensing system. In E. faecalis autolysis proceeds in a fratricide mode, resulting from a process similar to necrosis of eukaryotic cells. In Staphylococcus aureus autolysis originates by an altruistic suicide, i.e., a programmed cell death similar to apoptosis of eukaryotic cells. In S. aureus autolysis is mediated by murein hydrolase, while in S. epidermidis by the autolysin protein AtlE. In P. aeruginosa eDNA is located primarily in the stalks of mushroom-shaped multicellular structures. In S. aureus the crucial role of eDNA in stabilizing biofilm is highlighted by the disgregating effect of DNase I. eDNA represents an important mechanism for horizontal gene transfer in bacteria. eDNA and other microbial structural motifs are recognized by the innate immune system via the TLR family of pattern recognition receptors (PRRs).

Structure of supersonic jets with vortex generators at the nozzle exit

The spatial structure of the flow in a supersonic underexpanded jet exhausting from a convergent nozzle with vortex generators (chevrons) at the exit is experimentally studied. Disturbances of two types are observed during interaction of a single chevron and the main jet. The stronger disturbance is caused by the presence of the wake component and by generation of two streamwise vortices. The weaker disturbance is manifested in the form of perturbations of the Mach wave type propagating in the supersonic part of the shear layer of the main jet. Interaction of the set of chevrons with the jet flow leads to transformation of the stationary jet structure and to formation of mushroom-shaped large-scale vortex structures. The experimental and numerical data are demonstrated to be in reasonable agreement.

The Xanthomonas axonopodis pv. citri flagellum is required for mature biofilm and canker development

Xanthomonas axonopodis pv. citri (Xac) is the causative agent of citrus canker. This bacterium develops a characteristic biofilm on both biotic and abiotic surfaces. To evaluate the participation of the single flagellum of Xac in biofilm formation, mutants in the fliC (flagellin) and the flgE (hook) genes were generated. Swimming motility, assessed on 0.25 % agar plates, was markedly reduced in fliC and flgE mutants. However, the fliC and flgE mutants exhibited a flagellar-independent surface translocation on 0.5 % agar plates. Mutation of either the rpfF or the rpfC gene, which both encode proteins involved in cell-cell signalling mediated by diffusible signal factor (DSF), led to a reduction in both flagellar-dependent and flagellar-independent surface translocation, indicating a regulatory role for DSF in both types of motility. Confocal laser scanning microscopy of biofilms produced in static culture demonstrated that the flagellum is also involved in the formation of mushroom-shaped structures and water channels, and in the dispersion of biofilms. The presence of the flagellum was required for mature biofilm development on lemon leaf surfaces. The absence of flagellin produced a slight reduction in Xac pathogenicity and this reduction was more severe when the complete flagellum structure was absent.

Vortex Filament Simulation of the Turbulent Boundary Layer

A hybrid vortex filament scheme with the capability of simulating bounded turbulent flows is described. Viscous generation of new vortex elements at solid surfaces is accomplished through the intermediary step of solving the viscous vorticity transport equation on a thin boundary mesh via a finite difference and finite volume method. The transitional and turbulent boundary-layer flow past a wide, finite thickness, flat plate with rounded edges is computed with a view toward validating the methodology and gaining new insight into the structural aspects of transition. The predicted mean velocity and related statistics are well matched to experimental and numerical data. The representation of the flow through vortex filaments reveals that a distinction needs to be made between vortical structures, on one hand, and the rotational motion that they produce in the flowfield, on the other hand. In particular, hairpin-shaped regions that are commonly found by vortex identification schemes are found to not be structures in their own right, but rather the rotational signature of raised furrows in the surface vortex sheet. The latter overlie low-speed streaks and evolve to include ejected mushroom-shaped structures as well as spanwise vortices associated with roll-up.

