Down-regulation of MANNANASE7 gene in Brassica napus L. enhances silique dehiscence-resistance.

KEY MESSAGE: MANNANASE7 gene in Brassica napus L. encodes a hemicellulose which located at cell wall or extracellular space and dehiscence-resistance can be manipulated by altering the expression of MANNANASE7. Silique dehiscence is an important physiological process in plant reproductive development, but causes heavy yield loss in crops. The lack of dehiscence-resistant germplasm limits the application of mechanized harvesting and greatly restricts the rapeseed (Brassica napus L.) production. Hemicellulases, together with cellulases and pectinases, play important roles in fruit development and maturation. The hemicellulase gene MANNANASE7 (MAN7) was previously shown to be involved in the development and dehiscence of Arabidopsis (Arabidopsis thaliana) siliques. Here, we cloned BnaA07g12590D (BnMAN7A07), an AtMAN7 homolog from rapeseed, and demonstrate its function in the dehiscence of rapeseed siliques. We found that BnMAN7A07 was expressed in both vegetative and reproductive organs and significantly highly expressed in leaves, flowers and siliques where the abscission or dehiscence process occurs. Subcellular localization experiment showed that BnMAN7A07 was localized in the cell wall. The biological activity of the BnMAN7A07 protein isolated and purified through prokaryotic expression system was verified to catalyse the decomposition of xylan into xylose. Phenotypic studies of RNA interference (RNAi) lines revealed that down-regulation of BnMAN7A07 in rapeseed could significantly enhance silique dehiscence-resistance. In addition, the expression of upstream silique development regulators is altered in BnMAN7A07-RNAi plants, suggesting that a possible feedback regulation mechanism exists in the regulation network of silique dehiscence. Our results demonstrate that dehiscence-resistance can be manipulated by altering the expression of hemicellulase gene BnMAN7A07, which could provide an available genetic resource for breeding practice in rapeseed which is beneficial to mechanized harvest.

A novel urinary long non-coding RNA transcript improves diagnostic accuracy in patients undergoing prostate biopsy.

BACKGROUND: Long non-coding RNA (LncRNA) PCA3 has been a well-established urine biomarker for the detection of prostate cancer (PCa). Our previous study showed a novel LncRNA FR0348383 is up-regulated in over 70% of PCa compared with matched benign tissues. The aim of this study was to evaluate the diagnostic value of urinary FR0348383 for men undergoing prostate biopsy due to elevated PSA (PSA > 4.0 ng/ml) and/or abnormal digital rectal examination (DRE). METHODS: Post-DRE first-catch urine specimens prior to prostate biopsies were prospectively collected. After the whole transcriptome amplification, quantitative real time polymerase chain reaction was applied to quantify urine FR0348383 and PSA levels. The FR0348383 score was calculated as the ratio of PSA and FR0348383 mRNA (PSA mRNA/FR0348383 mRNA × 1000). The diagnostic value of FR0348383 score was evaluated by logistic regression and decision curve analysis. RESULTS: 213 cases with urine samples containing sufficient mRNA were included, 94 cases had serum PSA level 4.0-10.0 ng/ml. PCa was identified in 72 cases. An increasing FR0348383 score was correlated with an increasing probability of a positive biopsy (P < 0.001). Multivariable logistic analysis indicated FR0348383 score (P < 0.001), PSA (P = 0.004), age (P = 0.007), prostate volume (P < 0.001) were independent predictors of PCa. ROC analysis demonstrated FR0348383 score outperformed PSA, %free PSA, and PSA Density in the prediction of PCa in the subgroup of patients with grey area PSA (AUC: 0.815 vs. 0.562 vs. 0.599 vs. 0.645). When using a probability threshold of 30% in the grey zone cohort, The FR0348383 score would save 52.0% of avoidable biopsies without missing any high grade cancers. CONCLUSIONS: FR0348383 transcript in post-DRE urine may be a novel biomarker for detection of PCa with great diagnostic value, especially in the grey zone cohort. The application of FR0348383 score in clinical practice might avoid unnecessary prostate biopsies and increase the specificity of PCa diagnosis.

Nutrient addition alters plant community productivity but not the species diversity of a mountain meadow in Tajikistan.

