Unveiling unique alternative splicing responses to low temperature in Zoysia japonica through ZjRTD1.0, a high-quality reference transcript dataset.

Inadequate reference databases in RNA-seq analysis can hinder data utilization and interpretation. In this study, we have successfully constructed a high-quality reference transcript dataset, ZjRTD1.0, for Zoysia japonica, a widely-used turfgrass with exceptional tolerance to various abiotic stress, including low temperatures and salinity. This dataset comprises 113,089 transcripts from 57,143 genes. BUSCO analysis demonstrates exceptional completeness (92.4%) in ZjRTD1.0, with reduced proportions of fragmented (3.3%) and missing (4.3%) orthologs compared to prior datasets. ZjRTD1.0 enables more precise analyses, including transcript quantification and alternative splicing assessments using public datasets, which identified a substantial number of differentially expressed transcripts (DETs) and differential alternative splicing (DAS) events, leading to several novel findings on Z. japonica's responses to abiotic stresses. First, spliceosome gene expression influenced alternative splicing significantly under abiotic stress, with a greater impact observed during low-temperature stress. Then, a significant positive correlation was found between the number of differentially expressed genes (DEGs) encoding protein kinases and the frequency of DAS events, suggesting the role of protein phosphorylation in regulating alternative splicing. Additionally, our results suggest possible involvement of serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs) in generating inclusion/exclusion isoforms under low-temperature stress. Furthermore, our investigation revealed a significantly enhanced overlap between DEGs and differentially alternatively spliced genes (DASGs) in response to low-temperature stress, suggesting a unique co-regulatory mechanism governing transcription and splicing in the context of low-temperature response. In conclusion, we have proven that ZjRTD1.0 will serve as a reliable and useful resource for future transcriptomic analyses in Z. japonica.

RNF166 promotes colorectal cancer progression by recognizing and destabilizing poly-ADP-ribosylated angiomotins.

Activation of the Hippo pathway by angiomotins to limit colorectal cancer progression is prevalent, whereas the regulation of angiomotins remains elusive. In this study, we uncover the involvement of an upregulated E3 ubiquitin ligase called RNF166, which destabilizes angiomotins, activates YAP, and is associated with a poor prognosis in colorectal cancer patients. Mechanistically, RNF166 specifically recognizes PARsylated angiomotin, a modification mediated by tankyrase at specific amino acid residues (D506, E513, E516, and E528). The tankyrase inhibitor XAV939, effectively prevents RNF166-dependent destabilization of angiomotins and subsequent activation of YAP. Additionally, YAP-5SA, a constitutively active form of YAP, rescues colorectal cancer progression following knockdown of RNF166. Importantly, the C-terminus of RNF66, particularly the Di19-ZF domain, is the crucial region responsible for recognizing ADP-ribosylated angiomotins. Together, this work not only sheds light on the regulation of the Hippo pathway in colorectal cancer but also uncovers a novel poly(ADP-ribose)-binding domain, which may serve as a potential therapeutic target for intervention.

Influence of cathode materials on thermal characteristics of lithium-ion batteries.

In this work, the thermal stability of four types of 18,650 lithium-ion batteries with LiCoO2 (LCO), LiFePO4 (LFP), LiNi0.8Co0.1Mn0.1O2 (NCM811) and LiNi0.8Co0.15Al0.05O2 (NCA) materials as cathodes are experimentally investigated by the accelerating rate calorimeter (ARC) and the isothermal battery testing calorimeter (iso-BTC) under adiabatic and isothermal conditions, respectively. The thermal runaway danger level of these batteries can be ranked as LCO > NCA > NCM811 >> LFP by judging from the values of Tmax and HRmax, nominal. The higher the nickel and cobalt content, the higher the lithium-ion battery capacity, but the worse the thermal stability. The Qtotal of NCA is the largest in the complete standard charge and discharge process, due to that the capacity of NCA is significantly higher than that of the other three batteries, resulting in remarkable increase in Qirre proportioned to the square of the current. When the ambient temperature rises, the energy release decreases owing to the decrease in the internal resistance of the battery. These studies are expected to have important implications for the subsequent safe design of commercial lithium-ion batteries with different cathode materials.

Structural insights into the HDAC4-MEF2A-DNA complex and its implication in long-range transcriptional regulation.

