Jamming of nephron-forming niches in the developing mouse kidney creates cyclical mechanical stresses.

Urinary collecting tubules form during kidney embryogenesis through the branching of the ureteric bud epithelium. A travelling mesenchyme niche of nephron progenitor cells caps each branching ureteric bud tip. These 'tip domain' niches pack more closely over developmental time and their number relates to nephron endowment at birth. Yet, how the crowded tissue environment impacts niche number and cell decision-making remains unclear. Here, through experiments and mathematical modelling, we show that niche packing conforms to physical limitations imposed by kidney curvature. We relate packing geometries to rigidity theory to predict a stiffening transition starting at embryonic day 15 in the mouse, validated by micromechanical analysis. Using a method to estimate tip domain 'ages' relative to their most recent branch events, we find that new niches overcome mechanical resistance as they branch and displace neighbours. This creates rhythmic mechanical stress in the niche. These findings expand our understanding of kidney development and inform engineering strategies for synthetic regenerative tissues.

Planar cell polarity zebrafish models of congenital scoliosis reveal novel underlying defects in notochord morphogenesis.

Congenital scoliosis (CS) is a type of vertebral malformation whose etiology remains elusive. The notochord is pivotal for vertebrae development but its role in CS is still understudied. Zebrafish knockout of ptk7a, a planar cell polarity (PCP) gene that is essential for convergence and extension (C&E) of the notochord, developed congenital scoliosis-like vertebral malformations (CVM). Maternal zygotic ptk7a mutants displayed severe C&E defects of the notochord. Excessive apoptosis occurred in the malformed notochord, causing a significantly reduced number of vacuolated cells, and compromising the mechanical properties of the notochord. The latter manifested as a less stiff extracellular matrix along with a significant reduction in the number of the caveolae and severely loosened intercellular junctions in the vacuolated region. These defects led to focal kinks, abnormal mineralization, and CVM exclusively at the anterior spine. Loss of function of another PCP gene, vangl2, also revealed excessive apoptosis in the notochord associated with CVM. This study suggests a new model for CS pathogenesis that is associated with defects in notochord C&E and highlights an essential role of PCP signaling in vertebrae development.

Brillouin microscopy.

The field of Brillouin microscopy and imaging was established approximately 20 years ago, thanks to the development of non-scanning high-resolution optical spectrometers. Since then, the field has experienced rapid expansion, incorporating technologies from telecommunications, astrophotonics, multiplexed microscopy, quantum optics and machine learning. Consequently, these advancements have led to much-needed improvements in imaging speed, spectral resolution and sensitivity. The progress in Brillouin microscopy is driven by a strong demand for label-free and contact-free methods to characterize the mechanical properties of biomaterials at the cellular and subcellular scales. Understanding the local biomechanics of cells and tissues has become crucial in predicting cellular fate and tissue pathogenesis. This Primer aims to provide a comprehensive overview of the methods and applications of Brillouin microscopy. It includes key demonstrations of Brillouin microscopy and imaging that can serve as a reference for the existing research community and new adopters of this technology. The article concludes with an outlook, presenting the authors' vision for future developments in this vibrant field. The Primer also highlights specific examples where Brillouin microscopy can have a transformative impact on biology and biomedicine.

Enhancing Plant Stress Tolerance: The Role of LcWRKY40 Gene in Drought and Alkaline Salt Resistance in Tobacco and Yeast.

