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Abstract Enhancing wheat productivity by implementing a comprehensive approach that combines irrigation, nutrition, and organic amendments shows potential for collectively enhancing crop performance. This study examined the individual and combined effects of using irrigation systems (IS), foliar potassium bicarbonate (PBR) application, and compost application methods (CM) on nine traits related to the growth, physiology, and yield of the Giza-171 wheat cultivar. Analysis of variance revealed significant (P ≤ 0.05) main effects of IS, PBR, and CM on wheat growth, physiology, and yield traits over the two growing seasons of the study. Drip irrigation resulted in a 16% increase in plant height, leaf area index, crop growth rate, yield components, and grain yield compared to spray irrigation. Additionally, the application of foliar PBR at a concentration of 0.08 g/L boosted these parameters by up to 22% compared to the control. Furthermore, the application of compost using the role method resulted in enhanced wheat performance compared to the treatment including mix application. Importantly, the combined analysis revealed that the three-way interaction between the three factors had a significant effect (P ≤ 0.05) on all the studied traits, with drip irrigation at 0.08 g PBR rate and role compost application method (referred as Drip_0.08g_Role) resulting in the best performance across all traits, while sprinkle irrigation without PBR and conventional mixed compost method (referred as sprinkle_CK_Mix) produced the poorest results. This highlights the potential to synergistically improve wheat performance through optimized agronomic inputs.

Abstract Background As the most widely cultivated fiber crop, cotton production depends on hybridization to unlock the yield potential of current varieties. A deep understanding of genetic dissection is crucial for the cultivation of enhanced hybrid plants with desired traits, such as high yield and fine fiber quality. In this study, the general combining ability (GCA) and specific combining ability (SCA) of yield and fiber quality of nine cotton parents (six lines and three testers) and eighteen F1 crosses produced using a line × tester mating design were analyzed. Results The results revealed significant effects of genotypes, parents, crosses, and interactions between parents and crosses for most of the studied traits. Moreover, the effects of both additive and non-additive gene actions played a notably significant role in the inheritance of most of the yield and fiber quality attributes. The F1 hybrids of (Giza 90 × Aust) × Giza 86, Uzbekistan 1 × Giza 97, and Giza 96 × Giza 97 demonstrated superior performance due to their favorable integration of high yield attributes and premium fiber quality characteristics. Path analysis revealed that lint yield has the highest positive direct effect on seed cotton yield, while lint percentage showed the highest negative direct effect on seed cotton yield. Principal component analysis identified specific parents and hybrids associated with higher cotton yield, fiber quality, and other agronomic traits. Conclusion This study provides insights into identifying potential single- and three-way cross hybrids with superior cotton yield and fiber quality characteristics, laying a foundation for future research on improving fiber quality in cotton.

Emerging evidence has highlighted the capacity of hematogenous cells in skull and vertebral bone marrow to enter the meningeal borders via ossified vascular channels and maintain immune homeostasis in the central nervous system (CNS). CNS-adjacent skull and vertebral bone marrow comprises hematopoietic niches that can sense CNS injury and supply specialized immune cells to fine-tune inflammatory responses. Here, we review recent advances in our understanding of skull and vertebral bone marrow-derived immune cells in homeostasis and inflammatory CNS diseases. Further, we discuss the implications for future development of therapies to mitigate CNS inflammation and its detrimental sequelae in neurological disorders.

Maize is an economically vital cereal crop. However, water deficiency can severely impact its productivity. Thus, it is necessary to implement an essential approach to increase maize yield while navigating the limitations imposed by scarce water supplies. The present study aimed to investigate whether foliar applications of silicon (Si) and zinc (Zn) could mitigate the adverse effects of water deficiency and improve maize growth and yield. Field experiments were conducted in Egypt during two growing seasons (2021–2022) under three irrigation regimes: full irrigation (ET0), moderate stress (ET1), and severe stress (ET2). The treatments comprised foliar sprays of Si, Zn, Si + Zn, and water control. Phenological, growth, physiological, chemical, and yield-related traits were assessed. Results showed that adequate irrigation (ET0) enhanced most parameters compared to water stress treatments. Under ET0, the combined silicon and zinc treatment resulted in the highest values for plant height, leaf area, chlorophyll content, grains per ear, kernel weight, ear size, and yield compared to other foliar treatments. Under drought stress (ET1, ET2), Si + Zn applications maintained superiority in mitigating yield losses. Proline accumulation was highest under severe stress (ET2) in the absence of foliar sprays, indicating greater drought impacts. Correlation analysis revealed positive associations of grain yield with ear size, leaf area, kernel weight, and biological yield. Cluster analysis separated irrigation regimes and visualized the consistently beneficial effects of Si + Zn across all water levels. Overall, the results demonstrate the synergistic potential of Si and Zn supplementation to sustain maize performance and yields under varying water availability.

PurposeOsteosarcoma (OS) is the most common type of primary malignant bone tumor. Transducing a functional TP53 gene can effectively inhibit OS cell activity. Poly lactic acid-glycolic acid (PLGA) nanobubbles (NBs) mediated by focused ultrasound (US) can introduce exogenous genes into target cells in animal models, but this technique relies on the passive free diffusion of agents across the body. The inclusion of superparamagnetic iron oxide (SPIO) in microbubbles allows for magnetic-based tissue localization. A low-intensity-focused ultrasound (LIFU) instrument was developed at our institute, and different intensities of LIFU can either disrupt the NBs (RLI-LIFU) or exert cytocidal effects on the target tissues (RHI-LIFU). Based on these data, we performed US-magnetic-mediated TP53-NB destruction and investigated its ability to inhibit OS growth when combined with LIFU both in vitro and in vivo.MethodsSeveral SPIO/TP53/PLGA (STP) NB variants were prepared and characterized. For the in vitro experiments, HOS and MG63 cells were randomly assigned into five treatment groups. Cell proliferation and the expression of TP53 were detected by CCK8, qRT-PCR and Western blotting, respectively. In vivo, tumor-bearing nude mice were randomly assigned into seven treatment groups. The iron distribution of Perls’ Prussian blue-stained tissue sections was determined by optical microscopy. TUNEL-DAPI was performed to examine apoptosis. TP53 expression was detected by qRT-PCR and immunohistochemistry.ResultsSPIO/TP53/PLGA NBs with a particle size of approximately 200 nm were prepared successfully. For in vitro experiments, ultrasound-targeted transfection of TP53 overexpression in OS cells and efficient inhibition of OS proliferation have been demonstrated. Furthermore, in a tumor-bearing nude mouse model, RLI-LIFU-magnetic-mediated SPIO/TP53/PLGA NBs increased the transfection efficiency of the TP53 plasmid, resulting in apoptosis. Adding RHI-LIFU to the treatment regimen significantly increased the apoptosis of OS cells in vivo.ConclusionCombining LIFU and US-magnetic-mediated SPIO/TP53/PLGA NB destruction is potentially a novel noninvasive and targeted therapy for OS.

