Combined Analysis of Untargeted Metabolomics and Transcriptomics Revealed Seed Germination and Seedling Establishment in Zelkova schneideriana.

Zelkova schneideriana Hand.-Mazz is a valuable ornamental tree and timber source, whose seedling breeding and large-scale cultivation are restricted by low seed germination and seedling rates. The regulatory mechanisms underlying seed germination and seedling establishment in Z. schneideriana remain unknown. This study conducted metabolomic and transcriptomic analyses of seed germination and seedling establishment in Z. schneideriana. Regular expression of genes and metabolite levels has been observed in plant hormone signal transduction, starch and sucrose metabolism, linoleic acid metabolism, and phenylpropanoid biosynthesis. The reduction in abscisic acid during seed germination may lead to seed release from dormancy. After the seed is released from dormancy, the metabolic levels of auxin, cytokinins, brassinolide, and various sugars are elevated, and they are consumed in large quantities during the seedling establishment stage. Linoleic acid metabolism is gradually activated during seedling establishment. Transcriptome analysis showed that a large number of genes in different metabolic pathways are upregulated during plant establishment, and material metabolism may be accelerated during seedling establishment. Genes regulating carbohydrate metabolism are altered during seed germination and seedling establishment, which may have altered the efficiency of carbohydrate utilization. In addition, the syntheses of lignin monomers and cellulose have different characteristics at different stages. These results provide new insights into the complex mechanisms underlying seed germination and seedling establishment in Z. schneideriana and other woody plants.

An ultrasensitive and multiplexed miRNA one-step real time RT-qPCR detection system and its application in esophageal cancer serum.

MicroRNAs (miRNAs) are increasingly recognized as promising biomarkers for early disease diagnosis and prognosis. Therefore, the need for rapid, robust methods for multiplex miRNA detection in biological research and clinical diagnosis is crucial. This study introduces a novel multiplex miRNA detection method, SMOS-qPCR (Sensitive and Multiplexed One-Step RT-qPCR). The method integrates multiplexed reverse transcription and TaqMan-based qPCR into a single tube, employing a one-step operation on a real-time PCR system. We investigated the effect of 3' end phosphorylation of the Linker, Linker concentration and probe concentration on the SMOS-qPCR, resulted in a wide linear range from 1 fM to 0.1 zM (R2 ≥ 0.99 for each miRNA), surpassing the capabilities of stem-loop RT-qPCR and SYBR Green One-step RT-qPCR. The method showed excellent performance in distinguishing mature miRNA from miRNA precursor, and successfully detected four miRNAs in a single tube without cross-interference. Its high specificity enables precise differentiation of less than 1% nonspecific signal. Finally, we demonstrated the effectiveness of the SMOS-qPCR system in detecting circulating miRNAs in serum samples, distinguishing between esophageal cancers and health individuals with high AUC values (>0.940). In conclusion, the proposed SMOS-qPCR system offers a straightforward and promising approach for miRNA profiling in future clinical applications.

Responses of aquatic vegetables to biochar amended soil and water environments: a critical review.

Aquatic vegetables, including lotus root, water spinach, cress, watercress and so on, have been cultivated as commercial crops for a long time. Though aquatic vegetables have great edible and medicinal values, the increasing demands for aquatic vegetables with high quality have led to higher requirements of their soil and water environments. Unfortunately, the soil and water environment often face many problems such as nutrient imbalance, excessive fertilization, and pollution. Therefore, a new cost-effective and eco-friendly solution for addressing the above issues is urgently required. Biochars, one type of pyrolysis product obtained from agricultural and forestry waste, show great potential in reducing fertilizer application, upgrading soil quality and remediating pollution. Application of biochars in aquatic vegetable cultivation would not only improve the yield and quality, but also reduce its edible risk. Biochars can improve the soil micro-environment, soil microorganism and soil enzyme activities. Furthermore, biochars can remediate the heavy metal pollution, organic pollution and nitrogen and phosphorus non-point source pollution in the water and soil environments of aquatic vegetables, which promotes the state of cultivation conditions and thereby improves the yield and quality of aquatic vegetables. However, the harmful substances such as heavy metals, PAHs, etc. derived from biochars can cause environmental risks, which should be seriously considered. In this review, the application of biochars in aquatic vegetable cultivation is briefly summarized. The changes of soil physicochemical and biological properties, the effects of biochars in remediating water and soil environmental pollution and the impacts of biochars on the yield and quality of aquatic vegetables are also discussed. This review will provide a comprehensive overview of the research progress on the effects of biochars on soil and water environments for aquatic vegetable cultivation.

