Identification and Application of CLE Peptides for Drought Resistance in Solanaceae Crops.

The CLE (CLAVATA3/Embryo Surrounding Region-related) family, a group of peptides with hormone-like features, plays a pivotal role in plant growth, development, and adaptation to stress. Through homology-based blast analysis of 32 Arabidopsis thaliana CLE peptide sequences, we have identified 5, 14, and 10 CLE family members in Nicotiana tabacum, Capsicum annuum, and Solanum melongena, respectively. Chemical synthesis and functional assays of the peptides led to the discovery that NtCLE3 substantially enhances the drought resistance of these three Solanaceae crops. Our transcriptome, RT-qPCR, and antioxidant enzyme activity data showed that NtCLE3 increased antioxidant capacity and ABA synthesis in tobacco. Moreover, the recombinant protein RPNtCLE3, composed of 6*NtCLE3, preserved the capacity to foster drought resilience and proved to be a promising drought resistance regulator, which presents a more favorable alternative for field applications compared to ABA which degrades rapidly under sunlight exposure. This research unveils the prospective utility of NtCLE3 in enhancing drought tolerance in Solanaceae crops and provides new ideas for the development of novel bioregulators aimed at mitigating drought stress.

Dysfunction of duplicated pair rice histone acetyltransferases causes segregation distortion and an interspecific reproductive barrier.

Postzygotic reproductive isolation, which results in the irreversible divergence of species, is commonly accompanied by hybrid sterility, necrosis/weakness, or lethality in the F1 or other offspring generations. Here we show that the loss of function of HWS1 and HWS2, a couple of duplicated paralogs, together confer complete interspecific incompatibility between Asian and African rice. Both of these non-Mendelian determinants encode the putative Esa1-associated factor 6 (EAF6) protein, which functions as a characteristic subunit of the histone H4 acetyltransferase complex regulating transcriptional activation via genome-wide histone modification. The proliferating tapetum and inappropriate polar nuclei arrangement cause defective pollen and seeds in F2 hybrid offspring due to the recombinant HWS1/2-mediated misregulation of vitamin (biotin and thiamine) metabolism and lipid synthesis. Evolutionary analysis of HWS1/2 suggests that this gene pair has undergone incomplete lineage sorting (ILS) and multiple gene duplication events during speciation. Our findings have not only uncovered a pair of speciation genes that control hybrid breakdown but also illustrate a passive mechanism that could be scaled up and used in the guidance and optimization of hybrid breeding applications for distant hybridization.

[Difference between prostate cancer patients' Gleason scores from preoperative biopsy and those from postoperative pathology].

OBJECTIVE: To evaluate the consistency of the Gleason scores of PCa patients based on preoperative biopsy with those from postoperative pathology, identify the possible factors influencing results of scoring, and construct a risk scoring model. METHODS: We collected the demographic and clinical data on the patients with PCa confirmed by preoperative prostate biopsy or postoperative pathology and treated by radical prostatectomy within 6 months after diagnosis. Using paired sample t-test, we identified the difference between the Gleason scores based on preoperative biopsy and those from postoperative pathology, analyzed the demographic and clinical data on the patients for relevant factors affecting the consistency of the Gleason scores, and calculated and visualized the relative risk values of the factors through Poisson regression. From the continuous variables with statistical significance, we screened independent risk factors for the difference in the Gleason scores by Lasso regression analysis, established a risk scoring model, generated risk coefficients, and evaluated the predictive ability of the model using the ROC curve. Based on the results of imaging examination with statistically significant differences, we constructed a column chart by logistic regression and evaluated the predictive validity of the chart using calibration curves, decision curves and ROC curves. RESULTS: The results of paired sample t-test for 210 PCa patients showed statistically significant differences between the Gleason scores from preoperative biopsy and those from postoperative pathology (P < 0.001). There were significant differences in the body weight, BMI and PSA level as well as in all other factors but prostate calcification between the patients with consistent and those with inconsistent Gleason scores (all P < 0.05). An 8-factor prediction model was successfully constructed, which could predict the consistency of Gleason scores, with a better predicting performance than the single indicator within the model. The nomogram exhibited a C-index value of 0.85, with the calibration curve similar to the standard one, the threshold of the decision curve 0.10－0.92, and the area under the ROC curve higher than other predictive indicators. CONCLUSION: Based on the demographic and clinical data on PCa patients, a risk prediction model and a column chart were successfully constructed, which could effectively predict the difference between the Gleason scores from preoperative prostate biopsy and those from postoperative pathology.

An α/ß hydrolase family member negatively regulates salt tolerance but promotes flowering through three distinct functions in rice.