AbstractDrought has historically represented the greatest abiotic stress to adversely affect the stability of soybean (Glycine max (L.) Merr.) yields in non-irrigated field conditions. To investigate the genetic basis underlying drought tolerance in soybean, we screened the seed yield per plant (YP) in a natural diversity panel of 149 accessions under both water deficit (drought-stressed; YP-S) and well-watered (full irrigation; YP-W) conditions in field and greenhouse trials and calculated a drought susceptibility index (DSI) based on the differences in yield between treatments within each accession. A total of 19 quantitative trait loci (QTLs) were identified: eight were significantly associated with YP-W, 10 were associated with YP-S, 2 were associated with DSI and one QTL was associated with both YP-S and DSI. We then compared QTLs identified here with previously reported markers and found that these loci were located in regions associated with yield-related and other agronomic traits. In particular, YP-S-associated single nucleotide polymorphism (SNP) ss246509299 in chromosome (Chr.) 8, and YP-W-associated ss249310678 on Chr. 17 were both previously correlated with canopy wilt. Eight significant QTLs were located within eight genes. Glyma.18g092200, contained ss249600231 and annotated as GmWRKY168, is reportedly responsive to cadmium. This study helps to resolve which loci contribute to yield under drought stress in soybean, and can potentially serve as markers for selection of elite, high-yield and drought tolerant varieties.

Ship lock project currently demonstrates a distinct cyclical pattern, accumulating latent hazards that pose a significant threat to project safety. Seepage safety (the condition in which the seepage risk is reduced to an acceptable level) serves as a crucial indicator in the safety risk assessment index system for ship lock project construction, thus necessitating an in-depth analysis of the risk factors impacting seepage safety. Utilizing a ship lock project in China as a case study, this study employs the finite element method (FEM) to analyze the seepage field of the ship lock foundation pit basin and proposes a comprehensive set of methods for risk evaluation and warning models pertaining to seepage safety risks in ship lock engineering. This study reveals that the obstruction of dewatering wells and imperfections in the diaphragm wall are the primary factors contributing to seepage damage. The investigation conducted a quantitative analysis of the impact of these two factors on the seepage field of the ship lock pit, considering pore pressure, water head, gradient, and flow velocity. A comprehensive set of evaluation indicators for seepage safety was formulated, drawing on the principles of multi-objective optimization, and a method for delineating the safe range of ship lock pit excavation under seepage action was proposed. Subsequently, an integrated seepage safety risk assessment system for ship lock pit excavation engineering was established. These research findings offer a scientific foundation for the management of seepage safety in ship lock pit excavation engineering and provide valuable references and guidance for the development of anti-seepage systems.

Salt-alkali stress is a key factor affecting plant development and production, altering essential physiological and metabolic processes within plants. Particularly, soybean (Glycine max) exhibits a wide range of salt-alkali tolerance in soybean germplasms. Hence, the objective of this research was to pinpoint potential genes that react to salt-alkali stress through a comparative transcriptome analysis of two distinct soybean varieties exposed to such stress conditions. The two soybean varieties, including salt-tolerant Heinong531 and salt-sensitive 20_1846, were used for RNA-seq analysis. Nine physiological parameters including malondialdehyde (MDA), superoxide dismutase (SOD), glutathione (GSH), peroxidase (POD), proline, catalase (CAT), soluble protein, scavenging rate of hydroxyl radical, and soluble sugar activity were measured under the salt-alkaline treatment series of 0,1,2,3,4 days. The results showed that the levels of MDA, proline, and catalase contents decreased significantly, while levels of GSH and POD contents significantly increased. A total of 200 salt-alkali tolerance responsive differentially expressed genes (DEGs) were identified, comprising 93 up-regulated genes and 107 down-regulated. The functional gene ontology analysis for these 200 DEGs, where 29 key DEGs were found to be involved in the regulation of 14 GO pathways responding to salt-alkaline stress which have been previously considered as vital for salt resistance mechanisms in soybean. Remarkably, the association analysis between physiological parameters and differentially expressed genes (DEGs) under salt-alkali stress conditions demonstrated that distinct soybean cultivars exhibited unique patterns of gene expression, ultimately resulting in alterations in physiological indices as a response to such stress conditions. This study offers a compilation of potential genes worthy of additional exploration concerning their role in enhancing soybean's resistance to salt-alkali stress.

Abstract Salt is recognized as one of the most major factors that limits soybean yield in acidic soils. Soil enzyme activity and bacterial community have a critical function in improving the tolerance to soybean. Our aim was to assess the activities of soil enzyme, the structure of bacteria and their potential functions for salt resistance between Salt-tolerant (Salt-T) and -sensitive (Salt-S) soybean genotypes when subject to salt stress. Plant biomass, soil physicochemical properties, soil catalase, urease, sucrase, amylase, and acid phosphatase activities, and rhizosphere microbial characteristics were investigated in Salt-T and Salt-S soybean genotypes under salt stress with a pot experiment. Salt stress significantly decreased the soil enzyme activities and changed the rhizosphere microbial structure in a genotype-dependent manner. In addition, 46 ASVs which were enriched in the Salt-T geotype under the salt stress, such as ASV19 (Alicyclobacillus), ASV132 (Tumebacillus), ASV1760 (Mycobacterium) and ASV1357 (Bacillus), which may enhance the tolerance to soybean under salt stress. Moreover, the network structure of Salt-T soybean was simplified by salt stress, which may result in soil bacterial communities being susceptible to external factors. Salt stress altered the strength of soil enzyme activities and the assembly of microbial structure in Salt-T and Salt-S soybean genotypes. Na+, NO3 −–N, NH4 +–N and Olsen-P were the most important driving factors in the structure of bacterial community in both genotypes. Salt-T genotypes enriched several microorganisms that contributed to enhance salt tolerance in soybeans, such as Alicyclobacillus, Tumebacillus, and Bacillus. Nevertheless, the simplified network structure of salt-T genotype due to salt stress may render its bacterial community structure unstable and susceptible.

A biparental soybean population of 364 recombinant inbred lines (RILs) derived from Zhongdou 41 × ZYD 02.878 was used to identify quantitative trait loci (QTL) associated with hundred-seed weight (100-SW), pod length (PL), and pod width (PW). 100-SW, PL, and PW showed moderate correlations among one another, and 100-SW was correlated most strongly with PW (0.64–0.74). Respectively 74, 70, 75 and 19 QTL accounting for 38.7%–78.8% of total phenotypic variance were identified by inclusive composite interval mapping, restricted two-stage multi-locus genome-wide association analysis, 3 variance-component multi-locus random-SNP-effect mixed linear model analysis, and conditional genome-wide association analysis. Of these QTL, 189 were novel, and 24 were detected by multiple methods. Six loci were associated with 100-SW, PL, and PW and may be pleiotropic loci. A total of 284 candidate genes were identified in colocalizing QTL regions, including the verified gene Seed thickness 1 (ST1). Eleven genes with functions involved in pectin biosynthesis, phytohormone, ubiquitin-protein, and photosynthesis pathways were prioritized by examining single nucleotide polymorphism (SNP) variation, calculating genetic differentiation index, and inquiring gene expression. The prediction accuracies of genomic selection (GS) for 100-SW, PL, and PW based on single trait-associated markers reached 0.82, 0.76, and 0.86 respectively, but selection index (SI)-assisted GS strategy did not increase GS efficiency and inclusion of trait-associated markers as fixed effects reduced prediction accuracy. These results shed light on the genetic basis of 100-SW, PL, and PW and provide GS models for these traits with potential application in breeding programs.