Morphogenetic routes of long-term embryogenic callus culture of Areca catechu

Early morphogenetic events and repetitive embryogenesis from callus culture of betel nut palm (Areca catechu L.) were studied using scanning electron microscopy. On Murashige and Skoog (MS) medium supplemented with 2 mg dm-3 dicamba, callus culture has capacity to form plantlets via somatic embryogenesis and to form secondary embryos for about 4 years. However, various abnormal embryos without differentiation of the leaf sheath and shoot apical meristem were observed, which showed bell-shaped and then cup-shaped or mushroom-shaped structures. These abnormal embryos contained distinctive structures, including a disk-shape interior region, surfaces with grooves and a stalk-like posterior region. During subculture, these abnormal embryos enlarged, became deformed and gradually lose their shape and then converted into nodular, compact embryogenic callus. It was also found that secondary embryos originated from interior surfaces or posterior regions of abnormal embryos, and gave rise to the next cycle of normal and abnormal embryos.

Molecular Architecture of Synaptic Actin Cytoskeleton in Hippocampal Neurons Reveals a Mechanism of Dendritic Spine Morphogenesis

Excitatory synapses in the brain play key roles in learning and memory. The formation and functions of postsynaptic mushroom-shaped structures, dendritic spines, and possibly of presynaptic terminals, rely on actin cytoskeleton remodeling. However, the cytoskeletal architecture of synapses remains unknown hindering the understanding of synapse morphogenesis. Using platinum replica electron microscopy, we characterized the cytoskeletal organization and molecular composition of dendritic spines, their precursors, dendritic filopodia, and presynaptic boutons. A branched actin filament network containing Arp2/3 complex and capping protein was a dominant feature of spine heads and presynaptic boutons. Surprisingly, the spine necks and bases, as well as dendritic filopodia, also contained a network, rather than a bundle, of branched and linear actin filaments that was immunopositive for Arp2/3 complex, capping protein, and myosin II, but not fascin. Thus, a tight actin filament bundle is not necessary for structural support of elongated filopodia-like protrusions. Dynamically, dendritic filopodia emerged from densities in the dendritic shaft, which by electron microscopy contained branched actin network associated with dendritic microtubules. We propose that dendritic spine morphogenesis begins from an actin patch elongating into a dendritic filopodium, which tip subsequently expands via Arp2/3 complex-dependent nucleation and which length is modulated by myosin II-dependent contractility.

Dendritic Spine Remodeling After Spinal Cord Injury Alters Neuronal Signal Processing

Central sensitization, a prolonged hyperexcitability of dorsal horn nociceptive neurons, is a major contributor to abnormal pain processing after spinal cord injury (SCI). Dendritic spines are micron-sized dendrite protrusions that can regulate the efficacy of synaptic transmission. Here we used a computational approach to study whether changes in dendritic spine shape, density, and distribution can individually, or in combination, adversely modify the input-output function of a postsynaptic neuron to create a hyperexcitable neuronal state. The results demonstrate that a conversion from thin-shaped to more mature, mushroom-shaped spine structures results in enhanced synaptic transmission and fidelity, improved frequency-following ability, and reduced inhibitory gating effectiveness. Increasing the density and redistributing spines toward the soma results in a greater probability of action potential activation. Our results demonstrate that changes in dendritic spine morphology, documented in previous studies on spinal cord injury, contribute to the generation of pain following SCI.

Roles of type IV pili, flagellum‐mediated motility and extracellular DNA in the formation of mature multicellular structures in Pseudomonas aeruginosa biofilms

