The dynamic behavior of cytoplasmic F-actin in growing hyphae

Summary A dynamic population of cytoplasmic F-actin was observed with electroporated rhodamine phalloidin (RP) staining in growing hyphae ofSaprolegnia ferax. This central actin population was distinct from the fibrillar peripheral network previously described in chemically fixed hyphae in that it was diffuse, pervaded the entire cytoplasm and was most concentrated in the central cytoplasm 8.4 m from the tip. The peripheral network did not stain with electroporated RP. The apical concentration of central cytoplasmic actin was only present in growing hyphae and developed prior to tip extension. It co-localized with the polarized distribution of mitochondria and endoplasmic reticulum in the tip, suggesting that it functions in positioning these organelles during tip growth. Within the central actin there was a consistent apical cleft which only occurred in growing hyphae and whose position predicted the direction of tip growth. This cleft was coincident with the known accumulation of apical wall vesicles, suggesting that it is either established by vesicle exclusion of the central actin network or is permeated by a portion of the in vivo unstained peripheral network. Photobleaching studies showed that in both growing and non-growing hyphae, cytoplasmic actin continually and rapidly moved from subapical regions to the tip where it accumulated. It mostly moved forward at the rate of tip growth, while some also left the tip, presumably to populate subapical regions.Abbreviations RP rhodamine phalloidin - F-actin filamentous actin - DIC Nomarski differential interference contrast - FITC fluorescein isothiocyanate     

Evidence for the concentration of F-actin and myosin in synapses and in the plasmalemmal zone of axons

Fluorescent staining with phalloidin, a specific probe for F-actin, and antibodies to non-muscle myosin from thymus was used to localize actin and myosin in brain neurons of the rat. Phalloidin and anti-myosin displayed a preferential affinity for synaptic formations in the cerebellum, the brain stem, the spinal cord and the retina. The conclusion that F-actin and myosin are concentrated in synaptic terminals was further established by simultaneous staining of isolated rat brain synaptosomes with phalloidin and anti-thymus myosin as well as by the demonstration of a selective affinity of anti-thymus myosin for a 200 000-Mr protein band in gel electrophoretograms of synaptic fractions. Apart from synaptic areas, phalloidin and anti-thymus myosin reacted also, albeit rather weakly, with a narrow circumferential layer located in the area of the plasma membrane of virtually all axons in the white matter and the spinal roots. The spatial coexistence of myosin and actin in brain synapses and axons is of particular interest in view of various dynamic functions that have been proposed for axonal and synaptic actin.     

A deep dense inception network for protein beta-turn prediction

Beta-turn prediction is useful in protein function studies and experimental design. Although recent approaches using machine-learning techniques such as support vector machine (SVM), neural networks, and K nearest neighbor have achieved good results for beta-turn prediction, there is still significant room for improvement. As previous predictors utilized features in a sliding window of 4-20 residues to capture interactions among sequentially neighboring residues, such feature engineering may result in incomplete or biased features and neglect interactions among long-range residues. Deep neural networks provide a new opportunity to address these issues. Here, we proposed a deep dense inception network (DeepDIN) for beta-turn prediction, which takes advantage of the state-of-the-art deep neural network design of dense networks and inception networks. A test on a recent BT6376 benchmark data set shows that DeepDIN outperformed the previous best tool BetaTPred3 significantly in both the overall prediction accuracy and the nine-type beta-turn classification accuracy. A tool, called MUFold-BetaTurn, was developed, which is the first beta-turn prediction tool utilizing deep neural networks. The tool can be downloaded at http://dslsrv8.cs.missouri.edu/~cf797/MUFoldBetaTurn/download.html .     

