Proteomics mining of cancer hallmarks on a single-cell resolution.

Dysregulated proteome is an essential contributor in carcinogenesis. Protein fluctuations fuel the progression of malignant transformation, such as uncontrolled proliferation, metastasis, and chemo/radiotherapy resistance, which severely impair therapeutic effectiveness and cause disease recurrence and eventually mortality among cancer patients. Cellular heterogeneity is widely observed in cancer and numerous cell subtypes have been characterized that greatly influence cancer progression. Population-averaged research may not fully reveal the heterogeneity, leading to inaccurate conclusions. Thus, deep mining of the multiplex proteome at the single-cell resolution will provide new insights into cancer biology, to develop prognostic biomarkers and treatments. Considering the recent advances in single-cell proteomics, herein we review several novel technologies with particular focus on single-cell mass spectrometry analysis, and summarize their advantages and practical applications in the diagnosis and treatment for cancer. Technological development in single-cell proteomics will bring a paradigm shift in cancer detection, intervention, and therapy.

An AIEE-active Triphenylethylene Derivative with Photoresponsive Character for Latent Fingerprints Detection via a Simple Soaking Method.

Latent fingerprints (LFPs) is one of the most important physical evidence in the criminal scene, playing an important role in forensic investigations. Therefore, developing highly sensitive and convenient materials for the visualization of LFPs is of great significance. We designed and synthesized an organic fluorescent molecule TP-PH with aggregation-induced enhanced emission (AIEE) activity. By simply soaking, blue fluorescent images with high contrast and resolution are readily developed on various surfaces including tinfoil, steel, glass and plastic. Remarkably, LFPs can be visualized within 5 min including the first-, second- and tertiary-level details. In addition, TP-PH exhibits interesting photoactivated fluorescence enhancement properties. Under irradiation of 365 nm UV light with a power density of 382 mW/cm2, the fluorescence quantum yield displays approximately 21.5-fold enhancement. Mechanism studies reveals that the photoactivated fluorescence is attributed to the irreversible cyclodehydrogenation reactions under UV irradiation. This work provides a guideline for the design of multifunctional AIEE fluorescent materials.

The effect of triethylamine on dye-sensitized upconversion luminescence and its application in nanoprobes and photostability.

Triethylamine (TEA) is an effective medium for inhibiting dye aggregation and improving the luminescence of dye-sensitized lanthanide-doped upconversion nanoparticles (UCNPs). However, excessive TEA will cause quenching of upconversion luminescence. In this paper, the possible mechanism of TEA affecting upconversion luminescence is discussed. It is found that TEA can enhance the nucleophilicity of the solvent, leading to dye shedding from the nanoparticles. Reducing the dielectric constant of the solvent can make TEA play a more positive role in upconversion luminescence and photostability of dye-sensitized UCNPs. When heptanol is selected as the solvent for CyBSO-sensitized ß-NaYF4:20%Yb3+,2%Er3+ (UNs), TEA can increase the upconversion luminescence by 6.0 times relative to that in methanol. More importantly, the optimal content of TEA in heptanol is 3700 times more than that in methanol. Under the action of large amounts of TEA in heptanol, a novel upconversion nanoprobe for detecting ascorbic acid is developed with a limit of detection of 0.103 µM and high selectivity over potential interfering species. Meanwhile, the high concentration of TEA in heptanol can improve the photostability of CyBSO-sensitized UNs by 10.4 times, which is of paramount importance for the practical application of dye-sensitized UCNPs.

The crosstalk between reactive oxygen species and noncoding RNAs: from cancer code to drug role.