Vegetative soybean (maodou or edamame) serves as a nutrient-rich food source with significant potential for mitigating global nutritional deficiencies. This study undertook a thorough examination of the nutritional profiles and transcriptomic landscapes of six soybean cultivars, including three common cultivars (Heinong551, Heinong562, and Heinong63) and three fresh maodou cultivars (Heinong527, HeinongXS4, and HeinongXS5). Nutrient analysis of the seeds disclosed notable differences in the levels of protein, fat, soluble sugars, vitamin E, calcium, potassium, magnesium, manganese, iron, and zinc across the cultivars. Through comparative transcriptome profiling and RNA sequencing, distinct variations in differentially expressed genes (DEGs) were identified between fresh and traditional maodou cultivars. Functional enrichment analyses underscored the involvement of DEGs in critical biological processes, such as nutrient biosynthesis, seed development, and stress responses. Additionally, association studies demonstrated robust correlations between specific DEG expression patterns and seed nutrient compositions across the different cultivars. Sankey diagrams illustrated that DEGs are strongly linked with seed quality traits, revealing potential molecular determinants that govern variations in nutritional content. The identified DEGs and their relationships with nutritional profiles offer valuable insights for breeding programs focused on developing cultivars with improved nutritional quality, tailored to specific dietary needs or industrial applications.

A phase change materials (PCM) coupled mini-channel cooling plates model was established for the optimization of the battery thermal management system (BTMS). Specific cooling strategies with different discharge rates of the battery were discussed. For a discharge rate of under 2C, using PCM can meet the heat dissipation needs. Particularly, for a discharge rate below 1.2C, external cooling was not necessary. For a discharge rate above 2C, active cooling should be added to compensate for the lack of heat storage of PCM. In the research of optimization structure, it was found that the scheme of four cooling plates and each cooling plate with two mini-channels was the most ideal in this research, which not only reduced the battery temperature efficiently but also maintained a good temperature uniformity of the battery. For the optimization parameters, the effect of the ethylene glycol solution temperature, ethylene glycol solution volume fraction and the start-up time of active cooling on the maximum temperature of the battery and the melting fraction of PCM were discussed. After the multi-factor parameters optimization by Response Surface Methodology, three optimization schemes were put forward, which could reduce the driving power consumption by 35% – 40%. The research could provide valuable information support and optimization suggestions for the design of BTMS.

Microglia are first responders to acute brain insults and initiate neuroinflammation to drive secondary tissue injury. Yet the key molecular switches in control of the inflammatory activity of microglia remain poorly understood. Intracerebral hemorrhage (ICH) is a devastating stroke subtype whereby a hematoma is formed within the brain parenchyma and associated with high mortality. Using a mouse model of ICH, we found upregulation of CD22 that predominantly occurred in microglia. Antibody blockade of CD22 led to a reduction in neurological deficits, brain lesion and hematoma volume. This was accompanied by reduced inflammatory activity, increased expression of alternative activation markers (CD206 and IL-10) and enhanced phagocytosis activity in microglia after ICH. CD22 blockade also led to an increase of phosphorylated SYK and AKT after ICH. Notably, the benefits of CD22 blockade were ablated in ICH mice subjected to microglial depletion with a colony-stimulating factor 1 receptor inhibitor PLX5622. Additionally, the protective effects of CD22 blockade was diminished in ICH mice receiving a SYK inhibitor R406. Together, our findings highlight CD22 as a key molecular switch to control the detrimental effects of microglia after acute brain injury, and provide a novel strategy to improve the outcome of ICH injury.

IntroductionRhizosphere microorganisms can effectively promote the stress resistance of plants, and some beneficial rhizosphere microorganisms can significantly promote the growth of crops under salt stress, which has the potential to develop special microbial fertilizers for increasing the yield of saline-alkali land and provides a low-cost and environmentally friendly new strategy for improving the crop yield of saline-alkali cultivated land by using agricultural microbial technology.MethodsIn May 2022, a field study in a completely randomized block design was conducted at the Heilongjiang Academy of Agricultural Sciences to explore the correlation between plant rhizosphere microorganisms and soybean growth in saline-alkali soil. Two soybean cultivars (Hening 531, a salt-tolerant variety, and 20_1846, a salt-sensitive variety) were planted at two experimental sites [Daqing (normal condition) and Harbin (saline-alkali conditions)], aiming to investigate the performance of soybean in saline-alkali environments.ResultsSoybeans grown in saline-alkali soil showed substantial reductions in key traits: plant height (25%), pod number (26.6%), seed yield (33%), and 100 seed weight (13%). This underscores the unsuitability of this soil type for soybean cultivation. Additionally, microbial analysis revealed 43 depleted and 56 enriched operational taxonomic units (OTUs) in the saline-alkali soil compared to normal soil. Furthermore, an analysis of ion-associated microbes identified 85 mOTUs with significant correlations with various ions. A co-occurrence network analysis revealed strong relationships between specific mOTUs and ions, such as Proteobacteria with multiple ions. In addition, the study investigated the differences in rhizosphere species between salt-tolerant and salt-sensitive soybean varieties under saline-alkali soil conditions. Redundancy analysis (RDA) indicated that mOTUs in saline-alkali soil were associated with pH and ions, while mOTUs in normal soil were correlated with Ca2+ and K+. Comparative analyses identified significant differences in mOTUs between salt-tolerant and salt-sensitive varieties under both saline-alkali and normal soil conditions. Planctomycetes, Proteobacteria, and Actinobacteria were dominant in the bacterial community of saline-alkali soil, with significant enrichment compared to normal soil. The study explored the functioning of the soybean rhizosphere key microbiome by comparing metagenomic data to four databases related to the carbon, nitrogen, phosphorus, and sulfur cycles. A total of 141 KOs (KEGG orthologues) were identified, with 66 KOs related to the carbon cycle, 16 KOs related to the nitrogen cycle, 48 KOs associated with the phosphorus cycle, and 11 KOs linked to the sulfur cycle. Significant correlations were found between specific mOTUs, functional genes, and phenotypic traits, including per mu yield (PMY), grain weight, and effective pod number per plant.ConclusionOverall, this study provides comprehensive insights into the structure, function, and salt-related species of soil microorganisms in saline-alkali soil and their associations with salt tolerance and soybean phenotype. The identification of key microbial species and functional categories offers valuable information for understanding the mechanisms underlying plant-microbe interactions in challenging soil conditions.

Neurons communicate differently from non-neuronal cells. Here, authors present a method, NeuronChat, that utilizes scRNA-seq data and/or spatial transcriptomics to infer, visualize and analyze neural-specific cell-cell communication.

