Morphological Perturbations Research Articles

Chaetocin inhibits the progression of neuroblastoma by targeting JAK2/STAT3 signaling pathway in SH-SY5Y cells.

Chaetocin is a fungal mycotoxin that extensively found in various natural products and has anticancer and anti‑inflammatory activities. Herein, the anticancer effects of chaetocin against the progression of neuroblastoma were studied with SHSY-5Y human neuroblastoma cells and examined the underlying molecular mechanisms. The effects of chaetocin on cellular viability, apoptosis, cell migration, and invasion were investigated. The underlying mechanism of anticancer effects of chaetocin was found to mediate via activating JAK2/STAT3 signaling pathway. Furthermore, when SHSY-5Y cells were exposed to a higher concentration of chaetocin, the induction of cell apoptosis significantly increased by enhancing the expression of pro-apoptotic protein Bcl-2, resulting in anticancer activity against neuroblastoma. In addition, chaetocin significantly decreased the SHSY-5Y cell invasion and migration at 50μM treatment. Moreover, it was shown that increasing chaetocin treatments greatly decreased the activity of proteins connected to the JAK2/STAT3 signaling pathway. In conclusion, chaetocin exhibits a diverse range of actions on neuroblastoma cells, including the inhibition of proliferation, induction of apoptosis, perturbation of cellular morphology, and modulation of critical signaling pathways, with a specific focus on the JAK/STAT3 pathway. These results contribute valuable insights that underscore the potential therapeutic utility of chaetocin in the context of neuroblastoma treatment, suggesting its multifaceted impact on key cellular processes involved in cancer progression.

Maple samara flight is robust to morphological perturbation and united by a classic drag model

Winged, autorotating seeds from the genus Acer, have been the subject of study for botanists and aerodynamicists for decades. Despite this attention and the relative simplicity of these winged seeds, there are still considerable gaps in our understanding of how samara dynamics are informed by morphological features. Additionally, questions remain regarding the robustness of their dynamics to morphological alterations such as mass change by moisture or area change by damage. We here challenge the conventional approach of using wing-loading correlations and instead demonstrate the superiority of a classical aerodynamic model. Using allometry, we determine why some species deviate from interspecific aerodynamic behavior. We alter samara mass and wing area and measure corresponding changes to descent velocity, rotation rate, and coning angle, thereby demonstrating their remarkable ability to autorotate despite significant morphological alteration. Samaras endure mass changes greater than 100% while maintaining descent velocity changes of less than 15%, and are thus robust to changes in mass by moisture or damage. Additionally, samaras withstand up to a 40% reduction in wing area before losing their ability to autorotate, with the largest wings more robust to ablation. Thus, samaras are also robust to wing damage in their environment, a fact children joyfully exploit.

Wavy Ice Patterns as a Result of Morphological Instability of an Ice–Water Interface with Allowance for the Convective–Conductive Heat Transfer Mechanism

In this research, the wavy ice patterns that form due to the evolution of morphological perturbations on the water–ice phase transition interface in the presence of a fluid flow are studied. The mathematical model of heat transport from a relatively warm fluid to a cold wall includes the mechanism of convective–conductive heat transfer in liquid and small sinusoidal perturbations of the water–ice interface. The analytical solutions describing the main state with a flat phase interface as well as its small morphological perturbations are derived. Namely, the migration velocity of perturbations and the dispersion relation are found. We show that the amplification rate of morphological perturbations changes its sign with variation of the wavenumber. This confirms the existence of two different crystallization regimes with (i) a stable (flat) interfacial boundary and (ii) a wavy interfacial boundary. The maximum of the amplification rate representing the most dangerous (quickly growing) perturbations is found. The theory is in agreement with experimental data.

Unravelling the stabilization mechanism of mono-, di- and tri-cholinium citrate-ethylene glycol DESs towards α-chymotrypsin for preservation and activation of the enzyme.