When grown as a biofilm in laboratory flow chambers Pseudomonas aeruginosa can develop mushroom-shaped multicellular structures consisting of distinct subpopulations in the cap and stalk portions. We have previously presented evidence that formation of the cap portion of the mushroom-shaped structures in P. aeruginosa biofilms occurs via bacterial migration and depends on type IV pili (Mol Microbiol 50: 61-68). In the present study we examine additional factors involved in the formation of this multicellular substructure. While pilA mutants, lacking type IV pili, are deficient in mushroom cap formation, pilH and chpA mutants, which are inactivated in the type IV pili-linked chemosensory system, showed only minor defects in cap formation. On the contrary, fliM mutants, which are non-flagellated, and cheY mutants, which are inactivated in the flagellum-linked chemotaxis system, were largely deficient in cap formation. Experiments involving DNase treatment of developing biofilms provided evidence that extracellular DNA plays a role in cap formation. Moreover, mutants that are deficient in quorum sensing-controlled DNA release formed microcolonies upon which wild-type bacteria could not form caps. These results constitute evidence that type IV pili, flagellum-mediated motility and quorum sensing-controlled DNA release are involved in the formation of mature multicellular structures in P. aeruginosa biofilms.

Numerical Analysis of the Fluid Mixing Behaviors in a Microchannel with a Circular Cylinder and an Oscillating Stirrer

An active micromixer equipped successively with a circular cylinder and an oscillating stirrer is designed by analyzing the mixing behaviors, i.e., the effect of the Karman vortex, the flow structure after the stirrer, etc. The mixing is calculated by using the D2Q9 model of lattice Boltzmann methods. In this study, we use the time-averaged mixing index formula DI , which was recently proposed for time-dependent flow. Four models for microchannel flows driven from combinations of the above devices are tested and the calculated mixing indices are compared. In models III and IV, one type of fluid rolls with the other type of fluid caused by the scroll effect due to the oscillation of the stirrer. Therefore, the concentration distributions becomes mushroom-shaped structures at Re = 80. These behaviors are developed up to the channel outlet. Then, the contact area and the residence time of fluid particles between the two fluids for mixing by diffusion are increased infinitely. In model IV, the mixing is enhanced and stabilized much more by the Karman vortex from the circular cylinder. We found that successive mixing by the cylinder and stirrer is a very effective method.

Multiple Roles of Biosurfactants in Structural Biofilm Development by Pseudomonas aeruginosa

Recent studies have indicated that biosurfactants produced by Pseudomonas aeruginosa play a role both in maintaining channels between multicellular structures in biofilms and in dispersal of cells from biofilms. Through the use of flow cell technology and enhanced confocal laser scanning microscopy, we have obtained results which suggest that the biosurfactants produced by P. aeruginosa play additional roles in structural biofilm development. We present genetic evidence that during biofilm development by P. aeruginosa, biosurfactants promote microcolony formation in the initial phase and facilitate migration-dependent structural development in the later phase. P. aeruginosa rhlA mutants, deficient in synthesis of biosurfactants, were not capable of forming microcolonies in the initial phase of biofilm formation. Experiments involving two-color-coded mixed-strain biofilms showed that P. aeruginosa rhlA mutants were defective in migration-dependent development of mushroom-shaped multicellular structures in the later phase of biofilm formation. Experiments involving three-color-coded mixed-strain P. aeruginosa biofilms demonstrated that the wild-type and rhlA and pilA mutant strains formed distinct subpopulations on top of each other dependent on their ability to migrate and produce biosurfactants.

Differentiation and Distribution of Colistin- and Sodium Dodecyl Sulfate-Tolerant Cells inPseudomonas aeruginosaBiofilms

During Pseudomonas aeruginosa flow cell biofilm development, the cell population differentiates into a nonmotile subpopulation which forms microcolonies and a migrating subpopulation which eventually colonizes the top of the microcolonies, resulting in the development of mushroom-shaped multicellular structures. The cap-forming subpopulation was found to develop tolerance to membrane-targeting antimicrobial agents, such as the cyclic cationic peptide colistin and the detergent sodium dodecyl sulfate. The stalk-forming subpopulation, on the other hand, was sensitive to the membrane-targeting antibacterial agents. All biofilm-associated cells were sensitive to the antibacterial agents when tested in standard plate assays. A mutation eliminating the production of type IV pili, and hence surface-associated motility, prevented the formation of regular mushroom-shaped structures in the flow cell biofilms, and the development of tolerance to the antimicrobial agents was found to be affected as well. Mutations in genes interfering with lipopolysaccharide modification (pmr) eliminated the biofilm-associated colistin tolerance phenotype. Experiments with a PAO1 strain harboring a pmr-gfp fusion showed that only the cap-forming subpopulation in biofilms treated with colistin expresses the pmr operon. These results suggest that increased antibiotic tolerance in biofilms may be a consequence of differentiation into distinct subpopulations with different phenotypic properties.