Ongoing soil salinization drastically threatens crop growth, development, and yield worldwide. It is therefore crucial that we improve salt tolerance in rice by exploiting natural genetic variation. However, many salt-responsive genes confer undesirable phenotypes and therefore cannot be effectively applied to practical agricultural production. In this study, we identified a quantitative trait locus for salt tolerance from the African rice species Oryza glaberrima and named it as Salt Tolerance and Heading Date 1 (STH1). We found that STH1 regulates fatty acid metabolic homeostasis, probably by catalyzing the hydrolytic degradation of fatty acids, which contributes to salt tolerance. Meanwhile, we demonstrated that STH1 forms a protein complex with D3 and a vital regulatory factor in salt tolerance, OsHAL3, to regulate the protein abundance of OsHAL3 via the 26S proteasome pathway. Furthermore, we revealed that STH1 also serves as a co-activator with the floral integrator gene Heading date 1 to balance the expression of the florigen gene Heading date 3a under different circumstances, thus coordinating the regulation of salt tolerance and heading date. Notably, the allele of STH1 associated with enhanced salt tolerance and high yield is found in some African rice accessions but barely in Asian cultivars. Introgression of the STH1HP46 allele from African rice into modern rice cultivars is a desirable approach for boosting grain yield under salt stress. Collectively, our discoveries not only provide conceptual advances on the mechanisms of salt tolerance and synergetic regulation between salt tolerance and flowering time but also offer potential strategies to overcome the challenges resulted from increasingly serious soil salinization that many crops are facing.

A genetic module at one locus in rice protects chloroplasts to enhance thermotolerance.

How the plasma membrane senses external heat-stress signals to communicate with chloroplasts to orchestrate thermotolerance remains elusive. We identified a quantitative trait locus, Thermo-tolerance 3 (TT3), consisting of two genes, TT3.1 and TT3.2, that interact together to enhance rice thermotolerance and reduce grain-yield losses caused by heat stress. Upon heat stress, plasma membrane-localized E3 ligase TT3.1 translocates to the endosomes, on which TT3.1 ubiquitinates chloroplast precursor protein TT3.2 for vacuolar degradation, implying that TT3.1 might serve as a potential thermosensor. Lesser accumulated, mature TT3.2 proteins in chloroplasts are essential for protecting thylakoids from heat stress. Our findings not only reveal a TT3.1-TT3.2 genetic module at one locus that transduces heat signals from plasma membrane to chloroplasts but also provide the strategy for breeding highly thermotolerant crops.

[Basement membrane-related gene signature to predict biochemical recurrence in patients with prostate cancer after radical prostatectomy].

OBJECTIVE: To construct and verify a key gene signature of the basement membrane of prostate cancer (PCa) to predict the progression and biochemical recurrence of the malignancy after radical prostatectomy. METHODS: Based on the PCa-related transcriptome, gene mutation and clinical data from the Cancer Genome Atlas Project (TCGA) database, we analyzed the differentially expressed genes (DEG) related to the basement membrane in the PCa and adjacent normal prostate tissues, and subjected them to GO function enrichment and KEGG pathway enrichment analyses. We identified prognosis-related genes from the DEGs and analyzed their mutations. According to the follow-up data and biochemical recurrence after prostatectomy, we established a prognostic risk scoring model, verified its accuracy using the Gene Expression Omnibus (GEO) database, and performed survival analysis, principal component analysis (PCA), independent prognostic analysis and ROC curve analysis of the model. We constructed a protein-protein interaction network after verifying the correctness of the model by immunohistochemistry. We also established a nomogram and tested its accuracy using ROC and calibration curves. RESULTS: Totally, 85 DEGs were identified, among which 18 were up-regulated and 67 down-regulated. The prognostic risk scoring model was established with 11 of the genes. The risk of biochemical recurrence PCa was significantly higher in the high-risk than in the low-risk group (HR: 3.51, 95% CI: 2.32－5.32, P < 0.01), which was verified with the GEO database data (P < 0.01). In addition, the patients in the high-risk group were older with higher clinical T-stage, higher Gleason score, higher positive rate, larger numbers of positive lymph nodes, and a larger proportion of residual tumors than those in the low-risk group (P < 0.05). The nomogram constructed with the patients' age, pN, pT and cT stages, Gleason score and prognostic risk score manifested that the area under the ROC curve was higher than the other predictors. The calibration chart showed consistency of the predicted outcomes to the actual results. CONCLUSION: A prognostic risk scoring model of basement membrane-related genes and an effective nomogram were successfully constructed, which can predict the risk of biochemical recurrence in PCa patients after radical prostatectomy.

An Integrated Gut Microbiota and Network Pharmacology Study on Fuzi-Lizhong Pill for Treating Diarrhea-Predominant Irritable Bowel Syndrome.