Deep eutectic solvents (DESs) are considered as designer solvents that serve as alternatives to traditional solvents. Numerous favourable properties and advantageous characteristics promote their utility in bio-catalysis. Therefore, they have emerged as attractive sustainable media for different biomacromolecules. In the present work, we have synthesized cholinium-based DESs having a hydrogen bond acceptor (HBA) : hydrogen bond donor (HBD) molar ratio of 1 : 2 by varying the cationic ratio in the HBA, which led to the formation of the DESs such as monocholinium citrate ([Chn][Cit]), dicholinium citrate ([Chn]2[Cit]) and tricholinium citrate ([Chn]3[Cit]), keeping the HBD ethylene glycol (EG) constant to study their suitability for α-chymotrypsin (α-CT). Herein, we have systematically evaluated the influence of DES-1 ([Chn][Cit]-[EG]), DES-2 ([Chn]2[Cit]-[EG]) and DES-3 ([Chn]3[Cit]-[EG]) on the structural and thermal stability, thermodynamic profile, colloidal stability and enzymatic activity of α-CT using different spectroscopic techniques. The spectroscopic results explicitly show enhanced structural stability and activity of the enzyme as the cationic ratio in the HBA increases. Fascinatingly, temperature-dependent studies through both fluorescence and activity measurements showed that DES-2 and DES-3 have highly beneficial effects on α-CT stability. The transition temperature (Tm) of α-CT was augmented by 12.0 °C in DES-2, 10.0 °C in DES-3 and 9.1 °C in DES-1 when compared to the enzyme in buffer. Furthermore, transmission electron microscopy (TEM) analysis revealed that the morphology of α-CT in DES-2 and DES-3 closely mirrored the structure of α-CT, while DES-1 exhibited only minor structural deviations. These findings were corroborated by hydrodynamic size (dH) measurements and average decay time analysis, which confirmed the observed morphological similarities and perturbations. The long-term preservation ability and kinetics of DES-3 were eventually confirmed by Michaelis-Menten kinetics. Ultimately, these outcomes demonstrate that increasing the molar ratio of the cholinium cation in the HBA can enhance the ability of DESs to stabilize the α-CT structure. Our results also suggest that the effect imparted by DESs was due to DESs themselves rather than their constituent elements. Altogether, the present investigation provides a new insight into the dependence of protein's stability and conformational alterations on DES composition. Also, the biocompatibility of DESs towards enzymes can be varied by changing the molar ratios of the constituent components of DESs to facilitate the expansion of applicability of DESs in biocatalysis.

Disruption of Leishmania flagellum attachment zone architecture causes flagellum loss.

Leishmania are flagellated eukaryotic parasites that cause leishmaniasis and are closely related to the other kinetoplastid parasites such as Trypanosoma brucei. In all these parasites there is a cell membrane invagination at the base of the flagellum called the flagellar pocket, which is tightly associated with and sculpted by cytoskeletal structures including the flagellum attachment zone (FAZ). The FAZ is a complex interconnected structure linking the flagellum to the cell body and has critical roles in cell morphogenesis, function and pathogenicity. However, this structure varies dramatically in size and organisation between these different parasites, suggesting changes in protein localisation and function. Here, we screened the localisation and function of the Leishmania orthologues of T. brucei FAZ proteins identified in the genome-wide protein tagging project TrypTag. We identified 27 FAZ proteins and our deletion analysis showed that deletion of two FAZ proteins in the flagellum, FAZ27 and FAZ34 resulted in a reduction in cell body size, and flagellum loss in some cells. Furthermore, after null mutant generation, we observed distinct and reproducible changes to cell shape, demonstrating the ability of the parasite to adapt to morphological perturbations resulting from gene deletion. This process of adaptation has important implications for the study of Leishmania mutants.

What are the “dispersive shear bands” on the surfaces of layered heterostructured materials?

Hetero-deformation-induced (HDI) strengthening mechanism has been well investigated in heterostructured materials including layered/gradient materials prepared by surface attrition or other processing techniques. While the roles played by the geometrically necessary dislocations (GNDs) and the forward/back stresses on the grain scale have been a focus in nearly all these studies, some latest works reveal the peculiar formation of “dispersive shear bands” or strain localizations on the surfaces of layered/gradient materials. Feature sizes of these “shear bands” are commensurate with the macroscopic sample size, but not on the microstructural length scales, thus excluding the HDI strengthening as the primary mechanism. In this work, using a sandwich structure as an illustrative example, we demonstrate that the origin of these shear bands be localized necking with intermediate wavelengths and inclined orientations, which are critically dictated by the hardening behavior of the constituent layers, the geometric parameters, and the initial morphological perturbations. The layered structure under tension may not neck with an infinite wavelength (i.e., the Considère mode), but neck at intermediate wavelengths which actually correspond to a much larger uniform ductility than the commonly observed Considère necking mode. The arrangements of these shear bands can be further classified as I, X, and W types. Findings in this work not only resolve the origin of recent unusual experimental observations, but also suggest an alternative way of understanding and improving the ductility in heterostructured materials.