Oxidative stress (OS), characterized by the excessive accumulation of reactive oxygen species (ROS), is an emerging hallmark of cancer. Tumorigenesis and development driven by ROS require an aberrant redox homeostasis, that activates onco-signaling and avoids ROS-induced programmed death by orchestrating antioxidant systems. These processes are revealed to closely associate with noncoding RNAs (ncRNAs). On the basis of the available evidence, ncRNAs have been widely identified as multifarious modulators with the involvement of several key redox sensing pathways, such as NF-κB and Nrf2 signaling, therefore potentially becoming effective targets for cancer therapy. Furthermore, the vast majority of ncRNAs with property of easy detected in fluid samples (e.g., blood and urine) facilitate clinicians to monitor redox homeostasis, indicating a novel method for cancer diagnosis. Herein, focusing on carcinoma initiation, metastasis and chemoradiotherapy resistance, we aimed to discuss the ncRNAs-ROS network involved in cancer progression, and the potential clinical application as biomarkers and therapeutic targets.

Immunometabolic rewiring in tumorigenesis and anti-tumor immunotherapy.

Cellular metabolism constitutes a fundamental process in biology. During tumor initiation and progression, each cellular component in the cancerous niche undergoes dramatic metabolic reprogramming, adapting to a challenging microenvironment of hypoxia, nutrient deprivation, and other stresses. While the metabolic hallmarks of cancer have been extensively studied, the metabolic states of the immune cells are less well elucidated. Here we review the metabolic disturbance and fitness of the immune system in the tumor microenvironment (TME), focusing on the impact of oncometabolites to the function of immune cells and the clinical significance of targeting metabolism in anti-tumor immunotherapy. Metabolic alterations in the immune system of TME offer novel therapeutic insight into cancer treatment.

Effects of moisture and salinity on soil dissolved organic matter and ecological risk of coastal wetland.

Coastal wetland is the transitional area between land and ocean, which has a unique and sensitive ecosystem. In this study, the effects of moisture and salinity on dissolved organic matter (DOM) and adsorption of heavy metal ions (Cr(VI), Cd(II) and Pb(II)) by soil are investigated. Meanwhile, ecological risks for the potential release of N, P and heavy metals are also predicted. UV-Vis spectrophotometry and three-dimensional fluorescence spectroscopy are used to study the content and structural of DOM under different soil moisture and salinity. Soil adsorption of heavy metal ions is determined by inductively coupled plasma (ICP). The results show that soil moisture and salinity have significant effects on the basic physical and chemical properties of soil. DOM content is the highest in medium moisture and high salinity areas. In addition, the content of protein-like substances in DOM is the highest under all treatment conditions. The results also reveal that the increase of DOM promotes Cr(VI) adsorption and inhibits Cd(II) adsorption by soil. When Pb(II) concentration is high (150 mg/L), the increase of DOM inhibits Pb(II) adsorption by soil. The comprehensive ecological risk of heavy metals is the highest under high salinity. The potential release risk of N and P is the lowest at high moisture and low moisture, respectively. Base on above, effects of soil moisture and salinity on the surrounding ecological environment in coastal wetlands have been revealed, which provides a theoretical basis for the protection of coastal wetland ecological environment.

SiMYB3 in Foxtail Millet (Setaria italica) Confers Tolerance to Low-Nitrogen Stress by Regulating Root Growth in Transgenic Plants.

Foxtail millet (Setaria italica), which originated in China, has a strong tolerance to low nutrition stresses. However, the mechanism of foxtail millet tolerance to low-nitrogen stress is still unknown. In this study, the transcriptome of foxtail millet under low-nitrogen stress was systematically analyzed. Expression of 1891 genes was altered, including 1318 up-regulated genes and 573 down-regulated genes. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis revealed that 3% of these genes were involved in membrane transport and 5% were involved in redox processes. There were 74 total transcription factor (TF) genes in the DEGs (differentially expressed genes), and MYB-like transcription factors accounted for one-third (25) of the TF genes. We systematically analyzed the characteristics, expression patterns, chromosome locations, and protein structures of 25 MYB-like genes. The analysis of gene function showed that Arabidopsis and rice overexpressing SiMYB3 had better root development than WT under low-nitrogen stress. Moreover, EMSA results showed that SiMYB3 protein could specifically bind MYB elements in the promoter region of TAR2, an auxin synthesis related gene and MYB3-TAR2 regulate pair conserved in rice and foxtail millet. These results suggested that SiMYB3 can regulate root development by regulating plant root auxin synthesis under low-nitrogen conditions.

