Nanodysferlins support membrane repair and binding to TRIM72/MG53 but do not localize to t-tubules or stabilize Ca2+ signaling.

Mutations in the DYSF gene, encoding the protein dysferlin, lead to several forms of muscular dystrophy. In healthy skeletal muscle, dysferlin concentrates in the transverse tubules and is involved in repairing the sarcolemma and stabilizing Ca2+ signaling after membrane disruption. The DYSF gene encodes 7-8 C2 domains, several Fer and Dysf domains, and a C-terminal transmembrane sequence. Because its coding sequence is too large to package in adeno-associated virus, the full-length sequence is not amenable to current gene delivery methods. Thus, we have examined smaller versions of dysferlin, termed "nanodysferlins," designed to eliminate several C2 domains, specifically C2 domains D, E, and F; B, D, and E; and B, D, E, and F. We also generated a variant by replacing eight amino acids in C2G in the nanodysferlin missing domains D through F. We electroporated dysferlin-null A/J mouse myofibers with Venus fusion constructs of these variants, or as untagged nanodysferlins together with GFP, to mark transfected fibers We found that, although these nanodysferlins failed to concentrate in transverse tubules, three of them supported membrane repair after laser wounding while all four bound the membrane repair protein, TRIM72/MG53, similar to WT dysferlin. By contrast, they failed to suppress Ca2+ waves after myofibers were injured by mild hypoosmotic shock. Our results suggest that the internal C2 domains of dysferlin are required for normal t-tubule localization and Ca2+ signaling and that membrane repair does not require these C2 domains.

A novel image-based method for simultaneous counting of Lactobacillus and Saccharomyces in mixed culture fermentation.

Mixed microorganism cultures are prevalent in the food industry. A variety of microbiological mixtures have been used in these unique fermenting processes to create distinctive flavor profiles and potential health benefits. Mixed cultures are typically not well characterized, which may be due to the lack of simple measurement tools. Image-based cytometry systems have been employed to automatically count bacteria or yeast cells. In this work, we aim to develop a novel image cytometry method to distinguish and enumerate mixed cultures of yeast and bacteria in beer products. Cellometer X2 from Nexcelom was used to count of Lactobacillus plantarum and Saccharomyces cerevisiae in mixed cultures using fluorescent dyes and size exclusion image analysis algorithm. Three experiments were performed for validation. (1) Yeast and bacteria monoculture titration, (2) mixed culture with various ratios, and (3) monitoring a Berliner Weisse mixed culture fermentation. All experiments were validated by comparing to manual counting of yeast and bacteria colony formation. They were highly comparable with ANOVA analysis showing p-value > 0.05. Overall, the novel image cytometry method was able to distinguish and count mixed cultures consistently and accurately, which may provide better characterization of mixed culture brewing applications and produce higher quality products.

Propofol Anesthesia Alters Cortical Traveling Waves.

Oscillatory dynamics in cortex seem to organize into traveling waves that serve a variety of functions. Recent studies show that propofol, a widely used anesthetic, dramatically alters cortical oscillations by increasing slow-delta oscillatory power and coherence. It is not known how this affects traveling waves. We compared traveling waves across the cortex of non-human primates before, during, and after propofol-induced loss of consciousness (LOC). After LOC, traveling waves in the slow-delta (∼1 Hz) range increased, grew more organized, and traveled in different directions relative to the awake state. Higher frequency (8-30 Hz) traveling waves, by contrast, decreased, lost structure, and switched to directions where the slow-delta waves were less frequent. The results suggest that LOC may be due, in part, to increases in the strength and direction of slow-delta traveling waves that, in turn, alter and disrupt traveling waves in the higher frequencies associated with cognition.

The C2 domains of dysferlin: roles in membrane localization, Ca2+ signalling and sarcolemmal repair.