Leymus chinensis, a halophytic perennial grass belonging to the Poaceae family, thrives in saline-alkali grasslands and harbors a rich repository of resistance-related genetic resources. This study focused on deciphering the stress-responsive mechanisms of L. chinensis by conducting transcriptomic sequencing under NaHCO3 stress, which resulted in the annotation of a segment corresponding to the 51WRKY gene. The alkali-induced gene LcWRKY40 (QIG37591) was identified by phylogenetic analysis. Real-time quantitative PCR analysis was performed on L. chinensis plants subjected to PEG6000 and alkaline salt (NaHCO3) stress, and the results indicated that the LcWRKY40 gene was upregulated in both the leaves and roots. The localization of the LcWRKY40 protein was confirmed by the use of green fluorescent protein (GFP) fusion technology in transformed rice protoplast cells. The GAL4-driven transformation of the LcWRKY40 gene in INVScI yeast cells, which exhibited enhanced tolerance upon overexpression of the LcWRKY40 gene under mannitol and alkaline salt (NaHCO3) stress conditions. Under drought stress using mannitol, the fresh weight of Nicotiana tabacum overexpressing the LcWRKY40 gene was significantly higher than that of wild-type(WT) tobacco. Through drought and salt alkali stress, we found that overexpressed tobacco at different stages always outperformed the wild type in terms of fresh weight, SOD, MDA, and Fv/Fm. This study provides preliminary insights into the involvement of the LcWRKY40 gene in responding to drought and alkaline salt stresses, highlighting its role in enhancing plant resistance to drought and saline-alkaline conditions. These findings lay the foundation for future molecular breeding strategies aimed at improving grass resistance from different aspects.

splicekit: an integrative toolkit for splicing analysis from short-read RNA-seq.

Motivation: Analysis of alternative splicing using short-read RNA-seq data is a complex process that involves several steps: alignment of reads to the reference genome, identification of alternatively spliced features, motif discovery, analysis of RNA-protein binding near donor and acceptor splice sites, and exploratory data visualization. To the best of our knowledge, there is currently no integrative open-source software dedicated to this task. Results: Here, we introduce splicekit, a Python package that provides and integrates a set of existing and novel splicing analysis tools for conducting splicing analysis. Availability and implementation: The software splicekit is open-source and available at Github (https://github.com/bedapub/splicekit) and via the Python Package Index.

Laponite modified methacryloyl gelatin hydrogel with controlled release of vascular endothelial growth factor a for bone regeneration.

Reconstruction of bone defects has long been a major clinical challenge. Limited by the various shortcomings of conventional treatment like autologous bone grafting and inorganic substitutes, the development of novel bone repairing strategies is on top priority. Injectable biomimetic hydrogels that deliver stem cells and growth factors in a minimally invasive manner can effectively promote bone regeneration and thus represent a promising alternative. Therefore, in this study, we designed and constructed an injectable nanocomposite hydrogel co-loaded with Laponite (Lap) and vascular endothelial growth factor (VEGF) through a simplified and convenient scheme of physical co-mixing (G@Lap/VEGF). The introduced Lap not only optimized the injectability of GelMA by the electrostatic force between the nanoparticles, but also significantly delayed the release of VEGF-A. In addition, Lap promoted high expression of osteogenic biomarkers in mesenchymal stem cells (MSCs) and enhanced the matrix mineralization. Besides, VEGF-A exerted chemotactic effects recruiting endothelial progenitor cells (EPCs) and inducing neovascularization. Histological and micro-CT results demonstrated that the critical-sized calvarial bone defect lesions in the SD rats after treated with G@Lap/VEGF exhibited significant in vivo bone repairing. In conclusion, the injectable G@Lap/VEGF nanocomposite hydrogel constructed in our study is highly promising for clinical transformation and applications, providing a convenient and simplified scheme for clinical bone repairing, and contributing to the further development of the injectable biomimetic hydrogels.

Purinergic signaling through the P2Y2 receptor regulates osteocytes' mechanosensitivity.

Osteocytes' response to dynamic loading plays a crucial role in regulating the bone mass but quickly becomes saturated such that downstream induction of bone formation plateaus. The underlying mechanisms that downregulate osteocytes' sensitivity and overall response to loading remain unknown. In other cell types, purinergic signaling through the P2Y2 receptor has the potential to downregulate the sensitivity to loading by modifying cell stiffness through actin polymerization and cytoskeleton organization. Herein, we examined the role of P2Y2 activation in regulating osteocytes' mechanotransduction using a P2Y2 knockout cell line alongside conditional knockout mice. Our findings demonstrate that the absence of P2Y2 expression in MLO-Y4 cells prevents actin polymerization while increasing the sensitivity to fluid flow-induced shear stress. Deleting osteocytes' P2Y2 expression in conditional-knockout mice enabled bone formation to increase when increasing the duration of exercise. Overall, P2Y2 activation under loading produces a negative feedback loop, limiting osteocytes' response to continuous loading by shifting the sensitivity to mechanical strain through actin stress fiber formation.