The nascent-polypeptide-associated complex alpha subunit regulates the polygalacturonases expression negatively and influences the pathogenicity of Sclerotinia sclerotiorum.

Sclerotinia sclerotiorum is a necrotrophic plant-pathogenic fungus that infects more than 400 species of plants. In this study the nascent polypeptide-associated complex α subunit gene of S. sclerotiorum (SsNACα; accession No. XP_001593856.1) was cloned and characterized. The relative transcript expression of SsNACα at different morphological stages of asexual development of S. sclerotiorum were analyzed by quantitative real time PCR (qRT-PCR). RNAi-mediated gene silencing was successful for SsNACα, and the mutated strains exhibited less than 15% of the relative expression of SsNACα were obtained and used for studying the biological functions of the gene. A delay in sclerotial maturation for S. sclerotiorum was observed in the SsNACα mutants. The significant elevations for both the activities of pectin-degrading enzymes and the expression of polygalacturonase genes also were associated with the mutated strains, indicating that SsNACα could negatively influence polygalacturonases expression and modulate the pathogenicity of S. sclerotiorum.

[Rapid determination of beet sugar content using near infrared spectroscopy].

In order to classify and set different prices on basis of difference of beet sugar content in the acquisition process and promote the development of beet sugar industry healthily, a fast, nondestructive, accurate method to detect sugar content of beet was determined by applying near infrared spectroscopy technology. Eight hundred twenty samples from 28 representative varieties of beet were collected as calibration set and 70 samples were chosen as prediction set. Then near infrared spectra of calibration set samples were collected by scanning, effective information was extracted from NIR spectroscopy, and the original spectroscopy data was optimized by data preprocessing methods appropriately. Then partial least square(PLS)regression was used to establish beet sugar quantitative prediction mathematical model. The performances of the models were evaluated by the root mean square of cross-validation (RMSECV), the coefficient of determination (R2) of the calibration model and the standard error of prediction (SEP), and the predicted results of these models were compared. Results show that the established mathematical model by using first derivative (FD) and standard normal variate transformation (SNV) coupled with partial least squares has good predictive ability. The R2 of calibration models of sugar content of beet is 0.908 3, and the RMSECV is 0.376 7. Using this model to forecast the prediction set including 70 samples, the correlation coefficient is 0.921 4 between predicted values and measured values, and the standard error of prediction (SEP) is 0.439, without significant difference (p > 0.05) between predicted values and measured values. These results demonstrated that NIRS can take advantage of simple, rapid, nondestructive and environmental detection method and could be applied to predict beet sugar content. This model owned high accuracy and can meet the precision need of determination of beet sugar content. This detection method could be used to classify and set different prices on basis of difference of beet sugar content in the acquisition process.

The therapeutic effect of pelvic floor muscle training on stress urinary incontinence following prostatectomy: a systematic review and meta-analysis.

Background: Prostatectomy often causes urinary incontinence, especially stress Urinary incontinence, which has a serious impact on the quality of life of patients. Previous studies have proved that pelvic floor muscle training can help restore pelvic floor function and reduce Urinary incontinence, but the quantitative evaluation and systematic analysis of its effect have not yet been clear. This meta-analysis aimed to systematically evaluate the therapeutic effect of pelvic floor muscle training on managing stress urinary incontinence after prostatectomy. Methods: The literature on pelvic floor muscle training for patients after prostatectomy was searched in PubMed, Web of Science, EMBASE, CNKI, VIP, Wanfang, and China Biology Medical Literature Database (CBM) from database establishment up to January 30th, 2023. Risk bias assessment was conducted using RoB1, a risk assessment tool recommended by Cochrane for evaluating RCTs literature. Publication bias was evaluated through funnel plots. Meta-analysis of effect size was performed using R 4.2.2. Results: Eleven randomized controlled studies were included. The risk of bias assessment showed that three studies had a moderate risk of bias and eight had a low risk. The meta-analysis results showed that the patient-reported incontinence was improved after one month [odds ratio (OR): 2.71, 95% 95% confidence interval (CI): 1.86-3.94, P<0.01]; improved after three months (OR: 3.42, 95% CI: 1.96-5.98, P<0.01); improved after six months (OR: 3.77, 95% CI: 1.51-9.41, P<0.01); improved after 12 months (OR: 1.21, 95% CI: 1.11-1.31, P<0.01); and the International Consultation on Incontinence Questionnaire-Simple Form (ICIQ-SF) score decreased [mean difference (MD): -2.74, 95% CI: -4.96 to -0.52, P=0.02]. Subgroup analysis showed that the ICIQ-SF score decreased after one month (MD: -0.61, 95% CI: -0.81 to -0.40) and three months (MD: -3.43, 95% CI: -6.85 to -0.02). Conclusions: Pelvic floor muscle training significantly improves stress urinary incontinence after prostatectomy, which can be improved by 2.77 times at most. However, due to the limited number of studies included, further validation is needed.