MisMatch: Calibrated Segmentation via Consistency on Differential Morphological Feature Perturbations With Limited Labels.

Semi-supervised learning (SSL) is a promising machine learning paradigm to address the ubiquitous issue of label scarcity in medical imaging. The state-of-the-art SSL methods in image classification utilise consistency regularisation to learn unlabelled predictions which are invariant to input level perturbations. However, image level perturbations violate the cluster assumption in the setting of segmentation. Moreover, existing image level perturbations are hand-crafted which could be sub-optimal. In this paper, we propose MisMatch, a semi-supervised segmentation framework based on the consistency between paired predictions which are derived from two differently learnt morphological feature perturbations. MisMatch consists of an encoder and two decoders. One decoder learns positive attention for foreground on unlabelled data thereby generating dilated features of foreground. The other decoder learns negative attention for foreground on the same unlabelled data thereby generating eroded features of foreground. We normalise the paired predictions of the decoders, along the batch dimension. A consistency regularisation is then applied between the normalised paired predictions of the decoders. We evaluate MisMatch on four different tasks. Firstly, we develop a 2D U-net based MisMatch framework and perform extensive cross-validation on a CT-based pulmonary vessel segmentation task and show that MisMatch statistically outperforms state-of-the-art semi-supervised methods. Secondly, we show that 2D MisMatch outperforms state-of-the-art methods on an MRI-based brain tumour segmentation task. We then further confirm that 3D V-net based MisMatch outperforms its 3D counterpart based on consistency regularisation with input level perturbations, on two different tasks including, left atrium segmentation from 3D CT images and whole brain tumour segmentation from 3D MRI images. Lastly, we find that the performance improvement of MisMatch over the baseline might originate from its better calibration. This also implies that our proposed AI system makes safer decisions than the previous methods.

Tissue morphology influences the temporal program of human brain organoid development.

Progression through fate decisions determines cellular composition and tissue architecture, but how that same architecture may impact cell fate is less clear. We took advantage of organoids as a tractable model to interrogate this interaction of form and fate. Screening methodological variations revealed that common protocol adjustments impacted various aspects of morphology, from macrostructure to tissue architecture. We examined the impact of morphological perturbations on cell fate through integrated single nuclear RNA sequencing (snRNA-seq) and spatial transcriptomics. Regardless of the specific protocol, organoids with more complex morphology better mimicked invivo human fetal brain development. Organoids with perturbed tissue architecture displayed aberrant temporal progression, with cells being intermingled in both space and time. Finally, encapsulation to impart a simplified morphology led to disrupted tissue cytoarchitecture and a similar abnormal maturational timing. These data demonstrate that cells of the developing brain require proper spatial coordinates to undergo correct temporal progression.

Assessment of Drug-Induced Liver Injury through Cell Morphology and Gene Expression Analysis.

Drug-induced liver injury (DILI) is a significant concern in drug development, often leading to drug withdrawal. Although many studies aim to identify biomarkers and gene/pathway signatures related to liver toxicity and aim to predict DILI compounds, this remains a challenge in drug discovery. With a strong development of high-content screening/imaging (HCS/HCI) for phenotypic screening, we explored the morphological cell perturbations induced by DILI compounds. In the first step, cell morphological signatures were associated with two datasets of DILI chemicals (DILIRank and eTox). The mechanisms of action were then analyzed for chemicals having transcriptomics data and sharing similar morphological perturbations. Signaling pathways associated with liver toxicity (cell cycle, cell growth, apoptosis, ...) were then captured, and a hypothetical relation between cell morphological perturbations and gene deregulation was illustrated within our analysis. Finally, using the cell morphological signatures, machine learning approaches were developed to predict chemicals with a potential risk of DILI. Some models showed relevant performance with validation set balanced accuracies between 0.645 and 0.739. Overall, our findings demonstrate the utility of combining HCI with transcriptomics data to identify the morphological and gene expression signatures related to DILI chemicals. Moreover, our protocol could be extended to other toxicity end points, offering a promising avenue for comprehensive toxicity assessment in drug discovery.