Diarrhea-predominant irritable bowel syndrome (IBS-D) is one of the most common chronic functional gastrointestinal diseases with limited treatments. Gut microbiota play an important role in chronic gastrointestinal diseases. In traditional Chinese medicine (TCM), Spleen-Yang deficiency (SYD) is one of the root causes of IBS-D. Fuzi-Lizhong pill (FLZP) is well known for its powerful capacity for treating SYD and has a good clinical effect on IBS-D. However, the mechanism of FLZP on the gut microbiota of IBS-D has not been fully clarified. Our present study aimed to reveal the mechanism of FLZP regulating gut microbiota of IBS-D. The body mass, CCK, MTL, and Bristol fecal character score were used to verify the establishment of the IBS-D model. IL-6, TNF, IL-1ß, and IFN-γ were crucial targets screened by network pharmacology and preliminarily verified by ELISA. Eighteen gut microbiota were important for the treatment of IBS-D with FLZP. Bacteroidetes, Blautia, Turicibacter, and Ruminococcus_torques_group were the crucial gut microbiota that FLZP inhibits persistent systemic inflammation in the IBS-D model. Lactobacillus is the crucial gut microbiota that FLZP renovates intestinal immune barrier in the IBS-D model. In summary, FLZP can affect bacterial diversity and community structures in the host and regulate inflammation and immune system to treat IBS-D.

A rice QTL GS3.1 regulates grain size through metabolic-flux distribution between flavonoid and lignin metabolons without affecting stress tolerance.

Grain size is a key component trait of grain weight and yield. Numbers of quantitative trait loci (QTLs) have been identified in various bioprocesses, but there is still little known about how metabolism-related QTLs influence grain size and yield. The current study report GS3.1, a QTL that regulates rice grain size via metabolic flux allocation between two branches of phenylpropanoid metabolism. GS3.1 encodes a MATE (multidrug and toxic compounds extrusion) transporter that regulates grain size by directing the transport of p-coumaric acid from the p-coumaric acid biosynthetic metabolon to the flavonoid biosynthetic metabolon. A natural allele of GS3.1 was identified from an African rice with enlarged grains, reduced flavonoid content and increased lignin content in the panicles. Notably, the natural allele of GS3.1 caused no alterations in other tissues and did not affect stress tolerance, revealing an ideal candidate for breeding efforts. This study uncovers insights into the regulation of grain size though metabolic-flux distribution. In this way, it supports a strategy of enhancing crop yield without introducing deleterious side effects on stress tolerance mechanisms.

UDP-glucosyltransferase regulates grain size and abiotic stress tolerance associated with metabolic flux redirection in rice.

Grain size is an important component trait of grain yield, which is frequently threatened by abiotic stress. However, little is known about how grain yield and abiotic stress tolerance are regulated. Here, we characterize GSA1, a quantitative trait locus (QTL) regulating grain size and abiotic stress tolerance associated with metabolic flux redirection. GSA1 encodes a UDP-glucosyltransferase, which exhibits glucosyltransferase activity toward flavonoids and monolignols. GSA1 regulates grain size by modulating cell proliferation and expansion, which are regulated by flavonoid-mediated auxin levels and related gene expression. GSA1 is required for the redirection of metabolic flux from lignin biosynthesis to flavonoid biosynthesis under abiotic stress and the accumulation of flavonoid glycosides, which protect rice against abiotic stress. GSA1 overexpression results in larger grains and enhanced abiotic stress tolerance. Our findings provide insights into the regulation of grain size and abiotic stress tolerance associated with metabolic flux redirection and a potential means to improve crops.

Translational Regulation of Plant Response to High Temperature by a Dual-Function tRNAHis Guanylyltransferase in Rice.

As sessile organisms, plants have evolved numerous strategies to acclimate to changes in environmental temperature. However, the molecular basis of this acclimation remains largely unclear. In this study we identified a tRNAHis guanylyltransferase, AET1, which contributes to the modification of pre-tRNAHis and is required for normal growth under high-temperature conditions in rice. Interestingly, AET1 possibly interacts with both RACK1A and eIF3h in the endoplasmic reticulum. Notably, AET1 can directly bind to OsARF mRNAs including the uORFs of OsARF19 and OsARF23, indicating that AET1 is associated with translation regulation. Furthermore, polysome profiling assays suggest that the translational status remains unaffected in the aet1 mutant, but that the translational efficiency of OsARF19 and OsARF23 is reduced; moreover, OsARF23 protein levels are obviously decreased in the aet1 mutant under high temperature, implying that AET1 regulates auxin signaling in response to high temperature. Our findings provide new insights into the molecular mechanisms whereby AET1 regulates the environmental temperature response in rice by playing a dual role in tRNA modification and translational control.