Class IIa Histone deacetylases (HDACs), including HDAC4, 5, 7 and 9, play key roles in multiple important developmental and differentiation processes. Recent studies have shown that class IIa HDACs exert their transcriptional repressive function by interacting with tissue-specific transcription factors, such as members of the myocyte enhancer factor 2 (MEF2) family of transcription factors. However, the molecular mechanism is not well understood. In this study, we determined the crystal structure of an HDAC4-MEF2A-DNA complex. This complex adopts a dumbbell-shaped overall architecture, with a 2:4:2 stoichiometry of HDAC4, MEF2A and DNA molecules. In the complex, two HDAC4 molecules form a dimer through the interaction of their glutamine-rich domain (GRD) to form the stem of the 'dumbbell'; while two MEF2A dimers and their cognate DNA molecules are bridged by the HDAC4 dimer. Our structural observations were then validated using biochemical and mutagenesis assays. Further cell-based luciferase reporter gene assays revealed that the dimerization of HDAC4 is crucial in its ability to repress the transcriptional activities of MEF2 proteins. Taken together, our findings not only provide the structural basis for the assembly of the HDAC4-MEF2A-DNA complex but also shed light on the molecular mechanism of HDAC4-mediated long-range gene regulation.

A selenium-based NIR-II photosensitizer for a highly effective and safe phototherapy plan.

High efficiency, stability, long emission wavelength (NIR-II), and good biocompatibility are crucial for photosensitizers in phototherapy. However, current Food and Drug Administration (FDA)-approved organic fluorophores exhibit poor chemical stability and photostability as well as short emission wavelength, limiting their clinical usage. To address this, we developed Se-IR1100, a novel organic photosensitizer with a photostable and thermostable benzobisthiadiazole (BBTD) backbone. By incorporating selenium as a heavy atom and constructing a D-A-D structure, Se-IR1100 exhibits a maximum fluorescence emission wavelength of 1100 nm. Compared with FDA-approved indocyanine green (ICG), DSPE-PEGylated Se-IR1100 nanoparticles exhibit prominent photostability and long-lasting photothermal effects. Upon 808 nm laser irradiation, Se-IR1100 NPs efficiently convert light energy into heat and reactive oxygen species (ROS), inducing cancer cell death in cellular studies and living organisms while maintaining biocompatibility. With salient photostability and a photothermal conversion rate of 55.37%, Se-IR1100 NPs hold promise as a superior photosensitizer for diagnostic and therapeutic agents in oncology. Overall, we have designed and optimized a multifunctional photosensitizer Se-IR1100 with good biocompatibility that performs NIR-II fluorescence imaging and phototherapy. This dual-strategy method may offer novel approaches for the development of multifunctional probes using dual-strategy or even multi-strategy methods in bioimaging, disease diagnosis, and therapy.

Extracellular Vesicles Derived from Selenium-Deficient MAC-T Cells Aggravated Inflammation and Apoptosis by Triggering the Endoplasmic Reticulum (ER) Stress/PI3K-AKT-mTOR Pathway in Bovine Mammary Epithelial Cells.

Selenium (Se) deficiency disrupts intracellular REDOX homeostasis and severely deteriorates immune and anti-inflammatory function in high-yielding periparturient dairy cattle. To investigate the damage of extracellular vesicles derived from Se-deficient MAC-T cells (SeD-EV) on normal mammary epithelial cells, an in vitro model of Se deficiency was established. Se-deficient MAC-T cells produced many ROS, promoting apoptosis and the release of inflammatory factors. Extracellular vesicles were successfully isolated by ultrahigh-speed centrifugation and identified by transmission electron microscopy, particle size analysis, and surface markers (CD63, CD81, HSP70, and TSG101). RNA sequencing was performed on exosomal RNA. A total of 9393 lncRNAs and 63,155 mRNAs transcripts were identified in the SeC and SeD groups, respectively, of which 126 lncRNAs and 955 mRNAs were differentially expressed. Furthermore, SeD-EV promoted apoptosis of normal MAC-T cells by TUNEL analysis. SeD-EV significantly inhibited Bcl-2, while Bax and Cleaved Caspase3 were greatly increased. Antioxidant capacity (CAT, T-AOC, SOD, and GSH-Px) was inhibited in SeD-EV-treated MAC-T cells. Additionally, p-PERK, p-eIF2α, ATF4, CHOP, and XBP1 were all elevated in MAC-T cells supplemented with SeD-EV. In addition, p-PI3K, p-Akt, and p-mTOR were decreased strikingly by SeD-EV. In conclusion, SeD-EV caused oxidative stress, thus triggering apoptosis and inflammation through endoplasmic reticulum stress and the PI3K-Akt-mTOR signaling pathway, which contributed to explaining the mechanism of Se deficiency causing mastitis.