For the problem that the traceability parameters of sudden water pollution are difficult to determine, a fast traceability model based on a simplified mechanistic model coupled with an optimization algorithm is proposed to improve the accuracy of sudden water pollution traceability. In this paper, according to the diffusion law of pollutants, a quantitative formula of pollutant diffusion is proposed, and the differential calculation process of the pollutant convection equation is optimized. The Dynamic Programming and Beetle Antennae Search algorithm (DP-BAS) with dynamic step size is used in the reverse optimization process, which can avoid the problem of entering the local optimal solution in the calculation process. The DP-BAS is used to inverse solve the quantization equation to realize the decoupling of pollutant traceability parameters, transforming the multi-parameter coupled solution into a single-parameter solution, reducing the solution dimension, and optimizing the difficulty and solution complexity of pollutant traceability. The proposed traceability model is applied to the simulation case, the results show that the mean square errors of pollutant placement mass, location, and time are 2.39, 1.16, and 1.19 percent, respectively. To further verify the model reliability, the Differential Evolution and Markov Chain Monte Carlo simulation method (DE-MCMC) as well as Genetic Algorithms (GA) were introduced to compare with the proposed model to prove that the model has certain reliability and accuracy.

A critical task in spatial transcriptomics analysis is to understand inherently spatial relationships among cells. Here, the authors present a deep learning framework to integrate spatial and transcriptional information, spatially extending pseudotime and revealing spatiotemporal organization of cells.

Drought is one of the primary abiotic stress factors affecting the yield, growth, and development of soybeans. In extreme cases, drought can reduce yield by more than 50%. The seedling stage is an important determinant of soybean growth: the number and vigor of seedlings will affect growth and yield at harvest. Therefore, it is important to study the drought resistance of soybean seedlings. In this study, a recombinant inbred line (RIL) population comprising 234 F6:10 lines (derived from Zhonghuang 35 × Jindou 21) and a panel of 259 soybean accessions was subjected to drought conditions to identify the effects on phenotypic traits under these conditions. Using a genetic map constructed by single nucleotide polymorphism (SNPs) markers, 18 quantitative trait loci (QTL) on 7 soybean chromosomes were identified in two environments. This included 9 QTL clusters identified in the RIL population. Fifty-three QTL were identified in 19 soybean chromosomes by genome-wide association analysis (GWAS) in the panel of accessions, including 69 significant SNPs (−log10 (P) ≥ 3.97). A combination of the two populations revealed that two SNPs (−log10 (P) ≥ 3.0) fell within two of the QTL (qPH7-4 and qPH7-6) confidence intervals. We not only re-located several previously reported drought-resistance genes in soybean and other crops but also identified several non-synonymous stress-related mutation site differences between the two parents, involving Glyma.07g093000, Glyma.07g093200, Glyma.07g094100 and Glyma.07g094200. One previously unreported new gene related to drought stress, Glyma.07g094200, was found by regional association analysis. The significant SNP CHR7-17619 (G/T) was within an exon of the Glyma.07g094200 gene. In the RIL population, the DSP value of the “T” allele of CHR7-17619 was significantly (P

In this study, a liquid phase-change cooling module with mini-channels cold plate was designed. The temperature properties of a battery monomer with different cooling conditions and varying discharge rates were investigated. The heat dissipation contribution of latent heat transfer to the overall cooling performance of the mini-channels cold plate was analyzed based on the outlet vapor quality. Particularly, a cooling strategy with varying coolant flow rates was proposed and examined at 3C discharge rate. The results illustrated that the designed battery cooling module had an ideal effect on lowering the battery's surface temperature and increasing the battery's temperature uniformity. Compared to the cooling strategy with constant coolant flow rate, the proposed variable flow cooling strategy better matched the dynamic law of battery heat generation and increased the contribution of the latent heat transfer to the battery cooling, thereby efficiently reducing the coolant consumption and the pump power consumption of the BTMS (battery thermal management system) while providing the same or even superior cooling performance. The findings could assist the optimization of the BTMS and be the reference for the application of the varying flow rate cooling strategy in actual engineering.

For a long-distance open-channel water transfer project, the correctness of the hydrological state study and hydrodynamic numerical simulation is impacted directly by the spatiotemporal and consistency of the flow monitoring data along the project. Reported here is an inverted data cleaning model for flow monitoring stations based on the principle of water dynamic balance and the longest sequence method of interval flow, targeting the abnormal phenomenon of unequal flow at monitoring stations in the dispatching operation and using the middle route of the South-to-North Water Diversion Project in China as the research object. As an example, a hydrodynamic model is built for verification using flow and water level data after model cleaning as the upper and lower boundaries, respectively, for the middle-route project from the Baihe River to Huangjin River. The findings indicate that the cleaning model enhances the accuracy of flow monitoring data and reduces both the mean absolute error of the water level in front of the gate and the root-mean-square error by 0.0757 and 0.0895 m, respectively. In terms of data spatial consistency and logic, the cleaned flow data are superior to the measured flow data.

Glucose-6-phosphate dehydrogenase (G6PDH) is a key enzyme in the pentose phosphate pathway responsible for the generation of nicotinamide adenine dinucleotide phosphate (NADPH), thereby playing a central role in facilitating cellular responses to stress and maintaining redox homeostasis. This study aimed to characterize five G6PDH gene family members in maize. The classification of these ZmG6PDHs into plastidic and cytosolic isoforms was enabled by phylogenetic and transit peptide predictive analyses and confirmed by subcellular localization imaging analyses using maize mesophyll protoplasts. These ZmG6PDH genes exhibited distinctive expression patterns across tissues and developmental stages. Exposure to stressors, including cold, osmotic stress, salinity, and alkaline conditions, also significantly affected the expression and activity of the ZmG6PDHs, with particularly high expression of a cytosolic isoform (ZmG6PDH1) in response to cold stress and closely correlated with G6PDH enzymatic activity, suggesting that it may play a central role in shaping responses to cold conditions. CRISPR/Cas9-mediated knockout of ZmG6PDH1 on the B73 background led to enhanced cold stress sensitivity. Significant changes in the redox status of the NADPH, ascorbic acid (ASA), and glutathione (GSH) pools were observed after exposure of the zmg6pdh1 mutants to cold stress, with this disrupted redox balance contributing to increased production of reactive oxygen species and resultant cellular damage and death. Overall, these results highlight the importance of cytosolic ZmG6PDH1 in supporting maize resistance to cold stress, at least in part by producing NADPH that can be used by the ASA-GSH cycle to mitigate cold-induced oxidative damage.

Walker et al. review methods used to analyse spatial transcriptomics data and discuss open questions and areas of future development.

Due to the temperature of shallow aquifers being affected by atmospheric temperature, groundwater source heat pumps (GWSHPs) become unstable and the operation efficiency of GWSHP is constrained. In the study, the coupling numerical simulation model of the groundwater flow field and temperature field is established based on the continuous monitoring results in an actual experimental site, and the water and thermal migration of shallow aquifer is simulated under the influence of the atmospheric environment. The influence of the dynamic change in ground temperature is analyzed on a GWSHP. The results indicated that the temperature of the shallow aquifer is affected by the external temperature, and the recharge temperature in the summer cooling period was 33°C, and that in the winter heating period was 6°C in the actual site, to avoid the occurrence of thermal penetration when there is a gap between the actual situation and the design situation, the single cooler can balance the insufficient cooling capacity in summer under the most unfavorable situation. The research results can also provide a reference for the development and utilization of geothermal energy resources in shallow aquifers.