Introduction: Tajikistan is a typical mountainous country covered by different mountain grasslands that are important pasture resources. Recently, grassland degradation has become widespread due to climate change and human activities and fertilization has been used to improve grassland production. However, fertilizer inputs can substantially alter species diversity, but it is uncl\ear how productivity and species diversity respond to nutrient enrichment in the mountain meadows of Tajikistan. Methods: Therefore, a 5-year (2018-2022) continuous in-situ mineral fertilizer experiment was conducted to examine the effects of three nitrogen (N) levels (0, 30, and 90 kg N ha-1 year-1), two phosphorus (P) levels (0 and 30 kg P ha-1 year-1), and their combinations on above-ground biomass (AGB) and species diversity in a mountain meadow grassland in Ziddi, Varzob region, Tajikistan. Five species diversity metrics-Margalef's species richness (Dma), the Shannon-Wiener index (H), the Simpson index (C), Pielou's equitability index (Epi), and the Evar Species Evenness index (Evar)-were used to measure species diversity. Results and discussions: The results indicated that the addition of different N and P amounts and their various combinations considerably increased both total and dominant species AGB, with the highest increase occurring in the N90P30 (90 kg N ha-1 year-1 combined with 30 kg P ha-1 year-1) treatment in 2022; during the experiment, the importance value of Prangos pabularia (dominant species) first decreased and then increased, but its dominant status did not change or fluctuate among the years. Furthermore, N, P, and their different combinations had no significant effect on species diversity (Dma, H, C, Epi, and Evar). All the species diversity indexes fluctuated among years, but there was no interaction with mineral fertilizer addition. Total AGB had a negative relationship with species diversity and low concentration N fertilizer addition (N30; P30) strengthened this negative trend. However, this trend decreased under the high N fertilizer condition (N90P30). Overall, nutrient addition to the natural mountain grassland of the Varzob region improved AGB, which meant that there was more forage for local animals. Mineral fertilizers had no significant effect on species diversity, but may enhance P. pabularia dominance in the future, which will help maintain the stability of the plant community and improve the quality of the forage because P. pabularia is an excellent and important winter fodder. Our study suggests that scientific nutrient management could effectively promote grassland production, conserve plant variety, and regenerate degraded grassland, which will counteract the desertification process in northwest Tajikistan mountain meadows.

Effect of Nutrient Addition on the Productivity and Species Richness of Grassland Along With an Elevational Gradient in Tajikistan.

Grasslands provide key resource for the millions of people who are dependent on livestock in Tajikistan. Productivity and species richness (SR) are important characteristics of grassland ecosystems and are greatly affected by nutrient inputs. The effect that climate change might have on these characteristics remains unclear. Here, an in situ nitrogen (N) and phosphorus (P) fertilization experiment was conducted at four sites along with an elevational gradient (650, 1,100, 1,250, and 2,000 m) in western Tajikistan over 2 years (2018 and 2019) to examine the influences of nutrient availability and climate change on aboveground biomass (AGB) and SR; precipitation and temperature were also considered to analyze the responses. It demonstrated that enrichment with N, P, and their combinations significantly increased AGB along with an elevational gradient (p < 0.05). AGB increased as the concentrations of nutrients added increased. The maximum AGB, which was 2-fold higher compared with control, was observed when 90 kg N ha-1year-1 and 30 kg P ha-1year-1 were added. In addition, nitrogen addition alone stimulated greater AGB than P addition, although no significant difference was observed between these two treatments. Enrichment with N, P, and their combination had no significant effect on SR; however, SR significantly changed at different elevation. Elevation had direct effect on precipitation and temperature, which, in turn, resulted in variation in AGB and SR. Moreover, both nutrient and elevation had significant effect on AGB and SR, but there was no interaction effect of them. AGB and SR interacted with significant negative correlation. In the high-elevation area, plants grew better in the warmer year (2018); this indicates that grasslands in high mountain areas in Tajikistan might have higher productivity as the climate warms, which will positively affect the economic development of the country.

Prognostic Value of a Long Non-coding RNA Signature in Localized Clear Cell Renal Cell Carcinoma.