A characterization of DNA release in Pseudomonas aeruginosa cultures and biofilms

Pseudomonas aeruginosa produces extracellular DNA which functions as a cell-to-cell interconnecting matrix component in biofilms. Comparison of extracellular DNA and chromosomal DNA by the use of polymerase chain reaction and Southern analysis suggested that the extracellular DNA is similar to whole-genome DNA. Evidence that the extracellular DNA in P. aeruginosa biofilms and cultures is generated via lysis of a subpopulation of the bacteria was obtained through experiments where extracellular beta-galactosidase released from lacZ-containing P. aeruginosa strains was assessed. Experiments with the wild type and lasIrhlI, pqsA, pqsL and fliMpilA mutants indicated that the extracellular DNA is generated via a mechanism which is dependent on acyl homoserine lactone and Pseudomonas quinolone signalling, as well as on flagella and type IV pili. Microscopic investigation of flow chamber-grown wild-type P. aeruginosa biofilms stained with different DNA stains suggested that the extracellular DNA is located primarily in the stalks of mushroom-shaped multicellular structures, with a high concentration especially in the outer part of the stalks forming a border between the stalk-forming bacteria and the cap-forming bacteria. Biofilms formed by lasIrhlI, pqsA and fliMpilA mutants contained less extracellular DNA than biofilms formed by the wild type, and the mutant biofilms were more susceptible to treatment with sodium dodecyl sulphate than the wild-type biofilm.

Estimation of shock induced vorticity on irregular gaseous interfaces: a wavelet-based approach

We study the interaction of a shock with a density-stratified gaseous interface (Richtmyer–Meshkov instability) with localized jagged and irregular perturbations, with the aim of developing an analytical model of the vorticity deposition on the interface immediately after the passage of the shock. The jagged perturbations, meant to simulate machining errors on the surface of a laser fusion target, are characterized using Haar wavelets. Numerical solutions of the Euler equations show that the vortex sheet deposited on the jagged interface rolls into multiple mushroom-shaped dipolar structures which begin to merge before the interface evolves into a bubble-spike structure. The peaks in the distribution of x-integrated vorticity (vorticity integrated in the direction of the shock motion) decay in time as their bases widen, corresponding to the growth and merger of the mushrooms. However, these peaks were not seen to move significantly along the interface at early times i.e. t < 10 τ, where τ is the interface traversal time of the shock. We tested our analytical model against inviscid simulations for two test cases – a Mach 1.5 shock interacting with an interface with a density ratio of 3 and a Mach 10 shock interacting with a density ratio of 10. We find that this model captures the early time (t/τ ∼ 1) vorticity deposition (as characterized by the first and second moments of vorticity distributions) to within 5% of the numerical results.

Dynamics and Control of Biofilms of the Oligotrophic Bacterium Caulobacter crescentus