Dysferlin is an integral membrane protein of the transverse tubules of skeletal muscle that is mutated or absent in limb girdle muscular dystrophy 2B and Miyoshi myopathy. Here we examine the role of dysferlin's seven C2 domains, C2A through C2G, in membrane repair and Ca2+ release, as well as in targeting dysferlin to the transverse tubules of skeletal muscle. We report that deletion of either domain C2A or C2B inhibits membrane repair completely, whereas deletion of C2C, C2D, C2E, C2F or C2G causes partial loss of membrane repair that is exacerbated in the absence of extracellular Ca2+ . Deletion of C2C, C2D, C2E, C2F or C2G also causes significant changes in Ca2+ release, measured as the amplitude of the Ca2+ transient before or after hypo-osmotic shock and the appearance of Ca2+ waves. Most deletants accumulate in endoplasmic reticulum. Only the C2A domain can be deleted without affecting dysferlin trafficking to transverse tubules, but Dysf-ΔC2A fails to support normal Ca2+ signalling after hypo-osmotic shock. Our data suggest that (i) every C2 domain contributes to repair; (ii) all C2 domains except C2B regulate Ca2+ signalling; (iii) transverse tubule localization is insufficient for normal Ca2+ signalling; and (iv) Ca2+ dependence of repair is mediated by C2C through C2G. Thus, dysferlin's C2 domains have distinct functions in Ca2+ signalling and sarcolemmal membrane repair and may play distinct roles in skeletal muscle. KEY POINTS: Dysferlin, a transmembrane protein containing seven C2 domains, C2A through C2G, concentrates in transverse tubules of skeletal muscle, where it stabilizes voltage-induced Ca2+ transients and participates in sarcolemmal membrane repair. Each of dysferlin's C2 domains except C2B regulate Ca2+ signalling. Localization of dysferlin variants to the transverse tubules is not sufficient to support normal Ca2+ signalling or membrane repair. Each of dysferlin's C2 domains contributes to sarcolemmal membrane repair. The Ca2+ dependence of membrane repair is mediated by C2C through C2G. Dysferlin's C2 domains therefore have distinct functions in Ca2+ signalling and sarcolemmal membrane repair.

Traveling waves in the prefrontal cortex during working memory.

Neural oscillations are evident across cortex but their spatial structure is not well- explored. Are oscillations stationary or do they form "traveling waves", i.e., spatially organized patterns whose peaks and troughs move sequentially across cortex? Here, we show that oscillations in the prefrontal cortex (PFC) organized as traveling waves in the theta (4-8Hz), alpha (8-12Hz) and beta (12-30Hz) bands. Some traveling waves were planar but most rotated. The waves were modulated during performance of a working memory task. During baseline conditions, waves flowed bidirectionally along a specific axis of orientation. Waves in different frequency bands could travel in different directions. During task performance, there was an increase in waves in one direction over the other, especially in the beta band.

Ca2+ dependence and kinetics of cell membrane repair after electropermeabilization.

Electroporation, in particular with nanosecond pulses, is an efficient technique to generate nanometer-size membrane lesions without the use of toxins or other chemicals. The restoration of the membrane integrity takes minutes and is only partially dependent on [Ca2+]. We explored the impact of Ca2+ on the kinetics of membrane resealing by monitoring the entry of a YO-PRO-1 dye (YP) in BPAE and HEK cells. Ca2+ was promptly removed or added after the electric pulse (EP) by a fast-step perfusion. YP entry increased sharply after the EP and gradually slowed down following either a single- or a double-exponential function. In BPAE cells permeabilized by a single 300- or 600-ns EP at 14 kV/cm in a Ca2+-free medium, perfusion with 2 mM of external Ca2+ advanced the 90% resealing and reduced the dye uptake about twofold. Membrane restoration was accomplished by a combination of fast, Ca2+-independent resealing (τ = 13-15 s) and slow, Ca2+-dependent processes (τ ~70 s with Ca2+ and ~ 110 s or more without it). These time constants did not change when the membrane damage was doubled by increasing EP duration from 300 to 600 ns. However, injury by microsecond-range EP (300 and 600 µs) took longer to recover even when the membrane initially was less damaged, presumably because of the larger size of pores made in the membrane. Full membrane recovery was not prevented by blocking both extra- and intracellular Ca2+ (by loading cells with BAPTA or after Ca2+ depletion from the reticulum), suggesting the recruitment of unknown Ca2+-independent repair mechanisms.

The impact of a closed-loop thalamocortical model on the spatiotemporal dynamics of cortical and thalamic traveling waves.