Effect of biochar from peanut shell on speciation and availability of lead and zinc in an acidic paddy soil.

Biochar has been used to reduce the mobility and availability of heavy metals in contaminated paddy soils. A pot experiment was carried out to analyze the effects of peanut shell biochar (PBC) on the speciation and phytoavailability of Pb and Zn in contaminated acidic paddy soil using rice (Oryza sativa L.) as an indicator plant. Peanut shell biochar was applied to an acidic paddy soil contaminated with Pb and Zn at four rates (0%, 1%, 2%, and 5% w/w), and rice plants were grown in this soil. The soil pH, cation exchange capacity (CEC), water-soluble SO42-, dissolved organic carbon (DOC), CaCl2-extractable heavy metals, and speciation of heavy metals were determined. Additionally, biomass and concentrations of heavy metals in rice tissues were determined. The application of PBC significantly increased the pH, CEC, water-soluble SO42-, and DOC in the paddy soil, but decreased the content of CaCl2-extractable Pb and Zn. The CaCl2-extractable Pb and Zn showed significant negative correlations with the pH, CEC, water-soluble SO42-, and DOC (p < 0.05). Following the application of biochar to the contaminated paddy soil, the Pb and Zn concentrations in the CaCl2 extracts were reduced by 41.04-98.66% and 17.78-96.87% (p < 0.05), respectively. Sequential chemical extractions showed a reduction in the acid-soluble Pb and Zn fraction and an increase in the reducible fraction following the addition of biochars. PBC obviously inhibited the uptake and accumulation of Pb and Zn in the rice plants. The Pb concentrations in the rice grain were significantly reduced by 60.32%, with the addition of 5% PBC. Neither of the biochars significantly changed the Zn concentrations in the rice grain. The influence of biochar on Pb and Zn phytoavailability varied not only with the application rate of biochar, but also with the kind of metals. Overall, the use of peanut shell biochar at a high application rate is more effective in immobilizing Pb and Zn in the acidic paddy soil contaminated with heavy metals, especially in reducing the phytoavailability of Pb to the rice plants.

A three-season field study on the in-situ remediation of Cd-contaminated paddy soil using lime, two industrial by-products, and a low-Cd-accumulation rice cultivar.

To mitigate the serious problem of Cd-contaminated paddy soil, we investigated the remediation potential of combining in-situ immobilization with a low-Cd-accumulation rice cultivar. A three-season field experiment compared the soil pH, available Cd and absorption of Cd by three rice cultivars with different Cd accumulation abilities grown in Cd-contaminated paddy soil amended with lime (L), slag (S), and bagasse (B) alone or in combination. The three amendments applied alone and in combination significantly increased soil pH, reduced available Cd and absorption of Cd by rice with no effect on grain yield. Among these, the LS and LSB treatments reduced the brown rice Cd content by 38.3-69.1% and 58.3-70.9%, respectively, during the three seasons. Combined with planting of a low-Cd-accumulation rice cultivar (Xiang Zaoxian 32) resulted in a Cd content in brown rice that met the contaminant limit (≤0.2mgkg-1). However, the grain yield of the low-Cd-accumulation rice cultivar was approximately 30% lower than the other two rice cultivars. Applying LS or LSB as amendments combined with planting a low-Cd-accumulation rice cultivar is recommended for the remediation of Cd-contaminated paddy soil. The selection and breeding of low-Cd-accumulation rice cultivars with high grain production requires further research.

NRP-1 expression in bladder cancer and its implications for tumor progression.

Neuropilin-1 (NRP-1) overexpression has been reported in a variety of human cancers. However, the role of NRP-1 in bladder cancer (BC) remains unclear. The aim of present study was to analyze NRP-1 protein expression in BC tissues and to assess its prognostic significance for BC. NRP-1 messenger ribonucleic acid (mRNA) and protein expression were determined by real-time quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) and immunohistochemistry in specimens of primary cancer and their adjacent noncancerous tissues in BC patients. Additionally, NRP-1 protein expression in 139 archived paraffin-embedded BC samples was analyzed by immunohistochemistry and correlated with clinicopathological characteristics and survival. Student's t test, Spearman's rank correlation, Kaplan-Meier plots, and Cox's proportional hazards regression model were used to analyze the data. By qRT-PCR and immunohistochemistry, the levels of NRP-1 mRNA and protein were significantly higher in BC, compared to that in adjacent noncancerous tissues (P<0.001). High expression of NRP-1 was significantly associated with histologic grade (P=0.016) and tumor stage (P=0.001). Multivariate analysis showed that high expression of NRP-1 was an independent prognostic factor for overall survival. Our study suggests that overexpression of NRP-1 may play an important role in the progression of BC, and NRP-1 expression may serve as a biomarker for poor prognosis for BC.