Development of a Comprehensive Gene Signature Linking Hypoxia, Glycolysis, Lactylation, and Metabolomic Insights in Gastric Cancer through the Integration of Bulk and Single-Cell RNA-Seq Data.

BACKGROUND: Hypoxia and anaerobic glycolysis are cancer hallmarks and sources of the metabolite lactate. Intriguingly, lactate-induced protein lactylation is considered a novel epigenetic mechanism that predisposes cells toward a malignant state. However, the significance of comprehensive hypoxia-glycolysis-lactylation-related genes (HGLRGs) in cancer is unclear. We aimed to construct a model centered around HGLRGs for predicting survival, metabolic features, drug responsiveness, and immune response in gastric cancer. METHODS: The integration of bulk and single-cell RNA-Seq data was achieved using data obtained from the TCGA and GEO databases to analyze HGLRG expression patterns. A HGLRG risk-score model was developed based on univariate Cox regression and a LASSO-Cox regression model and subsequently validated. Additionally, the relationships between the identified HGLRG signature and multiple metabolites, drug sensitivity and various cell clusters were explored. RESULTS: Thirteen genes were identified as constituting the HGLRG signature. Using this signature, we established predictive models, including HGLRG risk scores and nomogram and Cox regression models. The stratification of patients into high- and low-risk groups based on HGLRG risk scores showed a better prognosis in the latter. The high-risk group displayed increased sensitivity to cytotoxic drugs and targeted inhibitors. The expression of the HGLRG BGN displayed a strong correlation with amino acids and lipid metabolites. Notably, a significant difference in immune infiltration, such as that of M1 macrophages and CD8 T cells, was correlated with the HGLRG signature. The abundant DUSP1 within the mesenchymal components was highlighted by single-cell transcriptomics. CONCLUSION: The innovative HGLRG signature demonstrates efficacy in predicting survival and providing a practical clinical model for gastric cancer. The HGLRG signature reflects the internal metabolism, drug responsiveness, and immune microenvironment components of gastric cancer and is expected to boost patients' response to targeted therapy and immunotherapy.

Electrochemical Synthesis of the Energetic Combustion Catalyst Co(BODN)·9H2O and Its Catalytic Effect on Ammonium Perchlorate Thermal Decomposition.

Safe, efficient, and green synthetic energetic combustion catalysts are of great importance for the application of ammonium perchlorate (AP) in solid propellants. In this study, a novel, simple, efficient, and green electrochemical method for synthesizing energetic combustion catalysts was designed and implemented to successfully synthesize Co(BODN)·9H2O (BODN = [2,2'-bi{1,3,4-oxadiazole}]-5,5'-dinitramide), a novel energetic combustion catalyst. The target products were characterized via single-crystal X-ray diffraction, powder X-ray diffraction, Fourier transform infrared spectroscopy, optical microscopy, scanning electron microscopy, differential scanning calorimetry, and thermogravimetric analysis. Results reveal that Co(BODN)·9H2O crystallizes in the triclinic P1̅ space group and has a density of 1.836 g cm-3. The size of the Co(BODN)·9H2O crystal increases gradually with the increase in the reaction current and the prolongation of the reaction time, respectively. However, the change in reaction current and time does not affect the crystal form. In addition, with the increase in Co(BODN)·9H2O content, the peak temperature of high-temperature decomposition (HTD) and apparent activation energy of AP/Co(BODN)·9H2O gradually decrease, and the heat release during thermal decomposition gradually increases. The HTD peak temperature and apparent activation energy of AP/Co(BODN) 9H2O (10%) decrease by 97.9 °C and 94.2 kJ·mol-1, respectively, compared with those of pure AP, and the heat release during thermal decomposition increases by 1613 J·g-1. Furthermore, compared with those of the propellant containing pure AP, the burning rate and flame temperature of the propellant containing AP/Co(BODN)·9H2O (10%) increase by 8.15 mm s-1 and 458.44 °C, respectively. Real-time Fourier transform infrared spectroscopy reveals that CoO catalyzes the thermal decomposition of AP mainly by promoting electron transfer to accelerate the oxidation of NH3 and the conversion of N2O to NO. In brief, this work provides new insights into synthesizing energetic combustion catalysts. Moreover, Co(BODN)·9H2O synthesized through the electrochemical method exhibits considerable application prospects for improving the thermal and energy performance of AP and the combustion performance of propellants.