Propagation of activity in spatially structured neuronal networks has been observed in awake, anesthetized, and sleeping brains. How these wave patterns emerge and organize across brain structures, and how network connectivity affects spatiotemporal neural activity remains unclear. Here, we develop a computational model of a two-dimensional thalamocortical network, which gives rise to emergent traveling waves similar to those observed experimentally. We illustrate how spontaneous and evoked oscillatory activity in space and time emerge using a closed-loop thalamocortical architecture, sustaining smooth waves in the cortex and staggered waves in the thalamus. We further show that intracortical and thalamocortical network connectivity, cortical excitation/inhibition balance, and thalamocortical or corticothalamic delay can independently or jointly change the spatiotemporal patterns (radial, planar and rotating waves) and characteristics (speed, direction, and frequency) of cortical and thalamic traveling waves. Computer simulations predict that increased thalamic inhibition induces slower cortical frequencies and that enhanced cortical excitation increases traveling wave speed and frequency. Overall, our results provide insight into the genesis and sustainability of thalamocortical spatiotemporal patterns, showing how simple synaptic alterations cause varied spontaneous and evoked wave patterns. Our model and simulations highlight the need for spatially spread neural recordings to uncover critical circuit mechanisms for brain functions.

An Excitable Ras/PI3K/ERK Signaling Network Controls Migration and Oncogenic Transformation in Epithelial Cells.

The Ras/PI3K/extracellular signal-regulated kinases (ERK) signaling network plays fundamental roles in cell growth, survival, and migration and is frequently activated in cancer. Here, we show that the activities of the signaling network propagate as coordinated waves, biased by growth factor, which drive actin-based protrusions in human epithelial cells. The network exhibits hallmarks of biochemical excitability: the annihilation of oppositely directed waves, all-or-none responsiveness, and refractoriness. Abrupt perturbations to Ras, PI(4,5)P2, PI(3,4)P2, ERK, and TORC2 alter the threshold, observations that define positive and negative feedback loops within the network. Oncogenic transformation dramatically increases the wave activity, the frequency of ERK pulses, and the sensitivity to EGF stimuli. Wave activity was progressively enhanced across a series of increasingly metastatic breast cancer cell lines. The view that oncogenic transformation is a shift to a lower threshold of excitable Ras/PI3K/ERK network, caused by various combinations of genetic insults, can facilitate the assessment of cancer severity and effectiveness of interventions.

Traveling and standing waves mediate pattern formation in cellular protrusions.

The mechanisms regulating protrusions during amoeboid migration exhibit excitability. Theoretical studies have suggested the possible coexistence of traveling and standing waves in excitable systems. Here, we demonstrate the direct transformation of a traveling into a standing wave and establish conditions for the stability of this conversion. This theory combines excitable wave stopping and the emergence of a family of standing waves at zero velocity, without altering diffusion parameters. Experimentally, we show the existence of this phenomenon on the cell cortex of some Dictyostelium and mammalian mutant strains. We further predict a template that encompasses a spectrum of protrusive phenotypes, including pseudopodia and filopodia, through transitions between traveling and standing waves, allowing the cell to switch between excitability and bistability. Overall, this suggests that a previously-unidentified method of pattern formation, in which traveling waves spread, stop, and turn into standing waves that rearrange to form stable patterns, governs cell motility.

Experimental demonstration of broadband solar absorption beyond the lambertian limit in certain thin silicon photonic crystals.

The tantalizing possibility of 31% solar-to-electric power conversion efficiency in thin film crystalline silicon solar cell architectures relies essentially on solar absorption well beyond the Lambertian light trapping limit (Bhattacharya and John in Nat Sci Rep 9:12482, 2019). Up to now, no solar cell architecture has exhibited above-Lambertian solar absorption, integrated over the broad solar spectrum. In this work, we experimentally demonstrate two types of photonic crystal (PhC) solar cells architectures that exceed Lambertian light absorption, integrated over the entire 300-1,200 nm wavelength band. These measurements confirm theoretically predicted wave-interference-based optical resonances associated with long lifetime, slow-light modes and parallel-to-interface refraction. These phenomena are beyond the realm of ray optics. Using two types of 10-µm thick PhC's, first an Inverted Pyramid PhC with lattice constant a = 2,500 nm and second a Teepee PhC with a = 1,200 nm, we observe solar absorption well beyond the Lambertian limit over λ = 950-1,200 nm. Our absorption measurements correspond to the maximum-achievable-photocurrent-density (MAPD), under AM1.5G illumination at 4-degree incident angle, 41.29 and 41.52 mA/cm2 for the Inverted Pyramid and Teepee PhC, respectively, in agreement with wave-optics, numerical simulations. Both of these values exceed the MAPD (= 39.63 mA/cm2) corresponding to the Lambertian limit for a 10-µm thick silicon for solar absorption over the 300-1,200 nm band.

Beyond 30% Conversion Efficiency in Silicon Solar Cells: A Numerical Demonstration.