Identification and analysis of the genetic integrity of different types of rice resources through SSR markers.

Seed aging is the key factor leading to the loss of genetic integrity. In this study, the seeds of Dongxiang wild rice, Xianggu, 9194 and Nipponbare were kept in a plant incubator with constant temperature and humidity for artificial aging treatment. The genetic integrity of germplasm resources with different germination gradients were analyzed using 44 SSR markers. The results suggested that different accessions could be ranked in order of aging resistance from highest to lowest as common wild rice > Xianggu > 9194 > Nipponbare. In order to maintain the genetic diversity of rice, the population size for reproduction and regeneration should be between 60 and 140. After aging, the number of polymorphic alleles, the number of specific single plant, the ratio of polymorphic bands, the number of alleles, the number of effective alleles, gene diversity index and Shannon index of different accessions all decreased with the decrease of germination rate. The germination rate of 60% was the critical value to maintain genetic integrity. Besides, the genetic integrity of eighteen SSR markers was rapidly lost or significantly increased. The regions of these markers were closely related to seed viability or genetic integrity. This study provides a theoretical basis for determining the population size for reproduction and regeneration and the critical value of germination rate of rice resources.

Development and validation of a novel anoikis-related gene signature in clear cell renal cell carcinoma.

Background: Despite numerous treatments available, clear cell renal cell carcinoma (ccRCC) remains a deadly and invasive cancer. Anoikis-related genes (ARGs) are essential regulators of tumor metastasis and development. However, the potential roles of ARGs in ccRCC remain unclear. Methods: Based on the TCGA-KIRC cohort and GeneCards database, we identified differentially expressed ARGs in ccRCC. Then a 4 ARGs risk model was created by Cox regression and LASSO. The Kaplan-Meier and receiver operating characteristic (ROC) curves were utilized to verify the predictive efficacy of the prognostic signature. Subsequently, the possible molecular mechanism of ARGs was investigated by functional enrichment analysis. To assess the immune infiltration, immune checkpoint genes, and immune function in various risk groups, single sample gene set enrichment (ssGSEA) algorithm was employed. Furthermore, the low-risk and high-risk groups were compared in terms of tumor mutation burden (TMB). Ultimately, we analyzed the protein expression of these four ARGs utilizing the western blot test. Results: Four genes were utilized to create a risk signature that may predict prognosis, enabling the classification of KIRC patients into groups with low or high risk. The reliability of the signature was examined utilizing survival analysis and ROC analysis. According to the multivariate Cox regression result, the risk score was a reliable independent prognostic predictor for KIRC patients. The novel risk model could differentiate between KIRC patients with various clinical outcomes and represent KIRC's specific immune status. An analysis of the correlation of TMB and risk score indicated a positive correlation between them, with high TMB being potentially linked to worse outcomes. Conclusion: Based on our findings, the prognostic signature of ARGs may be employed as an independent prognostic factor for ccRCC patients. It may introduce alternative perspectives on prognosis evaluation and serve as a prominent reference for personalized and precise therapy in KIRC.

TokenCut: Segmenting Objects in Images and Videos With Self-Supervised Transformer and Normalized Cut.

