Mechanistic insights into phosphoactivation of SLAC1 in guard cell signaling.

Stomata in leaves regulate gas (carbon dioxide and water vapor) exchange and water transpiration between plants and the atmosphere. SLow Anion Channel 1 (SLAC1) mediates anion efflux from guard cells and plays a crucial role in controlling stomatal aperture. It serves as a central hub for multiple signaling pathways in response to environmental stimuli, with its activity regulated through phosphorylation via various plant protein kinases. However, the molecular mechanism underlying SLAC1 phosphoactivation has remained elusive. Through a combination of protein sequence analyses, AlphaFold-based modeling and electrophysiological studies, we unveiled that the highly conserved motifs on the N- and C-terminal segments of SLAC1 form a cytosolic regulatory domain (CRD) that interacts with the transmembrane domain(TMD), thereby maintaining the channel in an autoinhibited state. Mutations in these conserved motifs destabilize the CRD, releasing autoinhibition in SLAC1 and enabling its transition into an activated state. Our further studies demonstrated that SLAC1 activation undergoes an autoinhibition-release process and subsequent structural changes in the pore helices. These findings provide mechanistic insights into the activation mechanism of SLAC1 and shed light on understanding how SLAC1 controls stomatal closure in response to environmental stimuli.

Structure and activity of SLAC1 channels for stomatal signaling in leaves.

Stomata in leaves regulate gas exchange between the plant and its atmosphere. Various environmental stimuli elicit abscisic acid (ABA); ABA leads to phosphoactivation of slow anion channel 1 (SLAC1); SLAC1 activity reduces turgor pressure in aperture-defining guard cells; and stomatal closure ensues. We used electrophysiology for functional characterizations of Arabidopsis thaliana SLAC1 (AtSLAC1) and cryoelectron microscopy (cryo-EM) for structural analysis of Brachypodium distachyon SLAC1 (BdSLAC1), at 2.97-Å resolution. We identified 14 phosphorylation sites in AtSLAC1 and showed nearly 330-fold channel-activity enhancement with 4 to 6 of these phosphorylated. Seven SLAC1-conserved arginines are poised in BdSLAC1 for regulatory interaction with the N-terminal extension. This BdSLAC1 structure has its pores closed, in a basal state, spring loaded by phenylalanyl residues in high-energy conformations. SLAC1 phosphorylation fine-tunes an equilibrium between basal and activated SLAC1 trimers, thereby controlling the degree of stomatal opening.

Inferring Users' Social Roles with a Multi-Level Graph Neural Network Model.

Users of social networks have a variety of social statuses and roles. For example, the users of Weibo include celebrities, government officials, and social organizations. At the same time, these users may be senior managers, middle managers, or workers in companies. Previous studies on this topic have mainly focused on using the categorical, textual and topological data of a social network to predict users' social statuses and roles. However, this cannot fully reflect the overall characteristics of users' social statuses and roles in a social network. In this paper, we consider what social network structures reflect users' social statuses and roles since social networks are designed to connect people. Taking an Enron email dataset as an example, we analyzed a preprocessing mechanism used for social network datasets that can extract users' dynamic behavior features. We further designed a novel social network representation learning algorithm in order to infer users' social statuses and roles in social networks through the use of an attention and gate mechanism on users' neighbors. The extensive experimental results gained from four publicly available datasets indicate that our solution achieves an average accuracy improvement of 2% compared with GraphSAGE-Mean, which is the best applicable inductive representation learning method.

Identification of novel cis-elements bound by BplMYB46 involved in abiotic stress responses and secondary wall deposition.

Transcription factors (TFs) play vital roles in various biological processes by binding to cis-acting elements to control expressions of their target genes. The MYB TF BplMYB46, from Betula platyphylla, is involved in abiotic stress responses and secondary wall deposition. In the present study, we used a TF-centered yeast one-hybrid technology (TF-centered Y1H) to identify the cis-acting elements bound by BplMYB46. We screened a short-insert random library and identified three cis-elements bound by BplMYB46: an E-box (CA(A/T/C)(A/G/C)TG) and two novel motifs, a TC-box (T(G/A)TCG(C/G)) and a GT-box (A(G/T)T(A/C)GT(T/G)C). Chromatin immunoprecipitation (ChIP) and effector-reporter coexpression assays in Nicotiana tabacum confirmed binding of BplMYB46 to the TC-box, GT-box, and E-box motifs in the promoters of the phenylalanine ammonia lyase (PAL), peroxidase (POD), and superoxide dismutase (SOD) genes, which function in abiotic stress tolerance and secondary wall biosynthesis. This finding improves our understanding of potential regulatory mechanisms in the response to abiotic stress and secondary wall deposition of BplMYB46 in B. platyphylla.