Character variation of root space microbial community composition in the response of drought-tolerant spring wheat to drought stress.

Drought is the most prevalent environmental stress in crop production, posing a significant danger to food security. Microorganisms in the crop root zone affect crop growth and development, enhance effective nutrient use, and resist adversity hazards. To analyze the changes and functional differences of root space microbial (endosphere-rhizosphere-bulk soil) communities in spring wheat under drought stress. In this study, the root, rhizosphere, and bulk soil of the drought-tolerant group (DTG, three varieties) and drought-sensitive group (DSG, three varieties) were collected. The control (CK, 25-28%), moderate drought (MD, 15-18%), and severe drought (SD, 9-12%) were analyzed by high-throughput sequencing and bioinformatics. The results showed significant differences in the diversity of Bacteria and Fungi in the root space of spring wheat under drought stress (P < 0.05), with the drought-tolerant group exhibiting higher microbial diversity. The microbial community change in spring wheat root space was mainly determined by the niche differentiation of endosphere, rhizosphere, and bulk soil and declined from endosphere to bulk soil due to drought. The antagonism between microbial and root-space species increased, and the community's complexity and stability deteriorated. Enriching drought-resistant preference groups like Actinobaciota, Variovorax, Streptomyces, and Conocybe altered the structure and function of the microbial community in the root space of spring wheat. Spring wheat's root space Bacteria and Fungi have different strategies to respond to drought.

Drought Sensitivity of Spring Wheat Cultivars Shapes Rhizosphere Microbial Community Patterns in Response to Drought.

Drought is the most important natural disaster affecting crop growth and development. Crop rhizosphere microorganisms can affect crop growth and development, enhance the effective utilization of nutrients, and resist adversity and hazards. In this paper, six spring wheat varieties were used as research material in the dry farming area of the western foot of the Greater Khingan Mountains, and two kinds of water control treatments were carried out: dry shed rain prevention (DT) and regulated water replenishment (CK). Phenotypic traits, including physiological and biochemical indices, drought resistance gene expression, soil enzyme activity, soil nutrient content, and the responses of potential functional bacteria and fungi under drought stress, were systematically analyzed. The results showed that compared with the control (CK), the leaf wilting, drooping, and yellowing of six spring wheat varieties were enhanced under drought (DT) treatment. The plant height, fresh weight (FW), dry weight (DW), net photosynthetic rate (Pn) and stomatal conductance (Gs), soil total nitrogen (TN), microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), microbial biomass phosphorus (MBP), organic carbon (SOC), and soil alkaline phosphatase (S-ALP) contents were significantly decreased, among which, FW, Gs and MBC decreased by more than 7.84%, 17.43% and 11.31%, respectively. By contrast, the soil total phosphorus (TP), total potassium (TK), and soil catalase (S-CAT) contents were significantly increased (p < 0.05). TaWdreb2 and TaBADHb genes were highly expressed in T.D40, T.L36, and T.L33 and were expressed at low levels in T.N2, T.B12, and T.F5. Among them, the relative expression of the TaWdreb2 gene in T.L36 was significantly increased by 2.683 times compared with CK. Soil TN and TP are the most sensitive to drought stress and can be used as the characteristic values of drought stress. Based on this, a drought-tolerant variety (T.L36) and a drought-sensitive variety (T.B12) were selected to further analyze the changes in rhizosphere microorganisms. Drought treatment and cultivar differences significantly affected the composition of the rhizosphere microbial community. Drought caused a decrease in the complexity of the rhizosphere microbial network, and the structure of bacteria was more complex than that of fungi. The Shannon index and network modular number of bacteria in these varieties (T.L36) increased, with rich small-world network properties. Actinobacteria, Chloroflexi, Firmicutes, Basidiomycota, and Ascomycota were the dominant bacteria under drought treatment. The beneficial bacteria Bacillus, Penicillium, and Blastococcus were enriched in the rhizosphere of T.L36. Brevibacillus and Glycomyce were enriched in the rhizosphere of T.B12. In general, drought can inhibit the growth and development of spring wheat, and spring wheat can resist drought hazards by regulating the expression of drought-related genes, regulating physiological metabolites, and enriching beneficial microorganisms.