Plant height affects crop production and breeding practices, while genetic control of dwarfism draws a broad interest of researchers. Dwarfism in soybean (Glycine max) is mainly unexplored. Here, we characterized a dwarf mutant dm screened from ethyl methanesulfonate (EMS) mutated seeds of the soybean cultivar Zhongpin 661(ZP). Phenotypically, dm showed shorter and thinner stems, smaller leaves, and more nodes than ZP under greenhouse conditions. Genetically, whole-genome sequencing and comparison revealed that 210K variants of SNPs and InDel in ZP relative to the soybean reference genome Williams82, and EMS mutagenesis affected 636 genes with variants predicted to have a large impact on protein function in dm. Whole-genome methylation sequencing found 704 differentially methylated regions in dm. Further whole-genome RNA-Seq based transcriptomic comparison between ZP and dm leaves revealed 687 differentially expressed genes (DEGs), including 263 up-regulated and 424 down-regulated genes. Integrated omics analyses revealed 11 genes with both differential expressions and DNA variants, one gene with differential expression and differential methylation, and three genes with differential methylation and sequence variation, worthy of future investigation. Genes in cellulose, fatty acids, and energy-associated processes could be the key candidate genes for the dwarf phenotype. This study provides genetic clues for further understanding of the genetic control of dwarfism in soybean. The genetic resources could help to inbreed new cultivars with a desirable dwarf characteristic.

Germination of soybean seed is the imminent vital process after sowing. The status of plumular axis and radicle determine whether soybean seed can emerge normally. Epicotyl, an organ between cotyledons and first functional leaves, is essential for soybean seed germination, seedling growth and early morphogenesis. Epicotyl length (EL) is a quantitative trait controlled by multiple genes/QTLs. Here, the present study analyzes the phenotypic diversity and genetic basis of EL using 951 soybean improved cultivars and landraces from Asia, America, Europe and Africa. 3VmrMLM was used to analyze the associations between EL in 2016 and 2020 and 1,639,846 SNPs for the identification of QTNs and QTN-by-environment interactions (QEIs)”.A total of 180 QTNs and QEIs associated with EL were detected. Among them, 74 QTNs (ELS_Q) and 16 QEIs (ELS_QE) were identified to be associated with ELS (epicotyl length of single plant emergence), and 60 QTNs (ELT_Q) and 30 QEIs (ELT_QE) were identified to be associated with ELT (epicotyl length of three seedlings). Based on transcript abundance analysis, GO (Gene Ontology) enrichment and haplotype analysis, ten candidate genes were predicted within nine genic SNPs located in introns, upstream or downstream, which were supposed to be directly or indirectly involved in the process of seed germination and seedling development., Of 10 candidate genes, two of them (Glyma.04G122400 and Glyma.18G183600) could possibly affect epicotyl length elongation. These results indicate the genetic basis of EL and provides a valuable basis for specific functional studies of epicotyl traits.

In recent years, many research methods have been developed for the traceability of groundwater contamination source, in which the numerical simulation and analytical methods are the most common methods to study on groundwater flow and solute transport. However, the establishment and solution of an optimization model is a very complex inverse problem. Given that many decision variables are needed to be identified, two relatively simple analytical and numerical methods are applied for the prediction of chloride migration range and duration process in source area, then the geophysical prospecting and drilling sampling analysis are also used for the verification, moreover, the source center is determined based on the difference between predicted results and measured results. In addition, the influence of the observation points layout, hydrodynamic dispersion parameters and groundwater flow rate on the traceability effect are also analyzed. The results show that located observation points can reflect the chloride distribution accurately, hydrodynamic dispersion parameters and groundwater flow rate have more significant impacts on the traceability effect compared with other factors. Lastly, the proposed model application process is also discussed in the limited scale site, and it provides the reference for source traceability and subsequent remediation design under the similar hydrogeological conditions.

When using the Laplace transform to solve a one-dimensional heat conduction model with Dirichlet boundary conditions, the integration and transformation processes become complex and cumbersome due to the varying properties of the boundary function f(t). Meanwhile, if f(t) has a complex functional form, e.g., an exponential decay function, the product of the image function of the Laplace transform and the general solution to the model cannot be obtained directly due to the difficulty in solving the inverse. To address this issue, operators are introduced to replace f(t) in the transformation process. Based on the properties of the Laplace transform and the convolution theorem, without the direct involvement of f(t) in the transformation, a general theoretical solution incorporating f(t) is derived, which consists of the product of erfc(t) and f(0), as well as the convolution of erfc(t) and the derivative of f(t). Then, by substituting f(t) into the general theoretical solution, the corresponding analytical solution is formulated. Based on the general theoretical solution, analytical solutions are given for f(t) as a commonly used function. Finally, combined with an exemplifying application demonstration based on the test data of temperature T(x, t) at point x away from the boundary and the characteristics of curve T(x, t) − t and curve 𝜕T(x, t)/𝜕t − t, the inflection point and curve fitting methods are established for the inversion of model parameters.

Effective nitrogen management practices by using two cultivation techniques can improve corn productivity and soil carbon components such as soil carbon storage, microbial biomass carbon (MBC), carbon management index (CMI), and water-soluble carbon (WSC). It is essential to ensure the long-term protection of dry-land agricultural systems. However, excessive application of nitrogen fertilizer reduces the efficiency of nitrogen use and also leads to increased greenhouse gas emissions from farming soil and several other ecological problems. Therefore, we conducted field trials under two planting methods during 2019–2020: P: plastic mulching ridges; F: traditional flat planting with nitrogen management practices, i.e., 0: no nitrogen fertilizer; FN: a common nitrogen fertilizer rate for farmers of 290 kg ha−1; ON: optimal nitrogen application rate of 230 kg ha−1; ON75%+DCD: 25% reduction in optimal nitrogen fertilizer rate + dicyandiamide; ON75%+NC: 25% reduction in optimal nitrogen rate + nano-carbon. The results showed that compared to other treatments, the PON75%+DCD treatment significantly increased soil water storage, water use efficiency (WUE), and nitrogen use efficiency (NUE) because total evapotranspiration (ET) and GHG were reduced. Under the PON75%+DCD or PON75%+NC, the soil carbon storage significantly (50% or 47%) increased. The PON75%+DCD treatment is more effective in improving MBC, CMI, and WSC, although it increases gaseous carbon emissions more than all other treatments. Compared with FFN, under the PON75%+DCD treatment, the overall CH4, N2O, and CO2 emissions are all reduced. Under the PON75%+DCD treatment, the area scale GWP (52.7%), yield scale GWP (90.3%), biomass yield (22.7%), WUE (42.6%), NUE (80.0%), and grain yield (32.1%) significantly increased compared with FFN, which might offset the negative ecological impacts connected with climate change. The PON75%+DCD treatment can have obvious benefits in terms of increasing yield and reducing emissions. It can be recommended to ensure future food security and optimal planting and nitrogen management practices in response to climate change.