G-PLIP: Knowledge graph neural network for structure-free protein-ligand bioactivity prediction.

Protein-ligand interactions (PLIs) determine the efficacy and safety profiles of small molecule drugs. Existing methods rely on either structural information or resource-intensive computations to predict PLI, casting doubt on whether it is possible to perform structure-free PLI predictions at low computational cost. Here we show that a light-weight graph neural network (GNN), trained with quantitative PLIs of a small number of proteins and ligands, is able to predict the strength of unseen PLIs. The model has no direct access to structural information about the protein-ligand complexes. Instead, the predictive power is provided by encoding the entire chemical and proteomic space in a single heterogeneous graph, encapsulating primary protein sequence, gene expression, the protein-protein interaction network, and structural similarities between ligands. This novel approach performs competitively with, or better than, structure-aware models. Our results suggest that existing PLI prediction methods may be improved by incorporating representation learning techniques that embed biological and chemical knowledge.

A liver immune rheostat regulates CD8 T cell immunity in chronic HBV infection.

Chronic hepatitis B virus (HBV) infection affects 300 million patients worldwide1,2, in whom virus-specific CD8 T cells by still ill-defined mechanisms lose their function and cannot eliminate HBV-infected hepatocytes3-7. Here we demonstrate that a liver immune rheostat renders virus-specific CD8 T cells refractory to activation and leads to their loss of effector functions. In preclinical models of persistent infection with hepatotropic viruses such as HBV, dysfunctional virus-specific CXCR6+ CD8 T cells accumulated in the liver and, as a characteristic hallmark, showed enhanced transcriptional activity of cAMP-responsive element modulator (CREM) distinct from T cell exhaustion. In patients with chronic hepatitis B, circulating and intrahepatic HBV-specific CXCR6+ CD8 T cells with enhanced CREM expression and transcriptional activity were detected at a frequency of 12-22% of HBV-specific CD8 T cells. Knocking out the inhibitory CREM/ICER isoform in T cells, however, failed to rescue T cell immunity. This indicates that CREM activity was a consequence, rather than the cause, of loss in T cell function, further supported by the observation of enhanced phosphorylation of protein kinase A (PKA) which is upstream of CREM. Indeed, we found that enhanced cAMP-PKA-signalling from increased T cell adenylyl cyclase activity augmented CREM activity and curbed T cell activation and effector function in persistent hepatic infection. Mechanistically, CD8 T cells recognizing their antigen on hepatocytes established close and extensive contact with liver sinusoidal endothelial cells, thereby enhancing adenylyl cyclase-cAMP-PKA signalling in T cells. In these hepatic CD8 T cells, which recognize their antigen on hepatocytes, phosphorylation of key signalling kinases of the T cell receptor signalling pathway was impaired, which rendered them refractory to activation. Thus, close contact with liver sinusoidal endothelial cells curbs the activation and effector function of HBV-specific CD8 T cells that target hepatocytes expressing viral antigens by means of the adenylyl cyclase-cAMP-PKA axis in an immune rheostat-like fashion.

Weight-adjusted waist index is a potential early predictor of degraded bone microarchitecture: A cross-sectional study of the national health and nutrition examination survey 2007-2008.

PURPOSE: This study aimed to investigate the association between weight-adjusted waist index (WWI) and trabecular bone score (TBS) and to assess the ability of WWI to identify individuals with degraded bone microarchitecture (DBMA). METHODS: This cross-sectional study included participants aged 20 and older from the National Health and Nutrition Examination Survey. Furthermore, WWI was calculated by waist circumference and body weight. In addition, linear regression models were employed to investigate the association between WWI and TBS, while logistic regression models were employed to determine the association between WWI and the risk of DBMA. Finally, the performance of WWI in identifying individuals with DBMA was using the receiver operating characteristic (ROC) curves with area under the ROC curve. RESULTS: A total of 4,179 participants with a mean age of 49.90 years were included in the final analysis. WWI was negatively associated with TBS and positively associated with an increased risk of DBMA. Furthermore, the associations between WWI and TBS, as well as DBMA risk, were stable regardless of stratification by age, sex, race, or body mass index (BMI). Moreover, WWI achieved good performances in identifying individuals with DBMA or low TBS. In addition, the combination of WWI and BMI showed better performances in identifying individuals with DBMA or low TBS than WWI or BMI alone. CONCLUSION: WWI established a negative association with TBS and a positive association with the risk of DBMA. Clinicians should be alert to the potential risk of DBMA among individuals with high WWI. Moreover, WWI, alone or in combination with BMI, has the potential to serve as an early screening strategy in identifying individuals with DBMA.