In this paper, we describe a graph-based algorithm that uses the features obtained by a self-supervised transformer to detect and segment salient objects in images and videos. With this approach, the image patches that compose an image or video are organised into a fully connected graph, in which the edge between each pair of patches is labeled with a similarity score based on the features learned by the transformer. Detection and segmentation of salient objects can then be formulated as a graph-cut problem and solved using the classical Normalized Cut algorithm. Despite the simplicity of this approach, it achieves state-of-the-art results on several common image and video detection and segmentation tasks. For unsupervised object discovery, this approach outperforms the competing approaches by a margin of 6.1%, 5.7%, and 2.6% when tested with the VOC07, VOC12, and COCO20 K datasets. For the unsupervised saliency detection task in images, this method improves the score for Intersection over Union (IoU) by 4.4%, 5.6% and 5.2%. When tested with the ECSSD, DUTS, and DUT-OMRON datasets. This method also achieves competitive results for unsupervised video object segmentation tasks with the DAVIS, SegTV2, and FBMS datasets.

Analysis of anthocyanins and total flavonoids content in functional rice and its recombination inbred lines.

Anthocyanin is one of the flavonoids, which has strong antioxidant properties. Functional rice rich in anthocyanins can not only improve immunity, but also anti-radiation, beauty, anti-aging effect, very popular in the market. In this study, we used Zibaoxiangnuo 1 (ZBXN 1), a functional rice variety which is rich in total flavonoids and anthocyanins, as the experimental material to construct Recombination Inbred Lines (RILs) with Minghui63 (MH63), a variety without anthocyanins. The contents of anthocyanins and total flavonoids of RILs and two parents were determined for three consecutive generations. The average anthocyanin content of parent ZBXN 1 was 319.31 mg/kg, and the anthocyanin inheritance of RIL population was relatively stable, with 10 samples higher than ZBXN 1. In addition, there was no significant difference in the total flavonoids content between the two parents, the total flavonoids content of Z25 in RIL population was 0.33%. Based on these studies, we believe that ZBXN 1 has abundant and stable anthocyanins, which can be used as an intermediate breeding material for breeding high-quality varieties with high anthocyanins, and lay a foundation for breeding more anthocyanin-rich rice varieties.

Overexpression of MYB-like transcription factor SiMYB30 from foxtail millet (Setaria italica L.) confers tolerance to low nitrogen stress in transgenic rice.

Nitrogen fertilizers significantly increase crop yield; however, the negative impact of excessive nitrogen use on the environment and soil requires urgent attention. Improving crop nitrogen use efficiency (NUE) is crucial to increase yields and protect the environment. Foxtail millet (Setaria italica L.), a gramineous crop with significant tolerance to barren croplands, is an ideal model crop for studying abiotic stress resistance in gramineous crops. However, knowledge of the regulatory network for NUE in foxtail millet is fragmentary. Herein, we identified an R2R3-like MYB transcription factor in foxtail millet, SiMYB30, which belongs to MYB subfamily 17. The expression of SiMYB30 is responsive to low nitrogen (LN) concentration. Compared with wildtype Kitaake, seedlings of rice lines overexpressing SiMYB30 showed significantly increased shoot fresh and dry weights, plant height, and root area under LN treatment indoors. Consistently, overexpression of SiMYB30 in field experiments significantly increased grain and stem nitrogen contents, grain yield per plant, and stem weight in rice. Furthermore, qRT-PCR revealed that SiMYB30 effectively activated the expression of nitrogen uptake-related genes-OsNRT1, OsNRT1.1B, and OsNPF2.4-and nitrogen assimilation-related genes-OsGOGAT1, OsGOGAT2, and OsNIA2. Notably, SiMYB30 directly bound to the promoter of OsGOGAT2 and regulated its expression. These results highlight the novel and pivotal role of SiMYB30 in improving crop NUE.

Improving the accuracy of nonpoint-source pollution estimates in inland waters with coupled satellite-UAV data.