Identification of key genes responsible for green and white colored spathes in Anthurium andraeanum (Hort.).

Modern anthuriums, Anthurium andraeanum (Hort.) are among the most popular flowering plants and widely used for interior decoration. Their popularity is largely attributed to the exotic spathes with different colors. Previous studies have reported color development in red spathe cultivars, but limited information is available on key genes regulating white and green colored spathes. This study analyzed anthocyanin, chlorophyll, and carotenoid contents as well as transcript differences in spathes of eight cultivars that differed in spathe colors ranging from red to white and green. Results showed that increased expression of a transcription factor AaMYB2 was associated with elevated levels of anthocyanin in spathes, but decreased expression of AaMYB2 and increased expression of AaLAR (leucoanthocyanidin reductase) and AaANR (anthocyanidin reductase) were accompanied with the accumulation of colorless proanthocyanidin, thus the white spathe. As to the green colored spathe, chlorophyll content in the green spathe cultivar was substantially higher than the other cultivars. Correspondingly, transcripts of chlorophyll biosynthesis-related genes AaHemB (porphobilinogen synthase) and AaPor (protochlorophyllide oxidoreductase) were highly upregulated but almost undetectable in white and red spathes. The increased expression of AaHemB and AaPor was correlated with the expression of transcription factor AaMYB124. Subsequently, qRT-PCR analysis confirmed their expression levels in nine additional cultivars with red, white, and green spathes. A working model for the formation of white and green spathes was proposed. White colored spathes are likely due to the decreased expression of AaMYB2 which results in increased expression of AaLAR and AaANR, and the green spathes are attributed to AaMYB124 enhanced expression of AaHemB and AaPor. Further research is warranted to test this working model.

Optimized N application improves N absorption, population dynamics, and ear fruiting traits of wheat.

Optimizing the N application amount and topdressing ratio can increase crop yield and decrease N loss, but its internal mechanisms have not been well studied, especially from the aspects of population dynamics and structure, ear fruiting traits. Here, field experiments, with three N rates 120 (N1), 180 (N2), and 240 (N3) kg N ha-1 and three N topdressing ratios T1 (7:3), T2 (6:4), and T3 (5:5) were conducted. At the same N level, results showed that the N accumulation amounts in the leaf, grain, and plant in T2 were higher than in T3 and T1, and increasing 60 kg N ha-1 (N3 compared to N2, N2 compared to N1) significantly enhanced N accumulation amounts. The effect of the N topdressing ratio on partial factor productivity of applied N was consistently T2 > T3 > T1, but T1 was more conducive to improving N utilization efficiency for grain and biomass production. After the jointing stage, compared to T1 and T3, T2 was more conducive to increasing the population growth rate of plant height, leaf area index, leaf area growth rate, dry matter weight, dry matter accumulation rate, light interception rate, and spikelets of population, and the above-mentioned indexes of population could be significantly enhanced by increasing 120 kg N ha-1. T2 increased the fruiting spikelets per ear, grains per ear, grain weight per ear, fruiting rate per ear, grain filling rate per ear, and yield but decreased the sterile spikelets at the top and bottom and imperfect grains per ear. Increasing N from 120 kg ha-1 to 180 kg ha-1 or from 180 kg ha-1 to 240 kg ha-1 significantly enhanced yield. The N accumulation amount in the grain, leaf, plant, leaf area growth rate, dry matter accumulation rate, light interception rate, population spikelets, fruiting spikelets per ear, grain filling rate, and yield were significantly positively correlated with each other. This study demonstrates a suitable N application rate with a N topdressing ratio 6:4 would more effectively improve N efficiency, population dynamics, structure, ear fruiting traits, and yield, but the effect of the N topdressing ratio is not as significant as that of increasing 60 kg N ha-1.