Stabilization of exocytosis by dynamic F-actin coating of zymogen granules in pancreatic acini

Reorganization of F-actin in the apical region of mouse pancreatic acinar cells during Ca(2+)-dependent exocytosis of zymogen granules was investigated by two-photon excitation microscopy with intact acini. Granules were rapidly coated with F-actin in response to either agonist stimulation or photolysis of a caged-Ca(2+) compound. Such F-actin coating occurred exclusively at the surface of granules undergoing exocytosis and was prevented either by latrunculin-A, which inhibits actin polymerization, or by Clostridium botulinum exoenzyme C3, which inhibits the small GTPase Rho. Latrunculin-A or exoenzyme C3 also triggered the formation of vacuoles in acinar cells, a characteristic of acute pancreatitis. Stimulation of acini with high concentrations of cholecystokinin, which cause acute pancreatitis in mice, also impaired the F-actin coating of granules and induced vacuole formation. Latrunculin-A reduced the latency to exocytosis but did not affect the total number of exocytic events, suggesting that F-actin slows and further stabilizes exocytosis by facilitating F-actin coating. Rho-dependent F-actin coating of granule membranes thus stabilizes exocytic structures and is necessary for physiological progression of sequetial compound exocytosis in the exocrine pancreas and for prevention of acute pancreatitis.     

A biologically inspired neural network for dynamic programming

An artificial neural network with a two-layer feedback topology and generalized recurrent neurons, for solving nonlinear discrete dynamic optimization problems, is developed. A direct method to assign the weights of neural networks is presented. The method is based on Bellmann's Optimality Principle and on the interchange of information which occurs during the synaptic chemical processing among neurons. The neural network based algorithm is an advantageous approach for dynamic programming due to the inherent parallelism of the neural networks; further it reduces the severity of computational problems that can occur in methods like conventional methods. Some illustrative application examples are presented to show how this approach works out including the shortest path and fuzzy decision making problems.     

Coupled myosin VI motors facilitate unidirectional movement on an F-actin network

Unconventional myosins interact with the dense cortical actin network during processes such as membrane trafficking, cell migration, and mechanotransduction. Our understanding of unconventional myosin function is derived largely from assays that examine the interaction of a single myosin with a single actin filament. In this study, we have developed a model system to study the interaction between multiple tethered unconventional myosins and a model F-actin cortex, namely the lamellipodium of a migrating fish epidermal keratocyte. Using myosin VI, which moves toward the pointed end of actin filaments, we directly determine the polarity of the extracted keratocyte lamellipodium from the cell periphery to the cell nucleus. We use a combination of experimentation and simulation to demonstrate that multiple myosin VI molecules can coordinate to efficiently transport vesicle-size cargo over 10 µm of the dense interlaced actin network. Furthermore, several molecules of monomeric myosin VI, which are nonprocessive in single molecule assays, can coordinate to transport cargo with similar speeds as dimers.     

Endocytosis and the development of cell polarity in yeast require a dynamic F-actin cytoskeleton

Studies using drugs that cause the disassembly of filamentous actin (F-actin) have demonstrated the importance of an intact actin cytoskeleton for polarised secretion by yeast cells [1,2]. To address the level of dynamic turnover needed for such processes, however, drugs or mutants that confer stabilising properties on F-actin are needed. Jasplakinolide is the only readily available drug that stabilises F-actin structures both in vivo and in vitro [3-6]. Yeast strains have been generated in which two of the ABC multidrug resistance transporter genes have been deleted, rendering normally jasplakinolide-resistant yeast cells sensitive to its effects. Treatment of these cells with jasplakinolide caused rapid and dramatic effects on the actin cytoskeleton, resulting in the accumulation of single large actin structures in cells. These structures, however, still contained components that are normally associated with cortical actin patches. A dynamic actin cytoskeleton was found to be critical for the generation of cell polarity and endocytosis.     

A two-scale network dynamic model for human mobility process

The technological changes and educational expansion have created the heterogeneity in the human species. Clearly, this heterogeneity generates a structure in the population dynamics, namely: citizen, permanent resident, visitor, and etc. Furthermore, as the heterogeneity in the population increases, the human mobility between meta-populations patches also increases. Depending on spatial scales, a meta-population patch can be decomposed into sub-patches, for examples: homes, neighborhoods, towns, etc. Members of the population can move between the sub-patches. The dynamics of human mobility in a heterogeneous and scaled structured population is still its infancy level. In this work, an attempt is made to investigate the human mobility dynamics of heterogeneous and scaled structured population. We present a two scaled human mobility model for a meta-population. The sub regions and regions are interlinked via intra-and inter regional transport network systems. Under various types of growth order assumptions on the intra and interregional residence times of the residents of a sub region, different patterns of static behavior of the mobility process is studied. In addition, the results reveal that the system has a natural tendency to quarantine itself without total breaking a link in the transportation network system. Moreover, there is a threshold point for the largest intra regional visiting time of residents of a given sub region that leads to either a total isolation of the residents from other sub regions within the region or a partial isolation of residents from some of the sub regions within the region.     