Functional and Morphological Adaptations in the Heart of Children Aged 12-14 Years following Two Different Endurance Training Protocols.

This study investigated the cardiac functional and the morphological adaptations because of two endurance training protocols. Untrained children (N = 30, age: 12-14 years) were divided into three groups (N = 10/group). The first group did not perform any session (CONTROL), the second performed ventilatory threshold endurance training (VTT) for 12 weeks (2 sessions/week) at an intensity corresponding to the ventilatory threshold (VT) and the third (IT) performed two sessions per week at 120% of maximal oxygen uptake (VO2max). Two other sessions (30 min running at 55-65% of VO2max) per week were performed in VVT and IT. Echocardiograms (Left Ventricular end Diastolic Diameter, LVEDd; Left Ventricular end Diastolic Volume, LVEDV; Stroke Volume, SV; Ejection Fraction, EF; Posterior Wall Thickness of the Left Ventricle, PWTLV) and cardiopulmonary ergospirometry (VO2max, VT, velocity at VO2max (vVO2max), time in vVO2max until exhaustion (Tlim) was conducted before and after protocols. Significant increases were observed in both training groups in LVEDd (VTT = 5%; IT = 3.64%), in LVEDV (VTT = 23.7%; ITT = 13.6%), in SV (VTT = 25%; IT = 16.9%) but not in PWTLV and EF, after protocols. No differences were noted in the CONTROL group. VO2max and VT increased significantly in both training groups by approximately 9% after training. Our results indicate that intensity endurance training does not induce meaningful functional and morphological perturbations in the hearts of children.

PE_PGRS45 (Rv2615c) protein of Mycobacterium tuberculosis perturbs mitochondria of macrophages.

The PE_PGRS proteins have coevolved with the antigenic ESX-V secretory system and are abundant in pathogenic Mycobacterium. Only a few PE_PGRS proteins have been characterized, and research suggests their role in organelle targeting, cell death pathways, calcium (Ca2+ ) homeostasis and disease pathogenesis. ThePE_PGRS45 (Rv2615c) protein was predicted to contain mitochondria targeting sequences by in silico evaluation. Therefore, we investigated the targeting of the Rv2615c protein to host mitochondria and its effect on mitochondrial functions. In vitro experiments showed the Rv2615c protein colocalized with the mitochondria and led to morphological mitochondrial perturbations. Recombinant Rv2615c was observed to cause increased levels of intracellular reactive oxygen species and the adenosine diphosphate-to-adenosine triphosphate ratio. The Rv2615c protein also induced mitochondrial membrane depolarization and the generation of mitochondrial superoxide. We observed the release of cytochrome C into the cytoplasm and increased expression of proapoptotic genes Bax and Bim with no significant change in anti-apoptotic Bcl2 in Rv2615c-stimulated THP1 macrophages. Ca2+ is a key signaling molecule in tuberculosis pathogenesis, modulating host cellresponses. As reported for other PE_PGRS proteins, Rv2615c also has Ca2+ -binding motifs and thus can modulate calcium homeostasis in the host. We also observed a high level of Ca2+ influx in THP1 macrophages stimulated with Rv2615c. Based on these findings, we suggest that Rv2615c may be an effector protein that could contribute to disease pathogenesis by targeting host mitochondria.

Optimizing the Cell Painting assay for image-based profiling.

In image-based profiling, software extracts thousands of morphological features of cells from multi-channel fluorescence microscopy images, yielding single-cell profiles that can be used for basic research and drug discovery. Powerful applications have been proven, including clustering chemical and genetic perturbations on the basis of their similar morphological impact, identifying disease phenotypes by observing differences in profiles between healthy and diseased cells and predicting assay outcomes by using machine learning, among many others. Here, we provide an updated protocol for the most popular assay for image-based profiling, Cell Painting. Introduced in 2013, it uses six stains imaged in five channels and labels eight diverse components of the cell: DNA, cytoplasmic RNA, nucleoli, actin, Golgi apparatus, plasma membrane, endoplasmic reticulum and mitochondria. The original protocol was updated in 2016 on the basis of several years' experience running it at two sites, after optimizing it by visual stain quality. Here, we describe the work of the Joint Undertaking for Morphological Profiling Cell Painting Consortium, to improve upon the assay via quantitative optimization by measuring the assay's ability to detect morphological phenotypes and group similar perturbations together. The assay gives very robust outputs despite various changes to the protocol, and two vendors' dyes work equivalently well. We present Cell Painting version 3, in which some steps are simplified and several stain concentrations can be reduced, saving costs. Cell culture and image acquisition take 1-2 weeks for typically sized batches of ≤20 plates; feature extraction and data analysis take an additional 1-2 weeks.This protocol is an update to Nat. Protoc. 11, 1757-1774 (2016): https://doi.org/10.1038/nprot.2016.105.