Quantitatively and accurately analyzing nonpoint-source (NPS) pollution is essential for efficiently preventing the input of NPS loads into inland waters. However, the accuracy of previous NPS pollution models is limited by the accuracy of ground parameter data. In addition, there are few effective methods that thoroughly verify modeling results at large scales. This paper presents a framework for accurate NPS pollution estimation by coupling satellite and unmanned aerial vehicle (UAV) monitoring data, and the results are verified by both field sampling and a newly developed inlet NPS pollution "observation" simulation method. Fractional vegetation coverage (FVC) data obtained by satellite were used to improve the accuracy of the runoff module of the framework. Satellite and UAV data were coupled to acquire livestock data, determine inlets, and identify reservoir buffer zones and vegetation types. These new data were then used to improve the accuracy of the livestock and runoff modules in the framework. The results show that the estimation accuracy of total nitrogen, total phosphorus, ammonia nitrogen, and chemical oxygen demand with FVC were improved by 39.96%, 69.29%, 54.05% and 47.22% (in relative error), respectively. The high-resolution livestock data acquisition improved the estimation accuracy of the NPS pollution load by 7-53%. The high-resolution inlet extraction improved the accuracy by 3-24%. The high-resolution buffer zone identification improved the accuracy with the estimated NPS pollutant concentration into reservoir decreasing by 60-99%. Finally, the high-resolution vegetation type identification improved the accuracy by 10-72%. The framework performs satisfactorily, which was verified based on the simulated NPS observations with an average relative error of 11.54-24.31%. We found that the FVC, livestock number, and inlet number are key parameters for NPS pollution modeling; the introduction of monthly variation in the FVC makes the modeled NPS pollution load much higher in areas with mature complex forested ecosystems or densely distributed vegetation but much lower in areas with sparsely distributed vegetation. The above methods provide a scientific reference for high-efficiency NPS pollution prevention in inland waters, laying a solid basis for decision-making regarding water quality management in data-scarce regions around the world.

Quantitative Trait Loci Mapping Analysis for Cold Tolerance Under Cold Stress and Brassinosteroid-Combined Cold Treatment at Germination and Bud Burst Stages in Rice.

Low temperature is one of the major abiotic stresses limiting seed germination and early seedling growth in rice. Brassinosteroid (BR) application can improve cold tolerance in rice. However, the regulatory relationship between cold tolerance and BR in rice remains undefined. Here, we constructed a population of 140 backcross recombinant inbred lines (BRILs) derived from a cross between a wild rice (Dongxiang wild rice, DXWR) and a super rice (SN265). The low-temperature germination rate (LTG), survival rate (SR), plant height (PH), and first leaf length (FLL) were used as indices for assessing cold tolerance under cold stress and BR-combined cold treatment at seed germination and bud burst stages. A high-resolution SNP genetic map, covering 1,145 bin markers with a distance of 3188.33 cM onto 12 chromosomes, was constructed using the GBS technique. A total of 73 QTLs were detected, of which 49 QTLs were identified under cold stress and 24 QTLs under BR-combined cold treatment. Among these, intervals of 30 QTLs were pairwise coincident under cold stress and BR-combined cold treatment, as well as different traits including SR and FLL, and PH and FLL, respectively. A total of 14 candidate genes related to cold tolerance or the BR signaling pathway, such as CBF/DREB (LOC_Os08g43200), bHLH (LOC_Os07g08440 and LOC_Os07g08440), WRKY (LOC_Os06g30860), MYB (LOC_Os01g62410 and LOC_Os05g51160), and BRI1-associated receptor kinase 1 precursor (LOC_Os06g16300), were located. Among these, the transcript levels of 10 candidate genes were identified under cold stress and BR-combined cold treatment by qRT-PCR. These findings provided an important basis for further mining the genes related to cold tolerance or the BR signaling pathway and understanding the molecular mechanisms of cold tolerance in rice.

Identification of QTL under Brassinosteroid-Combined Cold Treatment at Seedling Stage in Rice Using Genotyping-by-Sequencing (GBS).