High-Quality Genome Assembly and Genome-Wide Association Study of Male Sterility Provide Resources for Flax Improvement.

Flax is an economic crop with a long history. It is grown worldwide and is mainly used for edible oil, industry, and textiles. Here, we reported a high-quality genome assembly for "Neiya No. 9", a popular variety widely grown in China. Combining PacBio long reads, Hi-C sequencing, and a genetic map reported previously, a genome assembly of 473.55 Mb was constructed, which covers ~94.7% of the flax genome. These sequences were anchored onto 15 chromosomes. The N50 lengths of the contig and scaffold were 0.91 Mb and 31.72 Mb, respectively. A total of 32,786 protein-coding genes were annotated, and 95.9% of complete BUSCOs were found. Through morphological and cytological observation, the male sterility of flax was considered dominant nuclear sterility. Through GWAS analysis, the gene LUSG00017705 (cysteine synthase gene) was found to be closest to the most significant SNP, and the expression level of this gene was significantly lower in male sterile plants than in fertile plants. Among the significant SNPs identified in the GWAS analysis, only two were located in the coding region, and these two SNPs caused changes in the protein encoded by LUSG00017565 (cysteine protease gene). It was speculated that these two genes may be related to male sterility in flax. This is the first time the molecular mechanism of male sterility in flax has been reported. The high-quality genome assembly and the male sterility genes revealed, provided a solid foundation for flax breeding.

Dynamic changes of soil microorganisms in rotation farmland at the western foot of the Greater Khingan range.

Crop rotation and other tillage systems can affect soil microbial communities and functions. Few studies have reported the response of soil spatial microbial communities to rotation under drought stress. Therefore, the purpose of our study was to explore the dynamic changes of the soil space microbial community under different drought stress-rotation patterns. In this study, two water treatments were set up, control W1 (mass water content 25%-28%), and drought W2 (mass water content 9%-12%). Four crop rotation patterns were set in each water content, spring wheat continuous (R1), spring wheat-potato (R2), spring wheat-potato-rape (R3) and spring wheat-rape (R4), for a total of eight treatments (W1R1, W1R2, W1R3, W1R4, W2R1, W2R2, W2R3, W2R4). Endosphere, rhizosphere and bulk soil of spring wheat in each treatment were collected, and root space microbial community data were generated. The soil microbial community changed under different treatments and their relationship with soil factors were analyzed using a co-occurrence network, mantel test, and other methods. The results revealed that the alpha diversity of microorganisms in the rhizosphere and bulk soil did not differ significantly, but it was significantly greater than in the endosphere. The bacteria community structure was more stable, fungi alpha-diversity significant changes (p < 0.05), that were more sensitive to the response of various treatments than bacteria. The co-occurrence network between fungal species was stable under rotation patterns (R2, R3, R4), while the community stability was poor under continuous cropping pattern (R1), and interactions were strengthened. Soil organic matter (SOM), microbial biomass carbon (MBC), and pH value were the most important factors dominating the bacteria community structural changed in the endosphere, rhizosphere, and bulk soil. The dominant factor that affected the fungal community structural changed in the endosphere, rhizosphere, and bulk soil was SOM. Therefore, we conclude that soil microbial community changes under the drought stress-rotation patterns are mainly influenced by soil SOM and microbial biomass content.

Integrated Single-Cell and Transcriptome Sequencing Analyses Identify Dipeptidase 2 as an Immune-Associated Prognostic Biomarker for Lung Adenocarcinoma.

Dipeptidase 2 (DPEP2) is a dipeptidyl peptidase that plays an important role in the hydrolysis of leukotriene D4 (LTD4) to leukotriene E4 (LTE4). Previous studies have suggested that LTD4 promotes tumor progression and survival in non-small cell lung cancer (NSCLC). Therefore, we hypothesized that DPEP2 may play a pivotal role in this tumor. Given that lung adenocarcinoma (LUAD) is the most common subtype of NSCLC, our study aimed to examine the expression and function of DPEP2 in LUAD. Based on bioinformatics and the analysis of clinical samples, our findings revealed that DPEP2 is highly expressed in normal lung tissues, but downregulated in LUAD tissues, and its expression levels were significantly associated with clinical indicators of tumor grade and prognosis. Pathway enrichment analysis showed that DPEP2 is involved in biological processes such as chemokine signaling pathways, leukocyte trans-endothelial migration, and humoral immune responses in LUAD. In addition, DPEP2 expression was significantly associated with various immune cells, especially monocytes-macrophages. Single-cell transcriptome data further confirmed the expression of DPEP2 dominantly in macrophages from normal lung tissues. Analysis of the TCIA database revealed that high DPEP2 expression is associated with a stronger response to immune checkpoint inhibitors such as CTLA4 and PD1, and determines sensitivity to LUAD therapeutic agents. Furthermore, we found that DPEP2 inhibits the migration and invasion of LUAD cells. Therefore, DPEP2 may serve as a potential immune biomarker and therapeutic target for LUAD, providing novel therapeutic approaches for this disease.