In vitro cardiac modeling of desmin-related myofibrillar myopathy and deep learning-based image analysis to develop a high-content screening assay

Mutations of DES, the gene encoding desmin, the main intermediate filament of muscle cells, are one of the major cause of Myofibrillar myopathy(MFM). This disease is mainly characterized by a muscular dystrophy but also, in many cases, by the progressive emergence of cardiac dysfunctions evolving frequently from dilated cardiomyopathy to heart failure. For the moment, no specific treatment can revert this disease. The following study relied on the development of an automated tool base on deep-learning to discriminate efficiently mutant and control cardiomyocytes in the perspective of drug screening. We use cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs) obtained from control or patients carrying a DES mutation (E439K). Phenotyping of hiPSC-CMs was performed by immunocytostaining of the sarcomeres or the desmin network. After imaging, the morphological perturbations were evaluated manually based either on the sarcomeric organization or on the aspect of the desmin network at single cell level. Then an automated classification model was generated by using machine-learning method trained with the previous images annotated with the results of the manual classifications. In parallel, another automated classification model based on cell profiling from sarcomeric, desmin and mitochondrial staining by using the deep learning EfficientNet B0 model was setting up in order to distinguish Control cell and DES mutated cell. Manual classification based on sarcomeric organization was established on 4 classes ranging from cells with disorganized sarcomeres to cells with a well-organized sarcomeric network on 1500 single cells. We observed that the distribution of DES mutated cells is shifted toward the class of disorganized sarcomere compared to control cells. Identically, we also manually classified 1200 single cells based on the organization of the desmin network (4 classes). We also observed a shift of DES mutant cells to be classified as cells with aggregated desmin network compared to control cells. Finally, the various validation tests of the two automated classification methods showed significant correlation with the manual classification methods. Here we demonstrate the efficacy of our automated classification software to be able to discriminates mutant and control cells. This analysis platform will then be used to perform high throughput drug screening assays to discover new therapeutic molecules.

Infection of Endothelial Cells with Acinetobacter baumannii Reveals Remodelling of Mitochondrial Protein Complexes.

Acinetobacter baumannii is an antibiotic-resistant, Gram-negative pathogen that causes a multitude of nosocomial infections. However, pathogenicity mechanisms and the host cell response during infection remain unclear. In this study, we determined virulence traits of A. baumannii clinical isolates belonging to the most widely disseminated international clonal lineage, international cluster 2 (IC2), in vitro and in vivo. Complexome profiling of primary human endothelial cells with A. baumannii revealed that mitochondria, and in particular complexes of the electron transport chain, are important host cell targets. Infection with highly virulent A. baumannii remodelled assembly of mitochondrial protein complexes and led to metabolic adaptation. These were characterized by reduced mitochondrial respiration and glycolysis in contrast to those observed in infection with low-pathogenicity A. baumannii. Perturbation of oxidative phosphorylation, destabilization of mitochondrial ribosomes, and interference with mitochondrial metabolic pathways were identified as important pathogenicity mechanisms. Understanding the interaction of human host cells with the current global A. baumannii clone is the basis to identify novel therapeutic targets. IMPORTANCE Virulence traits of Acinetobacter baumannii isolates of the worldwide most prevalent international clonal lineage, IC2, remain largely unknown. In our study, multidrug-resistant IC2 clinical isolates differed substantially in their virulence potential despite their close genetic relatedness. Our data suggest that, at least for some isolates, mitochondria are important target organelles during infection of primary human endothelial cells. Complexes of the respiratory chain were extensively remodelled after infection with a highly virulent A. baumannii strain, leading to metabolic adaptation characterized by severely reduced respiration and glycolysis. Perturbations of both mitochondrial morphology and mitoribosomes were identified as important pathogenicity mechanisms. Our data might help to further decipher the molecular mechanisms of A. baumannii and host mitochondrial interaction during infection.