Mechanical evolution of metastatic cancer cells in three-dimensional microenvironment.

Cellular biomechanics plays critical roles in cancer metastasis and tumor progression. Existing studies on cancer cell biomechanics are mostly conducted in flat 2D conditions, where cells' behavior can differ considerably from those in 3D physiological environments. Despite great advances in developing 3D in vitro models, probing cellular elasticity in 3D conditions remains a major challenge for existing technologies. In this work, we utilize optical Brillouin microscopy to longitudinally acquire mechanical images of growing cancerous spheroids over the period of eight days. The dense mechanical mapping from Brillouin microscopy enables us to extract spatially resolved and temporally evolving mechanical features that were previously inaccessible. Using an established machine learning algorithm, we demonstrate that incorporating these extracted mechanical features significantly improves the classification accuracy of cancer cells, from 74% to 95%. Building on this finding, we have developed a deep learning pipeline capable of accurately differentiating cancerous spheroids from normal ones solely using Brillouin images, suggesting the mechanical features of cancer cells could potentially serve as a new biomarker in cancer classification and detection.

The Enhanced Photoluminescence Properties of Carbon Dots Derived from Glucose: The Effect of Natural Oxidation.

The investigation of the fluorescence mechanism of carbon dots (CDs) has attracted significant attention, particularly the role of the oxygen-containing groups. Dual-CDs exhibiting blue and green emissions are synthesized from glucose via a simple ultrasonic treatment, and the oxidation degree of the CDs is softly modified through a slow natural oxidation approach, which is in stark contrast to that aggressively altering CDs' surface configurations through chemical oxidation methods. It is interesting to find that the intensity of the blue fluorescence gradually increases, eventually becoming the dominant emission after prolonging the oxidation periods, with the quantum yield (QY) of the CDs being enhanced from ~0.61% to ~4.26%. Combining the microstructure characterizations, optical measurements, and ultrafiltration experiments, we hypothesize that the blue emission could be ascribed to the surface states induced by the C-O and C=O groups, while the green luminescence may originate from the deep energy levels associated with the O-C=O groups. The distinct emission states and energy distributions could result in the blue and the green luminescence exhibiting distinct excitation and emission behaviors. Our findings could provide new insights into the fluorescence mechanism of CDs.

Study on compaction characteristics and mechanical model of dry crushing filling material under lateral confinement condition.

The compaction characteristics and bearing capacity of dry filling materials in goaf have a significant influence on stope control and surface stability. Through acoustic emission monitoring and mechanical model analysis, a series of confined compression tests were conducted on crushed waste with varying particle sizes and Talbot coefficients. The deformation, fragmentation, and acoustic emission characteristics under corresponding working conditions were determined. The results indicate that the stress-strain curves of crushed stone with different particle sizes and Talbot coefficients exhibit similar nonlinear behavior during confined compression. However, the strain response varies with changing stress levels. By analyzing the slope change rate of the stress-strain curve, the lateral uniaxial compression process of waste rock can be divided into three deformation stages: rapid compression, stable crushing, and slow compaction. The compressive deformation characteristics of gravel differ based on particle size and Talbot coefficient. Specimens with a higher Talbot coefficient demonstrate stronger compressive resistance and weaker deformation resistance during initial compaction loading. Notably, the internal pressure structure strength is influenced by factors such as maximum particle size D, grading coefficient n, and particle size distribution continuity, rather than solely by the proportion of large particles. The evolution of acoustic emission signals and energy-time curve during waste rock confined axial compression synchronizes with the compaction process. Overall, compaction plays a critical role in maintaining the stability of goaf in dry crushed waste filling.