Transcriptomic and proteomic analyses uncover the drought adaption landscape of Phoebe zhennan.

BACKGROUND: Phoebe zhennan S.Lee (nanmu) is listed as a threatened tree species in China, whose growth and development, especially during the seedling stage, can be severely limited by drought. Previous studies on nanmu responses to drought stress involved physiological and biochemical analyses, while the molecular mechanisms remained unclear. Therefore, it is of great significance to carry out molecular biology research on the drought resistance of nanmu and reveal the genetic background and molecular regulation mechanism of nanmu drought resistance. RESULTS: Drought stress enhanced the soluble sugar (SS), free proline(PRO), superoxide anion (O2·-), and hydrogen peroxide (H2O2) contents as well as the peroxidase (POD) and monodehydroascorbate reductase (MDHAR) activities of nanmu. However, glutathione S-transferase (GST) activity was sensitive to drought stress. Further transcriptomic and proteomic analyses revealed the abundant members of the differentially expressed genes(DEGs) and differentially expressed proteins(DEPs) that were related to phenylpropanoid and flavonoid biosynthesis, hormone biosynthesis and signal transduction, chlorophyll metabolism, photosynthesis, and oxidation-reduction reaction, which suggested their involvement in the drought response of nanmu. These enhanced the osmotic regulation, detoxification, and enzyme-induced and non-enzyme-induced antioxidant ability of nanmu. Moreover, 52% (447/867) of proteins that were up-regulated and 34% (307/892) down-regulated ones were attributed to the increase and decrease of transcription abundance. Transcript up (TU) and protein up (PU) groups had 447 overlaps, while transcript down (TD) and protein down (PD) groups had 307 overlaps, accounting for 54% of up and 35% of down-regulated proteins. The lack of overlap between DEGs and DEPs also suggested that post-transcriptional regulation has a critical role in nanmu response to drought. CONCLUSIONS: Our research results provide significant insights into the regulatory mechanisms of drought stress in nanmu.

Effects of Biochar Application on Enzyme Activities in Tea Garden Soil.

Animal-manure biochar used as a sustainable amendment to garden soil has been widely applied, and the animal-manure pyrolysis temperatures would also have a regulatory effect on soil functions because of their affections on biochar physio-chemical properties. Here we studied the effects of different dosages of swine-manure biochar on tea garden soil functions, with the swine-manure pyrolysis temperature differed at 350 and 500°C. The results showed that the improvement of soil microbial biomass carbon and nitrogen and enzyme activities was closely related to the addition of 0.5-2% (biochar wt/soil wt) swine-manure biochar. Under different conditions of different carbon application rates and carbon type, the addition of 2% swine-manure biochar pyrolyzed at 350°C showed the best effects on soil enzyme activities and microbial biomass carbon and nitrogen contents. Compared to the control, after the addition of 2% swine-manure biochar, sucrase, phosphatase, catalase, and urease activities increased by 63.3, 23.2, 50.3, and 27.9%, respectively. Microbial biomass carbon and nitrogen contents also increased by 36.4 and 34.3%, respectively. Our study indicated that the effectiveness of using animal-manure swine-manure biochar as a sustainable amendment to soil would provide evidence of tea garden soil improvement and the environmental response to the usage of biochars.

[Value of airway pH monitoring in determining the association between chronic cough and laryngopharyngeal reflux in children].

OBJECTIVE: To study the value of airway pH monitoring in determining the association between chronic cough and laryngopharyngeal reflux (LPR) in children. METHODS: A total of 274 children with chronic cough who were treated from January 2016 to December 2019 were enrolled. The DX-pH detection system was used to conduct 24-hour airway pH monitoring. The association between chronic cough and LPR was analyzed. RESULTS: Among the 274 children, there were 168 boys and 106 girls, with a median age of 62.8 months and a median airway pH value of 7.3. Of all the 274 children, 99 (36.1%) had LPR, and the incidence rate of LPR was 36.9% (62/168) in boys and 34.9% (37/106) in girls (P=0.737). The comparison of the incidence rate of LPR among children aged < 1 year, 1-6 years, and > 6 years showed that the younger children had a significantly higher incidence rate of LPR than the older ones (P=0.003). There was no significant difference in the incidence of LPR between the two groups with chronic cough of unknown etiology and definite etiology. The incidence of chronic cough was positively correlated with that of LPR (rs=0.861, P < 0.01). Among the 99 children with positive RYAN index, 65 (66%) suffered from simple LPR. CONCLUSIONS: LPR is highly associated with the development of chronic cough, and airway pH monitoring may be a safe and effective method for the diagnosis of LPR.