OsPEX1, an extensin-like protein, negatively regulates root growth in a gibberellin-mediated manner in rice.

Leucine-rich repeat extensins (LRXs) are required for plant growth and development through affecting cell growth and cell wall formation. LRX gene family can be classified into two categories: predominantly vegetative-expressed LRX and reproductive-expressed PEX. In contrast to the tissue specificity of Arabidopsis PEX genes in reproductive organs, rice OsPEX1 is also highly expressed in roots in addition to reproductive tissue. However, whether and how OsPEX1 affects root growth is unclear. Here, we found that overexpression of OsPEX1 retarded root growth by reducing cell elongation likely caused by an increase of lignin deposition, whereas knockdown of OsPEX1 had an opposite effect on root growth, indicating that OsPEX1 negatively regulated root growth in rice. Further investigation uncovered the existence of a feedback loop between OsPEX1 expression level and GA biosynthesis for proper root growth. This was supported by the facts that exogenous GA3 application downregulated transcript levels of OsPEX1 and lignin-related genes and rescued the root developmental defects of the OsPEX1 overexpression mutant, whereas OsPEX1 overexpression reduced GA level and the expression of GA biosynthesis genes. Moreover, OsPEX1 and GA showed antagonistic action on the lignin biosynthesis in root. OsPEX1 overexpression upregulated transcript levels of lignin-related genes, whereas exogenous GA3 application downregulated their expression. Taken together, this study reveals a possible molecular pathway of OsPEX1mediated regulation of root growth through coordinate modulation of lignin deposition via a negative feedback regulation between OsPEX1 expression and GA biosynthesis.

Changes in the Microbial Community in Maize (Zea mays L.) Root Spatial Structure Following Short-Term Nitrogen Application.

The beneficial interactions between crop roots and microbiomes play a key role in crop nutrient availability, growth promotion, and disease suppression. Recent research, however, rarely reported the effects of nitrogen (N) application rate on microbial community composition at different spatial structures in the maize root zone. Therefore, one experiment was conducted to examine the influence of three N-application levels (0, 180, and 360 kg N ha-1) on microbial community composition in three root-associated compartments of maize (bulk soil, rhizoplane, and endosphere). The microbial diversity and community composition differed significantly among the various compartments. The effects of N application on fungal composition decreased in the order bulk soil > rhizosphere > endosphere at different sampling positions. Also, the fungal composition was more sensitive to the N-fertilizer rate in the bulk soil and the rhizosphere than the bacterial community. A total of 14.42, 9.46, and 3.55% of all taxonomic groups were sensitive to N fertilizer, respectively. The keystone species fungal groups were Humicola (bulk soil), Gibberella (rhizosphere soil), and Humicola (endosphere). Together, our results demonstrate that compared with that of the bacterial community, the fungal community composition was more susceptible to different N-application rates. N fertilization affected the distribution of microflora by changing soil physicochemical properties and enzyme activities. There were strong correlations between microbial communities in maize under the N180 treatment. Moreover, the N180 treatment had the maximum fresh yield and biomass at 64.5 and 24.3 kg·ha-1, respectively.

DNA methylation-mediated silencing of Neuronatin promotes hepatocellular carcinoma proliferation through the PI3K-Akt signaling pathway.