Co-administration of alcohol and combination antiretroviral therapy (cART) in male Sprague Dawley rats: A study on testicular morphology, oxidative and cytokines perturbations.

Alcohol consumption alongside combination antiretroviral therapy (cART) has attracted research interest, especially because of increasing male infertility. This study investigated the combined effects of alcohol and cART on testicular morphology, biomarkers of oxidative stress, inflammation, and apoptosis. Rats, weighing 330-370 g, were divided into four groups of six animals each; control, alcohol treated (A), cART, and alcohol plus cART treated (A+cART). Following 90 days treatment period, animals were euthanized, testis extracted, and routinely processed for histology and immunohistochemical analysis. Significantly decreased epithelial area fraction, increased luminal and connective tissue area fractions, and reduction of epithelial height and spermatocyte number, were recorded in the treated groups compared to control. Extensive seminiferous epithelial lesions including widened intercellular space, karyolysis, and sloughing of germinal epithelium were recorded in all the treated groups. Furthermore, upregulation of inducible nitric oxide synthase and 8-hydroxydeoxyguanosine, interleukin-6, and caspase 3 recorded in treated animals, was more significant in A+cART group. Also, the levels of interleukin-1β and tumor necrosis factor-α were more elevated in A and cART treated groups than in A+cART, while MDA was significantly elevated in cART and A+cART treated groups compared to control group. Altogether, the results indicate testicular toxicity of the treatments. It is concluded that consuming alcohol or cART induces oxidative stress, inflammation, and apoptosis in testis of rats, which lead to testicular structural and functional derangements, which are exacerbated when alcohol and cART are consumed concurrently. The result will invaluably assist clinicians in management of reproductive dysfunctions in male HIV/AIDS-alcoholic patients on cART.

Linking chemicals, genes and morphological perturbations to diseases

The progress in image-based high-content screening technology has facilitated high-throughput phenotypic profiling notably the quantification of cell morphology perturbation by chemicals. However, understanding the mechanism of action of a chemical and linking it to cell morphology and phenotypes remains a challenge in drug discovery.In this study, we intended to integrate molecules that induced transcriptomic perturbations and cellular morphological changes into a biological network in order to assess chemical-phenotypic relationships in humans. Such a network was enriched with existing disease information to suggest molecular and cellular profiles leading to phenotypes.Two datasets were used for this study. Firstly, we used the “Cell Painting morphological profiling assay” dataset, composed of 30,000 compounds tested on human osteosarcoma cells (named U2OS). Secondly, we used the “L1000 mRNA profiling assay” dataset, a collection of transcriptional expression data from cultured human cells treated with approximately 20,000 bioactive small molecules from the Library of Integrated Network-based Cellular Signatures (LINCS). Furthermore, pathways, gene ontology terms and disease enrichments were performed on the transcriptomics data.Overall, our study makes it possible to develop a biological network combining chemical-gene-pathway-morphological perturbation and disease relationships. It contains an ensemble of 9989 chemicals, 732 significant morphological features and 12,328 genes. Through diverse examples, we demonstrated that some drugs shared similar genes, pathways and morphological profiles that, taken together, could help in deciphering chemical-phenotype observations.

State-specific morphological deformations of the lipid bilayer explain mechanosensitive gating of MscS ion channels.

The force-from-lipids hypothesis of cellular mechanosensation posits that membrane channels open and close in response to changes in the physical state of the lipid bilayer, induced for example by lateral tension. Here, we investigate the molecular basis for this transduction mechanism by studying the mechanosensitive ion channel MscS from Escherichia coli and its eukaryotic homolog MSL1 from Arabidopsis thaliana. First, we use single-particle cryo-electron microscopy to determine the structure of a novel open conformation of wild-type MscS, stabilized in a thinned lipid nanodisc. Compared with the closed state, the structure shows a reconfiguration of helices TM1, TM2, and TM3a, and widening of the central pore. Based on these structures, we examined how the morphology of the membrane is altered upon gating, using molecular dynamics simulations. The simulations reveal that closed-state MscS causes drastic protrusions in the inner leaflet of the lipid bilayer, both in the absence and presence of lateral tension, and for different lipid compositions. These deformations arise to provide adequate solvation to hydrophobic crevices under the TM1-TM2 hairpin, and clearly reflect a high-energy conformation for the membrane, particularly under tension. Strikingly, these protrusions are largely eradicated upon channel opening. An analogous computational study of open and closed MSL1 recapitulates these findings. The gating equilibrium of MscS channels thus appears to be dictated by opposing conformational preferences, namely those of the lipid membrane and of the protein structure. We propose a membrane deformation model of mechanosensation, which posits that tension shifts the gating equilibrium towards the conductive state not because it alters the mode in which channel and lipids interact, but because it increases the energetic cost of the morphological perturbations in the membrane required by the closed state.