We demonstrate through precise numerical simulations the possibility of flexible, thin-film solar cells, consisting of crystalline silicon, to achieve power conversion efficiency of 31%. Our optimized photonic crystal architecture consists of a 15 µm thick cell patterned with inverted micro-pyramids with lattice spacing comparable to the wavelength of near-infrared light, enabling strong wave-interference based light trapping and absorption. Unlike previous photonic crystal designs, photogenerated charge carrier flow is guided to a grid of interdigitated back contacts with optimized geometry to minimize Auger recombination losses due to lateral current flow. Front and back surface fields provided by optimized Gaussian doping profiles are shown to play a vital role in enhancing surface passivation. We carefully delineate the drop in power conversion efficiency when surface recombination velocities exceed 100 cm/s and the doping profiles deviate from prescribed values. These results are obtained by exact numerical simulation of Maxwell's wave equations for light propagation throughout the cell architecture and a state-of-the-art model for charge carrier transport and Auger recombination.

Wave patterns organize cellular protrusions and control cortical dynamics.

Cellular protrusions are typically considered as distinct structures associated with specific regulators. However, we found that these regulators coordinately localize as propagating cortical waves, suggesting a common underlying mechanism. These molecular events fell into two excitable networks, the signal transduction network STEN and the cytoskeletal network CEN with different wave substructures. Computational studies using a coupled-network model reproduced these features and showed that the morphology and kinetics of the waves depended on strengths of feedback loops. Chemically induced dimerization at multiple nodes produced distinct, coordinated alterations in patterns of other network components. Taken together, these studies indicate: STEN positive feedback is mediated by mutual inhibition between Ras/Rap and PIP2, while negative feedback depends on delayed PKB activation; PKBs link STEN to CEN; CEN includes positive feedback between Rac and F-actin, and exerts fast positive and slow negative feedbacks to STEN The alterations produced protrusions resembling filopodia, ruffles, pseudopodia, or lamellipodia, suggesting that these structures arise from a common regulatory mechanism and that the overall state of the STEN-CEN system determines cellular morphology.

Publisher Correction: Integrating chemical and mechanical signals through dynamic coupling between cellular protrusions and pulsed ERK activation.

The original version of this Article contained an error in the spelling of the author Jr-Ming Yang, which was incorrectly given as J.-Ming Yang. This has now been corrected in both the PDF and HTML versions of the Article.

Publisher Correction: Integrating chemical and mechanical signals through dynamic coupling between cellular protrusions and pulsed ERK activation.

In the original version of this Article, the label "RTK" in Figure 6a was inadvertently changed to "RTE". This has now been corrected in the PDF and HTML versions of the Article.

Controlling excitable wave behaviors through the tuning of three parameters.

Excitable systems are a class of dynamical systems that can generate self-sustaining waves of activity. These waves are known to manifest differently under diverse conditions, whereas some travel as planar or radial waves, and others evolve into rotating spirals. Excitable systems can also form stationary stable patterns through standing waves. Under certain conditions, these waves are also known to be reflected at no-flux boundaries. Here, we review the basic characteristics of these four entities: traveling, rotating, standing and reflected waves. By studying their mechanisms of formation, we show how through manipulation of three critical parameters: time-scale separation, space-scale separation and threshold, we can interchangeably control the formation of all the aforementioned wave types.

U32 collagenase from Pseudoalteromonas agarivorans NW4327: Activity, structure, substrate interactions and molecular dynamics simulations.

A protease of the primary pathogen (Pseudoalteromonas agarivorans NW4327) of the disease affecting the Great Barrier Reef sponge Rhopaloeides odorabile was purified. Zymography demonstrated calcium-dependent collagenase and gelatinase activity of the purified protein. This metalloprotease was identified by matrix assisted laser desorption ionization time-of-flight mass spectrophotometry as a 52,509 Da U32 collagenase. Predicted tertiary structure of U32 collagenase (by Phyre2 fold recognition server) demonstrated 13% identity with known hydrolases establishing novelty of the enzyme. Molecular docking conceived two interacting loops of the collagenase that bound with collagen triple helices and two calcium ions remained centered between the loops. According to ConSurf multiple sequence alignment, the residues of loop1 of the collagenase were mostly conserved while variations among residues of loop2 were comparatively higher than loop1. Asp262, Glu263 of loop1 and Thr363, Lys364, Gln365 of loop2 participated in the interaction with Ca2+ and collagen. Root mean square deviation and root mean square fluctuation values signified higher stability of the collagen-Ca2+-collagenase complex and greater structural stability of the residues of the loops in the complex compared to apocollagenase. Observed properties of NW4327 U32 collagenase and its interaction with collagen were different from similar enzymes of thermophilic bacteria and terrestrial pathogens.