Caulobacter crescentus is an oligotrophic alpha-proteobacterium with a complex cell cycle involving sessile-stalked and piliated, flagellated swarmer cells. Because the natural lifestyle of C. crescentus intrinsically involves a surface-associated, sessile state, we investigated the dynamics and control of C. crescentus biofilms developing on glass surfaces in a hydrodynamic system. In contrast to biofilms of the well-studied Pseudomonas aeruginosa, Escherichia coli, and Vibrio cholerae, C. crescentus CB15 cells form biphasic biofilms, consisting predominantly of a cell monolayer biofilm and a biofilm containing densely packed, mushroom-shaped structures. Based on comparisons between the C. crescentus strain CB15 wild type and its holdfast (hfsA; DeltaCC0095), pili (DeltapilA-cpaF::Omegaaac3), motility (motA), flagellum (flgH) mutants, and a double mutant lacking holdfast and flagellum (hfsA; flgH), a model for biofilm formation in C. crescentus is proposed. For both biofilm forms, the holdfast structure at the tip of a stalked cell is crucial for mediating the initial attachment. Swimming motility by means of the single polar flagellum enhances initial attachment and enables progeny swarmer cells to escape from the monolayer biofilm. The flagellum structure also contributes to maintaining the mushroom structure. Type IV pili enhance but are not absolutely required for the initial adhesion phase. However, pili are essential for forming and maintaining the well-defined three-dimensional mushroom-shaped biofilm. The involvement of pili in mushroom architecture is a novel function for type IV pili in C. crescentus. These unique biofilm features demonstrate a spatial diversification of the C. crescentus population into a sessile, "stem cell"-like subpopulation (monolayer biofilm), which generates progeny cells capable of exploring the aqueous, oligotrophic environment by swimming motility and a subpopulation accumulating in large mushroom structures.

Position-Specified Formation of Epitaxial Si Grains on Thermally Oxidized Si(001) Surfaces via Isolated Nanodots

We report position-specified fabrication of epitaxial Si grains on an amorphous thermal oxide layer on Si(001) substrates. This process takes advantage of unique features of surface-sensitive deposition chemistry and nanoscale oxidation phenomena. To make the grown grains epitaxial with respect to the Si substrate, growth was initiated from Si nanodots that had been isolated from the substrate by the oxidation of mushroom-shaped overgrown structures. The position of each grain is controlled by the use of a lithographically patterned mask layer. Mechanisms of the oxidation-induced nanodot isolation, which is a key step in this fabrication process, are discussed. The present technique is applicable to the integration of various single-crystal materials onto Si substrates.

Involvement of bacterial migration in the development of complex multicellular structures in Pseudomonas aeruginosa biofilms.

Detailed knowledge of the developmental process from single cells scattered on a surface to complex multicellular biofilm structures is essential in order to create strategies to control biofilm development. In order to study bacterial migration patterns during Pseudomonas aeruginosa biofilm development, we have performed an investigation with time-lapse confocal laser scanning microscopy of biofilms formed by various combinations of colour-coded P. aeruginosa wild type and motility mutants. We show that mushroom-shaped multicellular structures in P. aeruginosa biofilms can form in a sequential process involving a non-motile bacterial subpopulation and a migrating bacterial subpopulation. The non-motile bacteria form the mushroom stalks by growth in certain foci of the biofilm. The migrating bacteria form the mushroom caps by climbing the stalks and aggregating on the tops in a process which is driven by type-IV pili. These results lead to a new model for biofilm formation by P. aeruginosa.

Experiments on the stability of sinusoidal flow over a circular cylinder

The instabilities in a sinusoidally oscillating non-separated flow over smooth circular cylinders in the range of Keulegan–Carpenter numbers, K, from about 0.02 to 1 and Stokes numbers, β, from about 103 to 1.4 × 106 have been observed from inception to chaos using several high-speed imagers and laser-induced fluorescence. The instabilities ranged from small quasi-coherent structures, as in Stokes flow over a flat wall (Sarpkaya 1993), to three-dimensional spanwise perturbations because of the centrifugal forces induced by the curvature of the boundary layer (Taylor–Görtler instability). These gave rise to streamwise-oriented counter-rotating vortices or mushroom-shaped coherent structures as K approached the Kh values theoretically predicted by Hall (1984). Further increases in K for a given β led first to complex interactions between the coherent structures and then to chaotic motion. The mapping of the observations led to the delineation of four states of flow in the (K, β)-plane: stable, marginal, unstable, and chaotic.