Expression of the MYB transcription factor gene BplMYB46 affects abiotic stress tolerance and secondary cell wall deposition in Betula platyphylla.

Plant MYB transcription factors control diverse biological processes, such as differentiation, development and abiotic stress responses. In this study, we characterized BplMYB46, an MYB gene from Betula platyphylla (birch) that is involved in both abiotic stress tolerance and secondary wall biosynthesis. BplMYB46 can act as a transcriptional activator in yeast and tobacco. We generated transgenic birch plants with overexpressing or silencing of BplMYB46 and subjected them to gain- or loss-of-function analysis. The results suggest that BplMYB46 improves salt and osmotic tolerance by affecting the expression of genes including SOD, POD and P5CS to increase both reactive oxygen species scavenging and proline levels. In addition, BplMYB46 appears to be involved in controlling stomatal aperture to reduce water loss. Overexpression of BplMYB46 increases lignin deposition, secondary cell wall thickness and the expression of genes in secondary cell wall formation. Further analysis indicated that BplMYB46 binds to MYBCORE and AC-box motifs and may directly activate the expression of genes involved in abiotic stress responses and secondary cell wall biosynthesis whose promoters contain these motifs. The transgenic BplMYB46-overexpressing birch plants, which have improved salt and osmotic stress tolerance, higher lignin and cellulose content and lower hemicellulose content than the control, have potential applications in the forestry industry.

ViRBase: a resource for virus-host ncRNA-associated interactions.

Increasing evidence reveals that diverse non-coding RNAs (ncRNAs) play critically important roles in viral infection. Viruses can use diverse ncRNAs to manipulate both cellular and viral gene expression to establish a host environment conducive to the completion of the viral life cycle. Many host cellular ncRNAs can also directly or indirectly influence viral replication and even target virus genomes. ViRBase (http://www.rna-society.org/virbase) aims to provide the scientific community with a resource for efficient browsing and visualization of virus-host ncRNA-associated interactions and interaction networks in viral infection. The current version of ViRBase documents more than 12,000 viral and cellular ncRNA-associated virus-virus, virus-host, host-virus and host-host interactions involving more than 460 non-redundant ncRNAs and 4400 protein-coding genes from between more than 60 viruses and 20 hosts. Users can query, browse and manipulate these virus-host ncRNA-associated interactions. ViRBase will be of help in uncovering the generic organizing principles of cellular virus-host ncRNA-associated interaction networks in viral infection.

ThWRKY4 from Tamarix hispida Can Form Homodimers and Heterodimers and Is Involved in Abiotic Stress Responses.

WRKY proteins are a large family of transcription factors that are involved in diverse developmental processes and abiotic stress responses in plants. However, our knowledge of the regulatory mechanisms of WRKYs participation in protein-protein interactions is still fragmentary, and such protein-protein interactions are fundamental in understanding biological networks and the functions of proteins. In this study, we report that a WRKY protein from Tamarix hispida, ThWRKY4, can form both homodimers and heterodimers with ThWRKY2 and ThWRKY3. In addition, ThWRKY2 and ThWRKY3 can both bind to W-box motif with binding affinities similar to that of ThWRKY4. Further, the expression patterns of ThWRKY2 and ThWRKY3 are similar to that of ThWRKY4 when plants are exposed to abscisic acid (ABA). Subcellular localization shows that these three ThWRKY proteins are nuclear proteins. Taken together, these results demonstrate that ThWRKY4 is a dimeric protein that can form functional homodimers or heterodimers that are involved in abiotic stress responses.

Exogenous GA3 Application Enhances Xylem Development and Induces the Expression of Secondary Wall Biosynthesis Related Genes in Betula platyphylla.