Soybean is a widespread crop in semi-arid regions of China, where soil salinity often increases and has a significant harmful impact on production, which will be a huge challenge in the coming years. Salicylic acid (SA) and pyraclostrobin are strobilurin-based bactericides (PBF). Under rainfall-harvesting conditions in covered ridges, the exogenous application of SA and PBF can improve the growth performance of soybeans, thereby reducing the adverse effects of soil salinity. The objectives of this research are to evaluate the potential effects of SA and PBF on soybean growth in two different regions, Harbin and Daqing. A two-year study was performed with the following four treatments: HCK: Harbin location with control; SA1+PBF1: salicylic acid (5 mL L−1) with pyraclostrobin (3 mL L−1); SA2+PBF2: salicylic acid (10 mL L−1) with pyraclostrobin (6 mL L−1); DCK: Daqing location with control. The results showed that in the Harbin region, SA2+PBF2 treatment reduced the evapotranspiration (ET) rate, increased soil water storage (SWS) during branching and flowering stages, and achieved a maximum photosynthesis rate. Moreover, this improvement is due to the reduction of MDA and oxidative damage in soybean at various growth stages. At different growth stages, the treatment of Harbin soybean with SA2+PBF2 significantly increased the activity of CAT, POD, SOD, and SP, while the content of MDA, H2O2, and O2− also decreased significantly. In the treatment of SA2+PBF2 in Harbin, the scavenging ability of free H2O2 and O2− was higher, and the activity of antioxidant enzymes was better. This was due to a worse level of lipid-peroxidation which successfully protected the photosynthesis mechanism and considerably increased water use efficiency (WUE) (46.3%) and grain yield (57.5%). Therefore, using plastic mulch with SA2+PBF2 treatment can be an effective water-saving management strategy, improving anti-oxidant enzyme activities, photosynthesis, and soybean production.

Abstract Background Cerebral ischemia–reperfusion (I/R) injury is a major cause of early complications and unfavorable outcomes after endovascular thrombectomy (EVT) therapy in patients with acute ischemic stroke (AIS). Recent studies indicate that modulating microglia/macrophage polarization and subsequent inflammatory response may be a potential adjunct therapy to recanalization. Annexin A1 (ANXA1) exerts potent anti-inflammatory and pro-resolving properties in models of cerebral I/R injury. However, whether ANXA1 modulates post-I/R-induced microglia/macrophage polarization has not yet been fully elucidated. Methods We retrospectively collected blood samples from AIS patients who underwent successful recanalization by EVT and analyzed ANXA1 levels longitudinally before and after EVT and correlation between ANXA1 levels and 3-month clinical outcomes. We also established a C57BL/6J mouse model of transient middle cerebral artery occlusion/reperfusion (tMCAO/R) and an in vitro model of oxygen–glucose deprivation and reoxygenation (OGD/R) in BV2 microglia and HT22 neurons to explore the role of Ac2-26, a pharmacophore N-terminal peptide of ANXA1, in regulating the I/R-induced microglia/macrophage activation and polarization. Results The baseline levels of ANXA1 pre-EVT were significantly lower in 23 AIS patients, as compared with those of healthy controls. They were significantly increased to the levels found in controls 2–3 days post-EVT. The increased post-EVT levels of ANXA1 were positively correlated with 3-month clinical outcomes. In the mouse model, we then found that Ac2-26 administered at the start of reperfusion shifted microglia/macrophage polarization toward anti-inflammatory M2-phenotype in ischemic penumbra, thus alleviating blood–brain barrier leakage and neuronal apoptosis and improving outcomes at 3 days post-tMCAO/R. The protection was abrogated when mice received Ac2-26 together with WRW4, which is a specific antagonist of formyl peptide receptor type 2/lipoxin A4 receptor (FPR2/ALX). Furthermore, the interaction between Ac2-26 and FPR2/ALX receptor activated the 5’ adenosine monophosphate-activated protein kinase (AMPK) and inhibited the downstream mammalian target of rapamycin (mTOR). These in vivo findings were validated through in vitro experiments. Conclusions Ac2-26 modulates microglial/macrophage polarization and alleviates subsequent cerebral inflammation by regulating the FPR2/ALX-dependent AMPK-mTOR pathway. It may be investigated as an adjunct strategy for clinical prevention and treatment of cerebral I/R injury after recanalization. Plasma ANXA1 may be a potential biomarker for outcomes of AIS patients receiving EVT.

Abstract The relationship between cerebral glucose metabolism and glucose transporter expression after intracerebral hemorrhage (ICH) is unclear. Few studies have used positron emission tomography (PET) to explore cerebral glucose metabolism after ICH in rodents. In this study, we produced ICH in mice with an intrastriatal injection of collagenase to investigate whether glucose metabolic changes in 18F-fluoro-2-deoxy-D-glucose (FDG)-PET images are associated with expression of glucose transporters (GLUTs) over time. On days 1 and 3 after ICH, the ipsilateral striatum exhibited significant hypometabolism. However, by days 7 and 14, glucose metabolism was significantly higher in the ipsilateral striatum than in the contralateral striatum. The contralateral hemisphere did not show hypermetabolism at any time after ICH. Qualitative immunofluorescence and Western blotting indicated that the expression of GLUT1 in ipsilateral striatum decreased on days 1 and 3 after ICH and gradually returned to baseline by day 21. The 18F-FDG uptake after ICH was associated with expression of GLUT1 but not GLUT3 or GLUT5. Our data suggest that ipsilateral cerebral glucose metabolism decreases in the early stage after ICH and increases progressively in the late stage. Changes in 18F-FDG uptake on PET imaging are associated with the expression of GLUT1 in the ipsilateral striatum.

Soybean is an important food crop that contains high amounts of isoflavones. However, due to the expression of multiple genes, different soybean seeds have different isoflavone compositions. The underlying mechanisms for this complexity remain unknown. In this study, we identified potential differentially expressed genes (DEGs) in two wild soybean cultivars, ZYD7068 (high isoflavone) and ZYD7194 (low isoflavone), at different seed developmental stages using RNA-seq technology and compared their differences in isoflavone content. A total of 1067 and 6479 differentially metabolized genes were identified at R6 and R8 stages, respectively. Subsequent analysis of the KEGG pathway revealed that three of these differential metabolized genes were involved in the Isoflavonoid biosynthesis and Flavone and flavonol biosynthesis at the R6 stage. A total of 80 TF genes encoding differential expression of MYB, bZIP, and WRKY were identified in A1 vs. B1 and A3 vs. B3. Eight differentially expressed genes were identified in duplicates at both stages, and three genes showed the same expression trend at both stages. To confirm the results of RNA-seq, qRT-PCR was performed to analyze the expression of the six identified differentially expressed genes (DEGs). The results of qRT-PCR were consistent with the results of RNA-seq. We found that four genes (Glyma.13G173300, Glyma.13G173600, Glyma.14G103100, and Glyma.17G158900) may be involved in the positive regulation of isoflavone synthesis, while two genes (Glyma.04G036700 and Glyma.19G030500) may be involved in the negative regulation of isoflavone synthesis. These findings suggest that the observed difference in isoflavone levels between the two cultivars may be attributable to the differential expression of these six genes at later stages of seed development.