Another string to your bow: machine learning prediction of the pharmacokinetic properties of small molecules.

INTRODUCTION: Prediction of pharmacokinetic (PK) properties is crucial for drug discovery and development. Machine-learning (ML) models, which use statistical pattern recognition to learn correlations between input features (such as chemical structures) and target variables (such as PK parameters), are being increasingly used for this purpose. To embed ML models for PK prediction into workflows and to guide future development, a solid understanding of their applicability, advantages, limitations, and synergies with other approaches is necessary. AREAS COVERED: This narrative review discusses the design and application of ML models to predict PK parameters of small molecules, especially in light of established approaches including in vitro-in vivo extrapolation (IVIVE) and physiologically based pharmacokinetic (PBPK) models. The authors illustrate scenarios in which the three approaches are used and emphasize how they enhance and complement each other. In particular, they highlight achievements, the state of the art and potentials of applying machine learning for PK prediction through a comphrehensive literature review. EXPERT OPINION: ML models, when carefully crafted, regularly updated, and appropriately used, empower users to prioritize molecules with favorable PK properties. Informed practitioners can leverage these models to improve the efficiency of drug discovery and development process.

Optical coherence tomography-guided Brillouin microscopy highlights regional tissue stiffness differences during anterior neural tube closure in the Mthfd1l murine mutant.

Neurulation is a highly synchronized biomechanical process leading to the formation of the brain and spinal cord, and its failure leads to neural tube defects (NTDs). Although we are rapidly learning the genetic mechanisms underlying NTDs, the biomechanical aspects are largely unknown. To understand the correlation between NTDs and tissue stiffness during neural tube closure (NTC), we imaged an NTD murine model using optical coherence tomography (OCT), Brillouin microscopy and confocal fluorescence microscopy. Here, we associate structural information from OCT with local stiffness from the Brillouin signal of embryos undergoing neurulation. The stiffness of neuroepithelial tissues in Mthfd1l null embryos was significantly lower than that of wild-type embryos. Additionally, exogenous formate supplementation improved tissue stiffness and gross embryonic morphology in nullizygous and heterozygous embryos. Our results demonstrate the significance of proper tissue stiffness in normal NTC and pave the way for future studies on the mechanobiology of normal and abnormal embryonic development.

Utility of somatosensory- and motor-evoked potential change thresholds in surgical treatment for thoracic spinal stenosis based on different pathologies.

BACKGROUND CONTEXT: Thoracic spinal stenosis (TSS) is secondary to different pathologies that differ in clinical characteristics and surgical outcomes. PURPOSE: This study aimed to determine the optimal warning thresholds for combined somatosensory-evoked potentials (SSEP) and motor-evoked potentials (MEP) for predicting postoperative neurological deterioration in surgical treatment for TSS based on different pathologies. Additionally, we explored the correlation between SSEP/MEP monitoring and postoperative spinal neurological function. STUDY SETTING: Retrospective study. PATIENT SAMPLE: Two hundred five patients. OUTCOME MEASURES: We obtained perioperative modified Japanese Orthopedic Association (mJOA) scores to assess spinal neurological function. METHODS: The data collected in this study included demographic data, intraoperative neurophysiological monitoring (IONM) signals, and perioperative neurological function assessments. To determine the optimal IONM warning threshold, a receiver operating characteristic (ROC) curve was used. Additionally, Pearson correlation analysis was conducted to determine the correlation between IONM signals and clinical neurological conditions. RESULTS: A total of 205 consecutive patients were eligible. Forty-one patients had thoracic disc herniation (TDH), 14 had ossification of the posterior longitudinal ligament (OPLL), 124 had ossification of the ligamentum flavum (OLF), and 26 had OPLL+OLF. The mean mJOA scores before surgery and 3 months after surgery were 7.0 and 7.9, respectively, resulting in a mean mJOA recovery rate (RR) of 23.1%. The average postoperative mJOA RRs for patients with TDH, OPLL, OLF, and OPLL+OLF were 24.8%, 10.4%, 26.8%, and 11.2%, respectively. Patients with OPLL+OLF exhibited a more stringent threshold for IONM changes. This included a lower amplitude cutoff value (a decrease of 49.0% in the SSEP amplitude and 57.5% in the MEP amplitude for short-term prediction) and a shorter duration of waveform change (19.5 minutes for SSEP and 22.5 minutes for MEP for short-term prediction). On the other hand, patients with TDH had more lenient IONM warning criteria (a decrease of 49.0% in SSEP amplitude and 77.5% in MEP amplitude for short-term prediction; durations of change of 25.5 minutes for SSEP and 32.5 minutes for MEP). However, OPLL patients or OLF patients had moderate and similar IONM warning thresholds. Additionally, there was a stronger correlation between the SSEP amplitude variability ratio and the JOA RR in OPLL+OLF patients, while the correlation was stronger between the MEP amplitude variability ratio and the JOA RR for the other three TSS pathologies. CONCLUSIONS: Optimal IONM change criteria for prediction vary depending on different TSS pathologies. The optimal monitoring strategy for prediction varies depending on TSS pathologies.