Gibberellin (GA) is a key signal molecule inducing differentiation of tracheary elements, fibers, and xylogenesis. However the molecular mechanisms underlying the effect of GA on xylem elongation and secondary wall development in tree species remain to be determined. In this study, Betula platyphylla (birch) seeds were treated with 300 ppm GA3 and/or 300 ppm paclobutrazol (PAC), seed germination was recorded, and transverse sections of hypocotyls were stained with toluidine blue; the two-month-old seedlings were treated with 50 µM GA3 and/or 50 µM PAC, transverse sections of seedling stems were stained using phloroglucinol-HCl, and secondary wall biosynthesis related genes expression was analyzed by real-time quantitative PCR. Results indicated that germination percentage, energy and time of seeds, hypocotyl height and seedling fresh weight were enhanced by GA3, and reduced by PAC; the xylem development was wider in GA3-treated plants than in the control; the expression of NAC and MYB transcription factors, CESA, PAL, and GA oxidase was up-regulated during GA3 treatment, suggesting their role in GA3-induced xylem development in the birch. Our results suggest that GA3 induces the expression of secondary wall biosynthesis related genes to trigger xylogenesis in the birch plants.

Characteristics of resistivity variation in deep granite and in-situ detection applications.

During the construction of deep vertical shafts, water inrush and flooding accidents are prone to occur, which seriously affect construction safety. Accurately determining the groundwater conditions is a prerequisite for effectively controlling water hazards and conducting risk management. In order to ensure the accuracy of the resistivity method in deep vertical well water exploration construction, a combination of indoor rock physics, mechanical testing, and on-site engineering measurements was used to analyze the influencing factors of granite resistivity. The corresponding relationship between resistivity and formation integrity was revealed, and water exploration experiments were conducted in the working face of deep underground mines. The results show that: (1) Rock resistivity is influenced by metallic minerals, saturation, temperature, ion content of fracture water, and joints. Regarding deep subsurface detection issues, the main factors affecting the detection results are water content and rock integrity. (2) During the loading process, rock resistivity exhibits significant stage response characteristics, which are closely related to rock integrity and damage accumulation. (3) A degradation model for aquifer zoning based on resistivity benchmark line was established. When the formation resistivity is higher than the benchmark line, it indicates a well-integrated formation with low water content. (4) Resistivity cloud maps and zoning degradation models can be used to visually determine and evaluate the occurrence status of formations and the effectiveness of grouting.

Mapping enhancer and chromatin accessibility landscapes charts the regulatory network of Alzheimer's disease.

BACKGROUND: Enhancers are regulatory elements that target and modulate gene expression and play a role in human health and disease. However, the roles of enhancer regulatory circuit abnormalities driven by epigenetic alterations in Alzheimer's disease (AD) are unclear. METHODS: In this study, a multiomic integrative analysis was performed to map enhancer and chromatin accessibility landscapes and identify regulatory network abnormalities in AD. We identified differentially methylated enhancers and constructed regulatory networks across brain regions using AD brain tissue samples. Through the integration of snATAC-seq and snRNA-seq datasets, we mapped enhancers with DNA methylation alterations (DMA) and chromatin accessibility landscapes. Core regulatory triplets that contributed to AD neuropathology in specific cell types were further prioritized. RESULTS: We revealed widespread DNA methylation alterations (DMA) in the enhancers of AD patients across different brain regions. In addition, the genome-wide transcription factor (TF) binding profiles showed that enhancers with DMA are pervasively regulated by TFs. The TF-enhancer-gene regulatory network analysis identified core regulatory triplets that are associated with brain and immune cell proportions and play important roles in AD pathogenesis. Enhancer regulatory circuits with DMA exhibited distinct chromatin accessibility patterns, which were further characterized at single-cell resolutions. CONCLUSIONS: Our study comprehensively investigated DNA methylation-mediated regulatory circuit abnormalities and provided novel insights into the potential pathogenesis of AD.

A neural m6A pathway regulates behavioral aggregation in migratory locusts.