AIMS: To explore the methylation status, function, and underlying mechanism of the imprinted gene Neuronatin (NNAT) in hepatocellular carcinoma (HCC) progression. MAIN METHODS: Immunohistochemistry (IHC) was performed to evaluate the expression of NNAT in HCC samples. Bisulfite genomic sequencing PCR (BSP) was applied to examine the methylation status of the NNAT promoter. In addition, colony formation, 5-Ethynyl-20-deoxyuridine (EdU) assays and subcutaneous xenograft nude models were used to explore the roles of NNAT in HCC cell proliferation. Furthermore, RNA-seq and phospho-specific protein microarray assays were conducted to illustrate the underlying mechanism by which NNAT regulates HCC progression. KEY FINDINGS: NNAT was obviously downregulated in HCC tissues, and its expression level was closely associated with tumor growth and patient prognosis. The downregulation of NNAT in HCC was induced by hypermethylation of CpG islands in the promoter region, and hypermethylation was correlated with overall survival of HCC. Moreover, the enforced expression of NNAT significantly inhibited HCC cell proliferation in vitro and in vivo. Transcriptome analysis showed that the alteration of NNAT expression was mainly related to dysregulation of the PI3K-Akt signaling pathway. Finally, phospho-specific antibody microarray detection further revealed that overexpressed NNAT can increase the phosphorylation levels of LKB1, Met, and elF4E and decrease the phosphorylation levels of PTEN, which are all involved in the PI3K-Akt signaling pathway. SIGNIFICANCE: Our research provides new insights into the epigenetic regulation of imprinted genes in tumorigenesis and implies that the imprinted gene NNAT may act as a prognostic biomarker and tumor suppressor in HCC.

UCHL1 promotes cancer stemness in triple-negative breast cancer.

BACKGROUND: Triple-negative breast cancer (TNBC) is a special kind of breast cancer with strong ability of invasion and metastasis. UCHL1 belongs to the ubiquitin carboxy-terminal hydrolase family and is found to be increased in a variety of malignancies, but its expression in TNBC is unknown. METHODS: First, we analyzed the expression of UCHL1 in 128 TNBC specimens and paired adjacent normal tissues from 17 TNBC patients undergoing curative resection by immunohistochemistry. Then, the relationship between UCHL1 and cancer stemness was investigated by cell flow cytometry, spheroid formation assays and western blot. Moreover, cell scratch assay and Transwell assays were performed to explore whether UCHL1 promotes the migration and invasion of TNBC cells. Finally, we constructed a xenografts model of TNBC cell lines to observe the effect of UCHL1 on tumorigenesis in vivo. RESULTS: UCHL1 was overexpressed in TNBC tissues and associated with poor prognosis. UCHL1 promoted stem cancer cells properties, including the percentage of CD44+/CD24- cells, sphere-forming ability and CSCs related markers. Furthermore, Scratch assay and Transwell assay proved that UCHL1 enhanced the migration and invasion of TNBC cells. The experimental results of xenografts model in nude mice showed that UCHL1 promoted tumorigenesis of TNBC in vivo. CONCLUSION: UCHL1 may play a role in the malignant progression of TNBC by maintaining the stemness and promoting cell invasion and is expected to become a potential therapeutic target for TNBC patients.

Chemical Constituents of Cyperus esculentus Leaves and the Protective Effect against Agricultural Fungicide-Induced Hepatotoxicity.

Cyperus esculentus is cultivated as a crop plant due to its edible and oily tubers (tiger nut). However, little is known about the phytochemicals and bioeffects of the leaves. This study was conducted to identify and quantify the chemical constituents of C. esculentus leaves and evaluate their bioactivities. By liquid chromatography-mass spectrometry, 30 compounds including flavan-3-ols, caffeic acid derivatives, and flavones, were identified from the leaves. The quantitative analysis revealed that gallocatechin (8), procyanidin B1 (15), catechin (16), chlorogenic acid (19), orientin (30), and luteolin 7-O-glucuronide (31) are the major chemical constituents of C. esculentus leaves. The contents of these six chemical constituents in the leaves collected in September in Hohhot, China, reached to 1460.85±7.66, 10178.77±302.65, 1048.35±17.37, 1722.15±26.13, 5318.62±277.16, and 1526.54±11.95 µg, respectively, in one gram of the dried leaves. The leaf extract (CELE) showed strong antioxidant activity in vitro, with compounds 8, 15, and 19 contributing the most. CELE showed significant protection against the agricultural fungicide tebuconazole-induced developmental toxicity and hepatotoxicity in zebrafish.