Wettability and Bactericidal Properties of Bioinspired ZnO Nanopillar Surfaces.

Nanomaterials of zinc oxide (ZnO) exhibit antibacterial activities under ambient illumination that result in cell membrane permeability and disorganization, representing an important opportunity for health-related applications. However, the development of antibiofouling surfaces incorporating ZnO nanomaterials has remained limited. In this work, we fabricate superhydrophobic surfaces based on ZnO nanopillars. Water droplets on these superhydrophobic surfaces exhibit small contact angle hysteresis (within 2-3°) and a minimal tilting angle of 1°. Further, falling droplets bounce off when impacting the superhydrophobic ZnO surfaces with a range of Weber numbers (8-46), demonstrating that the surface facilitates a robust Cassie-Baxter wetting state. In addition, the antibiofouling efficacy of the surfaces has been established against model pathogenic Gram-positive bacteria Staphylococcus aureus (S. aureus) and Gram-negative bacteria Escherichia coli (E. coli). No viable colonies of E. coli were recoverable on the superhydrophobic surfaces of ZnO nanopillars incubated with cultured bacterial solutions for 18 h. Further, our tests demonstrate a substantial reduction in the quantity of S. aureus that attached to the superhydrophobic ZnO nanopillars. Thus, the superhydrophobic ZnO surfaces offer a viable design of antibiofouling materials that do not require additional UV illumination or antimicrobial agents.

Ultrasound-guided versus fluoroscopy-guided lumbar selective nerve root block: a retrospective comparative study.

The purpose of this study is to compare the accuracy and effectiveness of ultrasound-guided and fluoroscopy-guided lumbar selective nerve root block (SNRB), and to explore the feasibility of ultrasound-guided methods. This retrospective study included patients with lumbar radicular pain who underwent ultrasound-guided and fluoroscopy-guided selective nerve root block at Honghui Hospital Affiliated to Xi'an Jiaotong University from August 2020 to August 2022. Patients were divided into U-SNRB group and F-SNRB group according to ultrasound-guided or fluoroscopy-guided selective nerve root block. There were 43 patients in U-SNRB group and 20 patients in F-SNRB group. The pain visual analogue scale (VAS) scores, Japanese Orthopaedic Association (JOA) scores, related indexes and complications were recorded and compared between the two groups before, 30 min, 1 month and 6 months after block. To evaluate the feasibility, accuracy and effectiveness of ultrasound-guided selective nerve root block. There were no complications in the process of selective nerve root block in both groups. The operating time and the times of closing needle angle adjustment in U-SNRB group were better than those in F-SNRB group, and the difference was statistically significant (P < 0.05). The VAS score and JOA score of patients in the two groups were significantly improved 30 min after block, 1 month and 6 months after block, and the difference was statistically significant (P < 0.05). There was no significant difference between the two groups (P > 0.05). The accuracy of ultrasound-guided selective nerve root block and the degree of pain relief of patients were similar to those of fluoroscopy guidance, but the operation time and needle angle adjustment times were significantly less than that of fluoroscopy, and could effectively reduce radiation exposure. Therefore, it can be used as a better way to guide for choice.