BACKGROUND: Long non-coding RNAs (lncRNAs) can be used as prognostic biomarkers in many types of cancer. OBJECTIVE: We sought to establish an lncRNA signature to improve postoperative risk stratification for patients with localized clear cell renal cell carcinoma (ccRCC). DESIGN, SETTING, AND PARTICIPANTS: Based on the RNA-seq data of 444 stage I-III ccRCC tumours from The Cancer Genome Atlas project, we built a four-lncRNA-based classifier using the least absolute shrinkage and selection operation (LASSO) Cox regression model in 222 randomly selected samples (training set) and validated the classifier in the remaining 222 samples (internal validation set). We confirmed this classifier in an external validation set of 88 patients with stage I-III ccRCC from a Japan cohort and using quantitative reverse transcription polymerase chain reaction (RT-PCR) in another three independent sets that included 1869 patients from China with stage I-III ccRCC. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Univariable and multivariable Cox regression, Harrell's concordance index (c-index), and time-dependent receiver operating characteristic curves were used to evaluate the association of the classifier with overall survival, disease-specific survival, and disease-free survival. RESULTS AND LIMITATIONS: Using the LASSO Cox regression model, we built a classifier named RCClnc4 based on four lncRNAs: ENSG00000255774, ENSG00000248323, ENSG00000260911, and ENSG00000231666. In the RNA-seq and RT-PCR data sets, the RCClnc4 signature significantly stratified patients into high-risk versus low-risk groups in terms of clinical outcome across and within subpopulations and remained as an independent prognostic factor in multivariate analyses (hazard ratio range, 1.34 [95% confidence interval {CI}: 1.03-1.75; p=0.028] to 1.89 [95% CI, 1.55-2.31; p<0.001]) after adjusting for clinical and pathologic factors. The RCClnc4 signature achieved a higher accuracy (mean c-index, 0.72) than clinical staging systems such as TNM (mean c-index, 0.62) and the stage, size, grade, and necrosis (SSIGN) score (mean c-index, 0.64), currently reported prognostic signatures and biomarkers for the estimation of survival. When integrated with clinical characteristics, the composite clinical and lncRNA signature showed improved prognostic accuracy in all data sets (TNM + RCClnc4 mean c-index, 0.75; SSIGN + RCClnc4 score mean c-index, 0.75). The RCClnc4 classifier was able to identify a clinically significant number of both high-risk stage I and low-risk stage II-III patients. CONCLUSIONS: The RCClnc4 classifier is a promising and potential prognostic tool in predicting the survival of patients with stage I-III ccRCC. Combining the lncRNA classifier with clinical and pathological parameters allows for accurate risk assessment in guiding clinical management. PATIENT SUMMARY: The RCClnc4 classifier could facilitate patient management and treatment decisions.

Exosome-Transmitted lncARSR Promotes Sunitinib Resistance in Renal Cancer by Acting as a Competing Endogenous RNA.

Sunitinib resistance is a major challenge for advanced renal cell carcinoma (RCC). Understanding the underlying mechanisms and developing effective strategies against sunitinib resistance are highly desired in the clinic. Here we identified an lncRNA, named lncARSR (lncRNA Activated in RCC with Sunitinib Resistance), which correlated with clinically poor sunitinib response. lncARSR promoted sunitinib resistance via competitively binding miR-34/miR-449 to facilitate AXL and c-MET expression in RCC cells. Furthermore, bioactive lncARSR could be incorporated into exosomes and transmitted to sensitive cells, thus disseminating sunitinib resistance. Treatment of sunitinib-resistant RCC with locked nucleic acids targeting lncARSR or an AXL/c-MET inhibitor restored sunitinib response. Therefore, lncARSR may serve as a predictor and a potential therapeutic target for sunitinib resistance.

[A research overview of methanogens].

Methane is the second most important greenhouse gas in the atmosphere with a concentration (rate by volume) of 1.7 x 10(-6). Approximately 75% of methane in atmosphere comes from the activity of methanogens in the worldwide. The methanogens are anaerobic archaebacteria, according to 16S rRNA and other biochemical taxonomy. The methanogens can use compounds such as acetic acid, hydrogen and CO2 athylamine as substrates for methane production. The biochemical metabolisms of methanogens are greatly affected by natural environment where they live in. This paper will present a general situation of methanogens in term of history, morphology, taxonomy, metabolisms and ecology.