The current calculation method of breakthrough time calculates the concentration value of the measuring point at different times based on the model solution, which is determined by approaching the concentration value corresponding to the breakthrough standard through trial calculations. However, it is necessary to research the breakthrough standard with practical applications of mathematical and physical significance, especially a one-dimensional mathematical model of contaminant migration under Dirichlet boundary conditions. A general algorithm for directly calculating the breakthrough time was established in this research. Moreover, the calculation standard of the breakthrough time was also discussed based on the similarity between the analytical solution and the mathematical law of thermal conduction. This research considered parameters of the seepage velocity, dispersion coefficient and characteristics of the impervious layer, and the sensitivity analysis of these factors was investigated. The results show that the proposed algorithm was basically consistent with the current method, and the concept of thermal penetration depth is also feasible for the calculation standard. This is not only suitable for different breakthrough standards, but also simple and convenient. This study can provide a reference for the design, management and subsequent remediation of actual sites.

Drought stress is an important factor affecting soybean yield. Improving drought tolerance of soybean varieties can increase yield and yield stability when the stress occurs. Identifying QTL related to drought tolerance using molecular marker-assisted selection is able to facilitate the development of drought-tolerant soybean varieties. In this study, we used a high-yielding and drought-sensitive cultivar ‘Zhonghuang 35’ and a drought-tolerant cultivar ‘Jindou 21’ to establish F6:9 recombinant inbred lines. We constructed a high-density genetic map using specific locus amplified fragment sequencing (SLAF-Seq) technology. The genetic map contained 8078 SLAF markers distributing across 20 soybean chromosomes with a total genetic distance of 3780.98 cM and an average genetic distance of 0.59 cM between adjacent markers. Two treatments (irrigation and drought) were used in the field tests, the Additive-Inclusive Composite Interval Mapping (ICIM-ADD) was used to call QTL, and plant height and seed weight per plant were used as the indicators of drought tolerance. We identified a total of 23 QTL related to drought tolerance. Among them, seven QTL (qPH2, qPH6, qPH7, qPH17, qPH19-1, qPH19-2, and qPH19-3) on chromosomes 2, 6, 7, 17, and 19 were related to plant height, and five QTL (qSWPP2, qSWPP6, qSWPP13, qSWPP17, and qSWPP19) on chromosomes 2, 6, 13, 17, and 19 were related to seed weight and could be considered as the major QTL. In addition, three common QTL (qPH6/qSWPP6, qPH17/qSWPP17, and qPH19-3/qSWPP19) for both plant height and seed weight per plant were located in the same genomic regions on the same chromosomes. Three (qPH2, qPH17, and qPH19-2) and four novel QTL (qSWPP2, qSWPP13, qSWPP17, and qSWPP19) were identified for plant height and seed weight per plant, respectively. Two pairs of QTL (qPH2/qSWPP2 and qPH17/qSWPP17) were also common for both plant height and seed weight per plant. These QTL and closely linked SLAF markers could be used to accelerate breeding for drought tolerant cultivars via MAS.

For the needs of the whole region’s emergency regulation of the nullah sudden water pollution event, the emergency regulation strategy of the accident section and upstream and downstream of the sudden water pollution event is studied. For the accident section, the duration of the whole emergency event is calculated using the parameter quantification method; for the upstream of the accident section, the NSGA-II is used to adjust the gate opening to ensure the water level stability of the upstream pools; for the downstream section, the optimized partition method is used to identify the unfavorable pools and close the unfavorable pool to extend the water supply time. Based on the example of an emergency event in the section of the Liyanghe gate–Guyunhe gate of the middle line project, the research results are as follows: the accident section is identified as the Xiaohe gate–Hutuohe gate, the upstream of the accident section is the Liyanghe gate–Xiaohe gate, and the downstream of the accident section is the Hutuohe gate–Gangtou Tunnel gate. The duration of the emergency event in the accident section is 7.9 h; the maximum average water level deviation before the gate upstream of the accident section is 0.05 m; two unfavorable canal pools are identified in the stream of the accident section, and the water supply time of the unfavorable pools is extended by 6.13 and 5.61 d.

One-dimensional heat-conduction models in a semi-infinite domain, although forced convection obeys Newton’s law of cooling, are challenging to solve using standard integral transformation methods when the boundary condition φ(t) is an exponential decay function. In this study, a general theoretical solution was established using Fourier transform, but φ(t) was not directly present in the transformation processes, and φ(t) was substituted into the general theoretical solution to obtain the corresponding analytical solution. Additionally, the specific solutions and corresponding mathematical meanings were discussed. Moreover, numerical verification and sensitivity analysis were applied to the proposed model. The results showed that T(x,t) was directly proportional to the thermal diffusivity (a) and was inversely proportional to calculation distance (x) and the coefficient of cooling ratio (λ). The analytical solution was more sensitive to the thermal diffusivity than other factors, and the highest relative error between numerical and analytical solutions was roughly 4% under the condition of 2a and λ. Furthermore, T(x,t) grew nonlinearly as the material’s thermal diffusivity or cooling ratio coefficient changed. Finally, the analytical solution was applied for parameter calculation and verification in a case study, providing the reference basis for numerical calculation under specific complex boundaries, especially for the study of related problems in the fields of fluid dynamics and peridynamics with the heat-conduction equation.

Intracerebral hemorrhage (ICH) is a highly fatal type of stroke that leads to various types of neuronal death. Recently, ferroptosis, a form of cell death resulting from iron-dependent lipid peroxide accumulation, was observed in a mouse ICH model. N-hydroxy-N′-(4-n-butyl-2-methylphenyl)-formamidine (HET0016), which inhibits synthesis of the arachidonic acid metabolite 20-hydroxyeicosatetraenoic acid (20-HETE), has shown a protective effect after ICH. However, the underlying mechanisms of the neuroprotective effect need further investigation. We explored whether 20-HETE participates in ICH-induced ferroptosis ex vivo by using hemoglobin-treated organotypic hippocampal slice cultures (OHSCs) and in vivo by using a collagenase-induced ICH mouse model. Ex vivo, we found that the 20-HETE synthesis inhibitor HET0016 and antagonist 20-6,15-HEDGE reduced hemoglobin-induced cell death, iron deposition, and lipid reactive oxygen species levels in OHSCs. Furthermore, 20-HETE inhibition in OHSCs increased the expression of glutathione peroxidase (GPX) 4, an antioxidant enzyme that serves as a main regulator of ferroptosis. In contrast, exposure of OHSCs to the 20-HETE stable mimetic 20-5,14-HEDGE induced cell death that was significantly inhibited by the ferroptosis inhibitor ferrostatin-1. In vivo, HET0016 treatment ameliorated focal deficits, reduced lesion volume, and decreased iron accumulation around the lesion at day 3 and 7 after ICH. In addition, lipid peroxidation was decreased and expression of GPX4 was increased in the HET0016-treated ICH group. The mitogen-activated protein kinase pathway also was inhibited by HET0016 in vivo. These results indicate that 20-HETE contributes to ICH-induced acute brain injury in part by activating ferroptosis pathways, thereby providing an upstream target for inhibiting ferroptosis.