A network model with auto-oscillating output and dynamic connections

A major problem that researchers attempting to elaborate mathematical models of neurophysiological and/or psychophysiological processes are confronted with is the identification of the mechanisms that give rise, in a neural network, to oscillatory behavior, either spontaneous or induced by external stimuli. The present work starts by considering a network model of a central pattern generator (CPG), introduced by Sompolinsky and co-authors. The present authors try to generalize this model to a wider range of biological situations, by introducing into it dynamic adjustments of connections among the processing units. Although the study performed so far is quite preliminary, some analytical considerations can be presented, supported by the results of numerical simulations, which show always a relaxation of the network toward specific stable states.     

A role for F-actin in hexokinase-mediated glucose signaling

HEXOKINASE1 (HXK1) from Arabidopsis (Arabidopsis thaliana) has dual roles in glucose (Glc) signaling and in Glc phosphorylation. The cellular context, though, for HXK1 function in either process is not well understood. Here we have shown that within normal experimental detection limits, AtHXK1 is localized continuously to mitochondria. Two mitochondrial porin proteins were identified as capable of binding to overexpressed HXK1 protein, both in vivo and in vitro. We also found that AtHXK1 can be associated with its structural homolog, F-actin, based on their coimmunoprecipitation from transgenic plants that overexpress HXK1-FLAG or from transient expression assays, and based on their localization in leaf cells after cryofixation. This association might be functionally important because Glc signaling in protoplast transient expression assays is compromised by disruption of F-actin. We also demonstrate that Glc treatment of Arabidopsis seedlings rapidly and reversibly disrupts fine mesh actin filaments. The possible roles of actin in HXK-dependent Glc signaling are discussed.     

A dynamic Bayesian network approach to protein secondary structure prediction

Background  

Protein secondary structure prediction method based on probabilistic models such as hidden Markov model (HMM) appeals to many because it provides meaningful information relevant to sequence-structure relationship. However, at present, the prediction accuracy of pure HMM-type methods is much lower than that of machine learning-based methods such as neural networks (NN) or support vector machines (SVM).     

Dexamethasone alters F-actin architecture and promotes cross-linked actin network formation in human trabecular meshwork tissue

Elevated intraocular pressure is an important risk factor for the development of glaucoma, a leading cause of irreversible blindness. This ocular hypertension is due to increased hydrodynamic resistance to the drainage of aqueous humor through specialized outflow tissues, including the trabecular meshwork (TM) and the endothelial lining of Schlemm's canal. We know that glucocorticoid therapy can cause increased outflow resistance and glaucoma in susceptible individuals, that the cytoskeleton helps regulate aqueous outflow resistance, and that glucocorticoid treatment alters the actin cytoskeleton of cultured TM cells. Our purpose was to characterize the actin cytoskeleton of cells in outflow pathway tissues in situ, to characterize changes in the cytoskeleton due to dexamethasone treatment in situ, and to compare these with changes observed in cell culture. Human ocular anterior segments were perfused with or without 10(-7) M dexamethasone, and F-actin architecture was investigated by confocal laser scanning microscopy. We found that outflow pathway cells contained stress fibers, peripheral actin staining, and occasional actin "tangles." Dexamethasone treatment caused elevated IOP in several eyes and increased overall actin staining, with more actin tangles and the formation of cross-linked actin networks (CLANs). The actin architecture in TM tissues was remarkably similar to that seen in cultured TM cells. Although CLANs have been reported previously in cultured cells, this is the first report of CLANs in tissue. These cytoskeletal changes may be associated with increased aqueous humor outflow resistance after ocular glucocorticoid treatment.     