RNA N6-methyladenosine (m6A), as the most abundant modification of messenger RNA, can modulate insect behaviors, but its specific roles in aggregation behaviors remain unexplored. Here, we conducted a comprehensive molecular and physiological characterization of the individual components of the methyltransferase and demethylase in the migratory locust Locusta migratoria. Our results demonstrated that METTL3, METTL14 and ALKBH5 were dominantly expressed in the brain and exhibited remarkable responses to crowding or isolation. The individual knockdown of methyltransferases (i.e., METTL3 and METTL14) promoted locust movement and conspecific attraction, whereas ALKBH5 knockdown induced a behavioral shift toward the solitary phase. Furthermore, global transcriptome profiles revealed that m6A modification could regulate the orchestration of gene expression to fine tune the behavioral aggregation of locusts. In summary, our in vivo characterization of the m6A functions in migratory locusts clearly demonstrated the crucial roles of the m6A pathway in effectively modulating aggregation behaviors.

Development of an m6A-Related lncRNAs Signature Predicts Tumor Stemness and Prognosis for Low-Grade Glioma Patients.

Background: Growing evidence has revealed that m6A modification of long noncoding RNAs (lncRNAs) dynamically controls tumor stemness and tumorigenesis-related processes. However, the prognostic significance of m6A-related lncRNAs and their associations with stemness in low-grade glioma (LGG) remain to be clarified. Methods: A multicenter transcriptome analysis of lncRNA expression in 1,247 LGG samples was performed in this study. The stemness landscape of LGG tumors was presented and associations with clinical features were revealed. The m6A-related lncRNAs were identified between stemness groups and were further prioritized via least absolute shrinkage and selection operator Cox regression analysis. A risk score model based on m6A-related lncRNAs was constructed and validated in external LGG datasets. Results: Based on the expression of LINC02984, PFKP-DT, and CRNDE, a risk model and nomogram were constructed; they successfully predicted the survival of patients and were extended to external datasets. Significant correlations were observed between the risk score and tumor stemness. Moreover, patients in different risk groups exhibited distinct tumor immune microenvironments and immune signatures. We finally provided several potential compounds suitable for specific risk groups, which may aid in LGG treatment. Conclusions: This novel signature presents noteworthy value in the prediction of prognosis and stemness status for LGG patients and will foster future research on the development of clinical regimens.

Hierarchical porous tri-metallic NiCoFe-Se/CFP derived from Ni-Co-Fe Prussian blue analogues as efficient electrocatalyst for oxygen evolution reaction.

The progress of inexpensive, high-efficiency, and steady oxygen evolution reaction (OER) electrocatalysts is of great importance to promoting water splitting for green hydrogen production. Herein, tri-metallic NiCoFe selenide catalyst backed up by carbon fiber paper (CFP) was synthesized by a facile selenization of NiCoFe Prussian blue analogues (PBAs) for OER in alkaline solutions. The NiCoFe-Se/CFP inherited the porous nanostructure of the metal-organic frameworks (MOFs) precursors prepared by rapid cyclic voltammetry electrodeposition. Benefiting from the 3D hierarchical porous structure, optimized electronic structure of NiCoFe selenides and high conductivity, the synthesized electrocatalyst exhibits outstanding catalytic activity to the corresponding mono-metallic or bi-metallic selenides. Specifically, the NiCoFe-Se/CFP electrode demands an overpotential of 221 mV to attain the 10 mA cm-2 current density in 1.0 M KOH solution and a low Tafel slope of 38.6 mV dec-1. The prepared catalyst also displays good stability and durability. These findings prove a feasible strategy to further improve the catalytic activities of non-precious metal based OER electrocatalysts by the cooperation of structure design and chemical component modification.

Identification of performance and cost in a new backwash method to clean the UF membrane: backwashing with low dosage of NaClO.