The function of boundary temperature variation with time, f(t) is generally defined according to measured data. For f(t), which has a complicated expression, a corresponding one-dimensional heat conduction model was constructed under the first type of boundary conditions (Dirichlet conditions) in a semi-infinite domain. By taking advantage of the Fourier transform properties, a theoretical solution was given for the model, under the condition that f(t) does not directly participate in the transformation process. The solution consists of the product of erfc(t) and f(0) and the convolution of erfc(t) and the derivative of f(t). The piecewise linear interpolation equation of f(t), based on the measured data of temperature, was substituted into the theoretical solution, thus quickly solving the model and deriving a corresponding analytical solution. Based on the analytical solution under the linear decay function boundary condition, the inflection point method and curve fitting method for calculating the thermal diffusivity were introduced and exemplified, and the variation laws of the appearance moment of the inflection point were discussed. The obtained results show that the values of thermal diffusivity calculated by the two methods are basically consistent, and that the inflection point values rise with the increasing values of the initial temperature variation of the boundary, the decrease in boundary temperature velocity, and the distance from the boundary, respectively.

Brain ischemia induces systemic immunosuppression and increases a host's susceptibility to infection. MicroRNAs (miRNAs) are molecular switches in immune cells, but the alterations of miRNAs in human immune cells in response to brain ischemia and their impact on immune defense remain elusive. Natural killer (NK) cells are critical for early host defenses against pathogens. In this study, we identified reduced counts, cytokine production, and cytotoxicity in human peripheral blood NK cells obtained from patients with acute ischemic stroke. The extent of NK cell loss of number and activity was associated with infarct volume. MicroRNA sequencing analysis revealed that brain ischemia significantly altered miRNA expression profiles in circulating NK cells, in which miRNA-451a and miRNA-122-5p were dramatically upregulated. Importantly, inhibition of miR-451a or miR-122-5p augmented the expression of activation-associated receptors in NK cells. These results provide the first evidence that brain ischemia alters miRNA signatures in human NK cells.

DNA methylation is a heritable epigenetic modification that plays an essential role in mammalian development. Genomic methylation patterns are dynamically maintained, with DNA methyltransferases mediating inheritance of methyl marks onto nascent DNA over cycles of replication. A recently developed experimental technique employing immunoprecipitation of bromodeoxyuridine labeled nascent DNA followed by bisulfite sequencing (Repli-BS) measures post-replication temporal evolution of cytosine methylation, thus enabling genome-wide monitoring of methylation maintenance. In this work, we combine statistical analysis and stochastic mathematical modeling to analyze Repli-BS data from human embryonic stem cells. We estimate site-specific kinetic rate constants for the restoration of methyl marks on >10 million uniquely mapped cytosines within the CpG (cytosine-phosphate-guanine) dinucleotide context across the genome using Maximum Likelihood Estimation. We find that post-replication remethylation rate constants span approximately two orders of magnitude, with half-lives of per-site recovery of steady-state methylation levels ranging from shorter than ten minutes to five hours and longer. Furthermore, we find that kinetic constants of maintenance methylation are correlated among neighboring CpG sites. Stochastic mathematical modeling provides insight to the biological mechanisms underlying the inference results, suggesting that enzyme processivity and/or collaboration can produce the observed kinetic correlations. Our combined statistical/mathematical modeling approach expands the utility of genomic datasets and disentangles heterogeneity in methylation patterns arising from replication-associated temporal dynamics versus stable cell-to-cell differences.

Single-cell transcriptomics is advancing discovery of the molecular determinants of cell identity, while spurring development of novel data analysis methods. Stochastic mathematical models of gene regulatory networks help unravel the dynamic, molecular mechanisms underlying cell-to-cell heterogeneity, and can thus aid interpretation of heterogeneous cell-states revealed by single-cell measurements. However, integrating stochastic gene network models with single cell data is challenging. Here, we present a method for analyzing single-cell gene-pair coexpression patterns, based on biophysical models of stochastic gene expression and interaction dynamics. We first developed a high-computational-throughput approach to stochastic modeling of gene-pair coexpression landscapes, based on numerical solution of gene network Master Equations. We then comprehensively catalogued coexpression patterns arising from tens of thousands of gene-gene interaction models with different biochemical kinetic parameters and regulatory interactions. From the computed landscapes, we obtain a low-dimensional “shape-space” describing distinct types of coexpression patterns. We applied the theoretical results to analysis of published single cell RNA sequencing data and uncovered complex dynamics of coexpression among gene pairs during embryonic development. Our approach provides a generalizable framework for inferring evolution of gene-gene interactions during critical cell-state transitions.

The nucleotide-binding oligomerization domain (NOD)-like receptor family pyrin domain containing 3 (NLRP3) inflammasome-mediated inflammatory response has emerged as a prominent contributor to the pathophysiological processes of traumatic brain injury (TBI). Recently, a potent, selective, small-molecule NLRP3 inflammasome inhibitor, MCC950, was described. Here, we investigated the effect of MCC950 on inflammatory brain injury and long-term neurological outcomes in a mouse model of TBI. Male C57/BL6 mice were subjected to TBI using the controlled cortical impact injury (CCI) system. Western blotting, flow cytometry, and immunofluorescence assays were utilized to analyze post-traumatic NLRP3 inflammasome expression and determine its cellular source. We found that NLRP3 inflammasome expression was significantly increased in the peri-contusional cortex and that microglia were the primary source of this expression. The effects of MCC950 on mice with TBI were then determined using post-assessments including analyses of neurological deficits, brain water content, traumatic lesion volume, neuroinflammation, blood-brain barrier (BBB) integrity, and cell death. MCC950 treatment resulted in a better neurological outcome after TBI by alleviating brain edema, reducing lesion volume, and improving long-term motor and cognitive functions. The therapeutic window for MCC950 against TBI was as long as 6 h. Furthermore, the neuroprotective effect of MCC950 was associated with reduced microglial activation, leukocyte recruitment, and pro-inflammatory cytokine production. In addition, MCC950 preserved BBB integrity, alleviated TBI-induced loss of tight junction proteins, and attenuated cell death. Notably, the efficacy of MCC950 was abolished in microglia-depleted mice. These results indicate that microglia-derived NLRP3 inflammasome may be primarily involved in the inflammatory response to TBI, and specific NLRP3 inflammasome inhibition using MCC950 may be a promising therapeutic approach for patients with TBI.

Astrocyte loss induced by neuromyelitis optica (NMO)-IgG and complement-dependent cytotoxicity (CDC) is the hallmark of NMO pathology. The survival of astrocytes is thought to reflect astrocyte exposure to environmental factors in the CNS and the response of astrocytes to these factors. However, still unclear are how astrocytes respond to NMO-IgG and CDC, and what CNS environmental factors may impact the survival of astrocytes. In a murine model of NMO induced by intracerebral injection of NMO-IgG and human complement, we found dramatic upregulation of IL-15 in astrocytes. To study the role of astrocytic IL-15 in NMO, we generated a transgenic mouse line with targeted expression of IL-15 in astrocytes (IL-15tg), in which the expression of IL-15 is controlled by a glial fibrillary acidic protein promoter. We showed that astrocyte-targeted expression of IL-15 attenuates astrocyte injury and the loss of aquaporin-4 in the brain. Reduced blood–brain barrier leakage and immune cell infiltration are also found in the lesion of IL-15tg mice subjected to NMO induction. IL-15tg astrocytes are less susceptible to NMO-IgG-mediated CDC than their wild-type counterparts. The enhanced resistance of IL-15tg astrocytes to cytotoxicity and cell death involves NF-κB signaling pathway. Our findings suggest that IL-15 reduces astrocyte loss and NMO pathology.