A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence

Pseudomonas aeruginosa is a metabolically versatile bacterium that is found in a wide range of biotic and abiotic habitats. It is a major human opportunistic pathogen causing numerous acute and chronic infections. The critical traits contributing to the pathogenic potential of P. aeruginosa are the production of a myriad of virulence factors, formation of biofilms and antibiotic resistance. Expression of these traits is under stringent regulation, and it responds to largely unidentified environmental signals. This review is focused on providing a global picture of virulence gene regulation in P. aeruginosa. In addition to key regulatory pathways that control the transition from acute to chronic infection phenotypes, some regulators have been identified that modulate multiple virulence mechanisms. Despite of a propensity for chaotic behaviour, no chaotic motifs were readily observed in the P. aeruginosa virulence regulatory network. Having a ‘birds-eye’ view of the regulatory cascades provides the forum opportunities to pose questions, formulate hypotheses and evaluate theories in elucidating P. aeruginosa pathogenesis. Understanding the mechanisms involved in making P. aeruginosa a successful pathogen is essential in helping devise control strategies.     

A dynamic neural network with temporal coding and functional connectivity

A neural network model capable of altering its pattern classifying properties by program input is proposed. Here the “program input” is another source of input besides the pattern input. Unlike most neural network models, this model runs as a deterministic point process of spikes in continuous time; connections among neurons have finite delays, which are set randomly according to a normal distribution. Furthermore, this model utilizes functional connectivity which is dynamic connectivity among neurons peculiar to temporal-coding neural networks with short neuronal decay time constants. Computer simulation of the proposed network has been performed, and the results are considered in light of experimental results shown recently for correlated firings of neurons. Received: 6 December 1996 / Accepted in revised form: 15 September 1997     

Yeast-to-hyphal transition triggers formin-dependent Golgi localization to the growing tip in Candida albicans

Rapid and long-distance secretion of membrane components is critical for hyphal formation in filamentous fungi, but the mechanisms responsible for polarized trafficking are not well understood. Here, we demonstrate that in Candida albicans, the majority of the Golgi complex is redistributed to the distal region during hyphal formation. Randomly distributed Golgi puncta in yeast cells cluster toward the growing tip during hyphal formation, remain associated with the distal portion of the filament during its extension, and are almost absent from the cell body. This restricted Golgi localization pattern is distinct from other organelles, including the endoplasmic reticulum, vacuole and mitochondria, which remain distributed throughout the cell body and hypha. Hyphal-induced positioning of the Golgi and the maintenance of its structural integrity requires actin cytoskeleton, but not microtubules. Absence of the formin Bni1 causes a hyphal-specific dispersal of the Golgi into a haze of finely dispersed vesicles with a sedimentation density no different from that of normal Golgi. These results demonstrate the existence of a hyphal-specific, Bni1-dependent cue for Golgi integrity and positioning at the distal portion of the hyphal tip, and suggest that filamentous fungi have evolved a novel strategy for polarized secretion, involving a redistribution of the Golgi to the growing tip.     

Thiol oxidation of actin produces dimers that enhance the elasticity of the F-actin network

Slow oxidation of sulfhydryls, forming covalently linked actin dimers and higher oligomers, accounts for increases in the shear elasticity of purified actin observed after aging. Disulfide-bonded actin dimers are incorporated into F-actin during polymerization and generate cross-links between actin filaments. The large gel strength of oxidized actin (>100 Pa for 1 mg/ml) in the absence of cross-linking proteins falls to within the theoretically predicted order of magnitude for uncross-linked actin filament networks (1 Pa) with the addition of sufficient concentrations of reducing agents such as 5 mM dithiothreitol or 10 mM beta-mercaptoethanol. As little as 1 gelsolin/1000 actin subunits also lowers the high storage modulus of oxidized actin. The effects of gelsolin may be both to increase filament number as it severs F-actin and to cover the barbed end of an actin filament, which otherwise might cross-link to the side of another filament via an actin dimer. These new findings may explain why previous studies of actin rheology report a wide range of values when purified actin is polymerized without added regulatory proteins.