Atomic layer deposition of Er-doped yttrium aluminum gallium garnet nanofilms with tunable crystallization and electroluminescence properties.

Polycrystalline erbium-doped Y3(AlxGa1-x)5O12 (Er-YAGG) nanofilms with various Al/Ga compositions are deposited on silicon using atomic layer deposition followed by annealing at different temperatures. The Al/Ga ratios and the corresponding annealing temperatures required for crystallization are confirmed by investigating the diffraction patterns and micro-morphologies. The co-alloying of Al and Ga compositions controllably changes the lattice constant and impacts the grain growth. The crystal-field splitting of doped Er3+ ions is also modified, manifesting different electroluminescence (EL) spectra that also indicate the crystallization of garnet matrices. The EL performance of a device based on the Y3Al2Ga3O12 nanofilm (1.39 at% Er dopant) annealed at 900 °C is improved due to the adjustment of morphology and microstructural perturbations that are beneficial for radiative transition. The optimal EL device exhibits a low onset voltage of ∼25 V and a maximum external quantum efficiency of 3.29%. The excitation cross-section under electrical pumping is estimated to be 1.18 × 10-15 cm2. The carrier transport of these co-alloyed Er-YAGG devices conforms to the Poole-Frenkel mechanism. Both the EL decay lifetime and the device operation time increase with the incorporation of Ga within the Er-YAGG nanofilms. These Er-YAGG devices with tunable optoelectronic properties manifest promising potential for the engineering of light sources compatible with CMOS technology.

Polarity-driven laminar pattern formation by lateral-inhibition in 2D and 3D bilayer geometries

Abstract Fine-grain patterns produced by juxtacrine signalling have previously been studied using static monolayers as cellular domains. However, analytic results are usually restricted to a few cells due to the algebraic complexity of non-linear dynamical systems. Motivated by concentric patterning of Notch expression observed in the mammary gland, we combine concepts from graph and control theory to represent cellular connectivity and behaviour. The resulting theoretical framework allows us to exploit the symmetry of multicellular bilayer structures in 2D and 3D, thereby deriving analytical conditions that drive the dynamical system to form laminar patterns, consistent with the formation of cell polarity by activator localization. Critically, the patterning conditions are independent of the precise dynamical details, thus the framework allows for generality in understanding the influence of cellular geometry and signal polarity on patterning using lateral-inhibition systems. Applying the analytic conditions to mammary organoids suggests that intense cell signalling polarity is required for the maintenance of stratified cell types within a static bilayer using a lateral-inhibition mechanism. Furthermore, by employing 2D and 3D cell-based models, we highlight that the cellular polarity conditions derived from static domains can generate laminar patterning in dynamic environments. However, they are insufficient for the maintenance of patterning when subjected to substantial morphological perturbations. In agreement with the mathematical implications of strict signalling polarity induced on the cells, we propose an adhesion-dependent Notch-Delta biological process that has the potential to initiate bilayer stratification in a developing mammary organoid.

Cellular Sensing Governs the Stability of Chemotactic Fronts.

In contexts ranging from embryonic development to bacterial ecology, cell populations migrate chemotactically along self-generated chemical gradients, often forming a propagating front. Here, we theoretically show that the stability of such chemotactic fronts to morphological perturbations is determined by limitations in the ability of individual cells to sense and thereby respond to the chemical gradient. Specifically, cells at bulging parts of a front are exposed to a smaller gradient, which slows them down and promotes stability, but they also respond more strongly to the gradient, which speeds them up and promotes instability. We predict that this competition leads to chemotactic fingering when sensing is limited at too low chemical concentrations. Guided by this finding and by experimental data on E. coli chemotaxis, we suggest that the cells' sensory machinery might have evolved to avoid these limitations and ensure stable front propagation. Finally, as sensing of any stimuli is necessarily limited in living and active matter in general, the principle of sensing-induced stability may operate in other types of directed migration such as durotaxis, electrotaxis, and phototaxis.