Cold stress is a major threat to the sustainability of rice yield. Brassinosteroids (BR) application can enhance cold tolerance in rice. However, the regulatory mechanism related to cold tolerance and the BR signaling pathway in rice has not been clarified. In the current study, the seedling shoot length (SSL), seedling root length (SRL), seedling dry weight (SDW), and seedling wet weight (SWW) were used as the indices for identifying cold tolerance under cold stress and BR-combined cold treatment in a backcross recombinant inbred lines (BRIL) population. According to the phenotypic characterization for cold tolerance and a high-resolution SNP genetic map obtained from the GBS technique, a total of 114 QTLs were identified, of which 27 QTLs were detected under cold stress and 87 QTLs under BR-combined cold treatment. Among them, the intervals of many QTLs were coincident under different treatments, as well as different traits. A total of 13 candidate genes associated with cold tolerance or BR pathway, such as BRASSINAZOLE RESISTANT1 (OsBZR1), OsWRKY77, AP2 domain-containing protein, zinc finger proteins, basic helix-loop-helix (bHLH) protein, and auxin-induced protein, were predicted. Among these, the expression levels of 10 candidate genes were identified under different treatments in the parents and representative BRIL individuals. These results were helpful in understanding the regulation relationship between cold tolerance and BR pathway in rice.

Genomic insights on the contribution of introgressions from Xian/Indica to the genetic improvement of Geng/Japonica rice cultivars.

Hybridization between Xian/indica (XI) and Geng/japonica (GJ) rice combined with utilization of plant ideotypes has greatly contributed to yield improvements in modern GJ rice in China over the past 50 years. To explore the genomic basis of improved yield and disease resistance in GJ rice, we conducted a large-scale genomic landscape analysis of 816 elite GJ cultivars representing multiple eras of germplasm from China. We detected consistently increasing introgressions from three XI subpopulations into GJ cultivars since the 1980s and found that the XI genome introgressions significantly increased the grain number per panicle (GN) and decreased the panicle number per plant. This contributed to the improvement of plant type during modern breeding, changing multi-tiller plants to moderate tiller plants with a large panicle size and increasing the blast resistance. Notably, we found that key gene haplotypes controlling plant architecture, yield components, and pest and disease resistance, including IPA1, SMG1, DEP3, Pib, Pi-d2, and Bph3, were introduced from XI rice by introgression. By GWAS analysis, we detected a GN-related gene Gnd5, which had been consistently introgressed from XI into GJ cultivars since the 1980s. Gnd5 is a GRAS transcription factor gene, and Gnd5 knockout mutants showed a significant reduction in GN. The estimated genetic effects of genes varied among different breeding locations, which explained the distinct introgression levels of XI gene haplotypes, including Gnd5, DEP3, etc., to these GJ breeding pedigrees. These findings reveal the genomic contributions of introgressions from XI to the trait improvements of GJ rice cultivars and provide new insights for future rice genomic breeding.

Accumulation and cross-linkage of ß-1,3/1,6-glucan lead to loss of basal stipe cell wall extensibility in mushroom Coprinopsis cinerea.

The mature basal stipe of mushroom Coprinopsis cinerea loses wall extensibility. We found that an endo-ß-1,3-glucanase ENG from C. cinerea could restore mature basal stipe wall extensibility via pretreatment such that the ENG-pretreated basal stipe walls could be induced to extend by chitinase ChiIII. ENG pretreatment released glucose, laminaribiose, and 3-O-D-gentiobiose-D-glucose from the basal stipe walls, consistent with ENG-digested products of ß-1,6-branched ß-1,3-glucan. Different effects of endo-ß-1,3-glucanase ENG and exo-ß-1,3-glucanase EXG pretreatment on the structure, amount and ratio (ß-1,3-glucoside bonds to ß-1,6-glucoside bonds) of products from the basal stipe and the apical stipe cell walls, respectively, and on the cell wall extensibility and the cell wall ultra-architecture of the basal stipes were analyzed. All results demonstrate that the more accumulation and cross-linkage of ß-1,6-branched ß-1,3-glucan with wall maturation lead to loss of wall extensibility of the basal stipe regions compared to the apical stipe cell walls.