Ultrafiltration (UF) is widely used in wastewater reclamation treatments. Conventional backwashing is usually performed at regular time intervals (10-120 min) with permeate and without the addition of chemicals. Chemical enhanced backwashing (CEB) is usually applied after 70-90 filtration cycles with added chemicals. These cleaning methods cause membrane fouling and require costly chemicals. Instead of conventional backwashing, we propose herein a new backwashing method involving backwashing the effluent with low doses of sodium hypochlorite (NaClO) named as BELN. The performance and cost of UF backwashing were investigated with Beijing wastewater reclamation treatment. The results showed that the transmembrane pressure (TMP) increased from 33.2 to 48.2 kPa during hydraulic backwashing after 80 filtration cycles but increased from 33.3 to 39.3 kPa during backwashing with a low NaClO content of 20 mg/L. It was also noticed that the hydraulic-irreversible fouling index decreased from 5.58 × 10-3 m2/L to 3.58 × 10-3 m2/L with the new method. According to the three-dimensional fluorescence excitation-emission (3D-EEM), the response increased from 11.9 to 15.2% with BELN. Protein-like material was identified as the main component causing membrane fouling by blocking the membrane pores. The results indicated that the low dosage of NaClO effectively stripped the fouling layer. Finally, based on an economic evaluation, the capacity of the UF process was increased from 76,959 to 109,133 m3/d with the new method. The amount of NaClO consumed for Beijing wastewater reclamation treatment was similarly compared with the conventional backwashing in per year under BELN. The new method has good potential for application.

Epigenetically regulated lncRNAs dissect the intratumoural heterogeneity and facilitate immune evasion of glioblastomas.

Background: Glioblastomas are the most common and malignant central nervous system (CNS) tumors that occupied a highly heterogeneous tumor microenvironment (TIME). Long noncoding RNAs (lncRNAs), whose expression can be modified by DNA methylation, are emerging as critical regulators in the immune system. However, knowledge about the epigenetic changes in lncRNAs and their contribution to the immune heterogeneity of glioma is still lacking. Methods: In this study, we integrated paired methylome and transcriptome datasets of glioblastomas and identified 2 robust immune subtypes based on lncRNA methylation features. The immune characteristics of glioma subtypes were compared. Furthermore, immune-related lncRNAs were identified and their relationships with immune evasion were evaluated. Results: Glioma immunophenotypes exhibited distinct immune-related characteristics as well as clinical and epigenetic features. 149 epigenetically regulated (ER) lncRNAs were recognized that possessed inverse variation in epigenetic and transcriptional levels between glioma subtypes. Immune-related lncRNAs were further identified through the investigation of their correlation with immune cell infiltrations and immune-related pathways. In particular, the 'Hot' glioma subtype with higher immunoactivity while a worse survival outcome was found to character immune evasion features. We finally prioritized candidate ER lncRNAs associated with immune evasion markers and response to glioma immunotherapy. Among them, CD109-AS1 and LINC02447 were validated as novel immunoevasive biomarkers for glioma through in vitro experiments. Conclusion: In summary, our study systematically reveals the crosstalk among DNA methylation, lncRNA, and immune regulation in glioblastomas, and will facilitate the development of epigenetic immunotherapy approaches.

Structure and activation mechanism of the rice Salt Overly Sensitive 1 (SOS1) Na+/H+ antiporter.

Salinity is one of the most severe abiotic stresses that adversely affect plant growth and agricultural productivity. The plant Na+/H+ antiporter Salt Overly Sensitive 1 (SOS1) located in the plasma membrane extrudes excess Na+ out of cells in response to salt stress and confers salt tolerance. However, the molecular mechanism underlying SOS1 activation remains largely elusive. Here we elucidate two cryo-electron microscopy structures of rice (Oryza sativa) SOS1, a full-length protein in an auto-inhibited state and a truncated version in an active state. The SOS1 forms a dimeric architecture, with an NhaA-folded transmembrane domain portion in the membrane and an elongated cytosolic portion of multiple regulatory domains in the cytoplasm. The structural comparison shows that SOS1 adopts an elevator transport mechanism accompanied by a conformational transition of the highly conserved Pro148 in the unwound transmembrane helix 5 (TM5), switching from an occluded conformation in the auto-inhibited state to a conducting conformation in the active state. These findings allow us to propose an inhibition-release mechanism for SOS1 activation and elucidate how SOS1 controls Na+ homeostasis in response to salt stress.

A maize epimerase modulates cell wall synthesis and glycosylation during stomatal morphogenesis.