Integrating chemical and mechanical signals through dynamic coupling between cellular protrusions and pulsed ERK activation.

The Ras-ERK signaling pathway regulates diverse cellular processes in response to environmental stimuli and contains important therapeutic targets for cancer. Recent single cell studies revealed stochastic pulses of ERK activation, the frequency of which determines functional outcomes such as cell proliferation. Here we show that ERK pulses are initiated by localized protrusive activities. Chemically and optogenetically induced protrusions trigger ERK activation through various entry points into the feedback loop involving Ras, PI3K, the cytoskeleton, and cellular adhesion. The excitability of the protrusive signaling network drives stochastic ERK activation in unstimulated cells and oscillations upon growth factor stimulation. Importantly, protrusions allow cells to sense combined signals from substrate stiffness and the growth factor. Thus, by uncovering the basis of ERK pulse generation we demonstrate how signals involved in cell growth and differentiation are regulated by dynamic protrusions that integrate chemical and mechanical inputs from the environment.

Mutually inhibitory Ras-PI(3,4)P2 feedback loops mediate cell migration.

Signal transduction and cytoskeleton networks in a wide variety of cells display excitability, but the mechanisms are poorly understood. Here, we show that during random migration and in response to chemoattractants, cells maintain complementary spatial and temporal distributions of Ras activity and phosphatidylinositol (3,4)-bisphosphate [PI(3,4)P2]. In addition, depletion of PI(3,4)P2 by disruption of the 5-phosphatase, Dd5P4, or by recruitment of 4-phosphatase INPP4B to the plasma membrane, leads to elevated Ras activity, cell spreading, and altered migratory behavior. Furthermore, RasGAP2 and RapGAP3 bind to PI(3,4)P2, and the phenotypes of cells lacking these genes mimic those with low PI(3,4)P2 levels, providing a molecular mechanism. These findings suggest that Ras activity drives PI(3,4)P2 down, causing the PI(3,4)P2-binding GAPs to dissociate from the membrane, further activating Ras, completing a positive-feedback loop essential for excitability. Consistently, a computational model incorporating such a feedback loop in an excitable network model accurately simulates the dynamic distributions of active Ras and PI(3,4)P2 as well as cell migratory behavior. The mutually inhibitory Ras-PI(3,4)P2 mechanisms we uncovered here provide a framework for Ras regulation that may play a key role in many physiological processes.

The threshold of an excitable system serves as a control mechanism for noise filtering during chemotaxis.

Chemotaxis, the migration of cells in the direction of a chemical gradient, is of utmost importance in various biological processes. In recent years, research has demonstrated that the underlying mechanism that controls cell migration is an excitable network. One of the properties that characterizes excitability is the presence of a threshold for activation. Here, we show that excitable systems possess noise filtering capabilities that enable faster and more efficient directed migration compared to other systems that also include a threshold, such as ultrasensitive switches. We demonstrate that this filtering ability is a consequence of the varying responses of excitable systems to step and pulse stimuli. Whereas the response to step inputs is determined solely by the magnitude of the stimulus, for pulse stimuli, the response depends on both the magnitude and duration of the stimulus. We then show that these two forms of threshold behavior can be decoupled from one another, allowing finer control in chemotaxis. Finally, we use a simple model of chemotaxis to demonstrate that cells that rely on an excitable system display faster and more effective directed migration that a hypothetical cell guided by an ultra-sensitive switch.

Altered membrane integrity in the progression of muscle diseases.

Sarcolemmal integrity is orchestrated through the interplay of preserving membrane strength and fast tracking the membrane repair process during an event of compromised membrane fragility. Several molecular players have been identified that act in a concerted fashion to maintain the barrier function of the muscle membrane. Substantial research findings in the field of muscle biology point out the importance of maintaining membrane integrity as a key contributory factor to cellular homeostasis. Innumerable data on the progression of membrane pathology associated with compromised muscle membrane integrity support targeting sarcolemmal integrity in skeletal and cardiac muscle as a model therapeutic strategy to alleviate some of the pathologic conditions. This review will discuss strategies that researchers have undertaken to compensate for an imbalance in sarcolemma membrane fragility and membrane repair to maintain muscle membrane integrity.