The unique dumbbell-shape of grass guard cells (GCs) is controlled by their cell walls which enable their rapid responses to the environment. The molecular mechanisms regulating the synthesis and assembly of GC walls are as yet unknown. Here we have identified BZU3, a maize gene encoding UDP-glucose 4-epimerase that regulates the supply of UDP-glucose during GC wall synthesis. The BZU3 mutation leads to significant decreases in cellular UDP-glucose levels. Immunofluorescence intensities reporting levels of cellulose and mixed-linkage glucans are reduced in the GCs, resulting in impaired local wall thickening. BZU3 also catalyzes the epimerization of UDP-N-acetylgalactosamine to UDP-N-acetylglucosamine, and the BZU3 mutation affects N-glycosylation of proteins that may be involved in cell wall synthesis and signaling. Our results suggest that the spatiotemporal modulation of BZU3 plays a dual role in controlling cell wall synthesis and glycosylation via controlling UDP-glucose/N-acetylglucosamine homeostasis during stomatal morphogenesis. These findings provide insights into the mechanisms controlling formation of the unique morphology of grass stomata.

The generation mechanism of Turing-pattern in a Tree-grass competition model with cross diffusion and time delay.

In this paper, we study the general mechanism of Turing-pattern in a tree-grass competition model with cross diffusion and time delay. The properties of four equilibrium points, the existence of Hopf bifurcation and the sufficient conditions for Turing instability caused by cross-diffusion are analyzed, respectively. The amplitude equation of tree-grass competition model is derived by using multi-scale analysis method, and its nonlinear stability is studied. The sensitivity analysis also verified that fire frequency plays a key role in tree-grass coexistence equilibrium. Finally, the Turing pattern of tree-grass model obtained by numerical simulation is consistent with the spatial structure of tree-grass density distribution observed in Hulunbuir grassland, China.

Artificial Intelligence Algorithm-Based Intraoperative Magnetic Resonance Navigation for Glioma Resection.

The study aimed to analyze the application value of artificial intelligence algorithm-based intraoperative magnetic resonance imaging (iMRI) in neurosurgical glioma resection. 108 patients with glioma in a hospital were selected and divided into the experimental group (intraoperative magnetic resonance assisted glioma resection) and the control group (conventional surgical experience resection), with 54 patients in each group. After the resection, the tumor resection rate, NIHSS (National Institute of Health Stroke Scale) score, Karnofsky score, and postoperative intracranial infection were calculated in the two groups. The results revealed that the average tumor resection rate in the experimental group was significantly higher than that in the control group (P < 0.05). There was no significant difference in Karnofsky score before and after the operation in the experimental group (P > 0.05). There was no significant difference in NIHSS score between the experimental group and the control group after resection (P > 0.05). The number of patients with postoperative neurological deficits in the experimental group was smaller than that in the control group. In addition, there was no significant difference in infection rates between the two groups after glioma resection (P > 0.05). In summary, intraoperative magnetic resonance navigation on the basis of a segmentation dictionary learning algorithm has great clinical value in neurosurgical glioma resection. It can maximize the removal of tumors and ensure the integrity of neurological function while avoiding an increased risk of postoperative infection, which is of great significance for the treatment of glioma.

Cryo-EM structure and electrophysiological characterization of ALMT from Glycine max reveal a previously uncharacterized class of anion channels.

Aluminum-activated malate transporters (ALMTs) form an anion channel family that plays essential roles in diverse functions in plants. Arabidopsis ALMT12, also named QUAC1 (quick anion channel 1), regulates stomatal closure in response to environmental stimuli. However, the molecular basis of ALMT12/QUAC1 activity remains elusive. Here, we describe the cryo-EM structure of ALMT12/QUAC1 from Glycine max at 3.5-Å resolution. GmALMT12/QUAC1 is a symmetrical dimer, forming a single electropositive T-shaped pore across the membrane. The transmembrane and cytoplasmic domains are assembled into a twisted two-layer architecture, with their associated dimeric interfaces nearly perpendicular. GmALMT12/QUAC1-mediated currents display rapid kinetics of activation/deactivation and a bell-shaped voltage dependency, reminiscent of the rapid (R)-type anion currents. Our structural and functional analyses reveal a domain-twisting mechanism for malate-mediated activation. Together, our study uncovers the molecular basis for a previously uncharacterized class of anion channels and provides insights into the gating and modulation of the ALMT12/QUAC1 anion channel.