NRTPredictor: identifying rice root cell state in single-cell RNA-seq via ensemble learning.

BACKGROUND: Single-cell RNA sequencing (scRNA-seq) measurements of gene expression show great promise for studying the cellular heterogeneity of rice roots. How precisely annotating cell identity is a major unresolved problem in plant scRNA-seq analysis due to the inherent high dimensionality and sparsity. RESULTS: To address this challenge, we present NRTPredictor, an ensemble-learning system, to predict rice root cell stage and mine biomarkers through complete model interpretability. The performance of NRTPredictor was evaluated using a test dataset, with 98.01% accuracy and 95.45% recall. With the power of interpretability provided by NRTPredictor, our model recognizes 110 marker genes partially involved in phenylpropanoid biosynthesis. Expression patterns of rice root could be mapped by the above-mentioned candidate genes, showing the superiority of NRTPredictor. Integrated analysis of scRNA and bulk RNA-seq data revealed aberrant expression of Epidermis cell subpopulations in flooding, Pi, and salt stresses. CONCLUSION: Taken together, our results demonstrate that NRTPredictor is a useful tool for automated prediction of rice root cell stage and provides a valuable resource for deciphering the rice root cellular heterogeneity and the molecular mechanisms of flooding, Pi, and salt stresses. Based on the proposed model, a free webserver has been established, which is available at https://www.cgris.net/nrtp .

Content Determination of Geniposide in Biyuanshu Oral Liquid by Micellar Electrokinetic Capillary Chromatography / 中国中医药信息杂志

Objective To establish a micellar electrokinetic capillary chromatography method for content determination of geniposide in Biyuanshu Oral Liquid. Methods Acetaminophen was used as an internal standard, and the separation was performed on an uncoated fused silica capillary of 52 cm × 50 μm ID (42 cm effective length) with the separation voltage of 25.0 kV. The running buffer contained 50 mmol/L borax, 100 mmol/L sodium dodecyl sulfate and 15％ acetonitrile (pH=10). The sample was injected by pressure (10 s, 0.5 psi) and detected at 238 nm. Results Geniposide was in good linearity range of 15.02–320.48 μg/mL (r=0.9995). The repeatability (low, medium and high concentration of samples) and intermediate precision assays gave satisfactory RSD values of less than 1.77％and 2.01％, respectively. The average recovery of geniposide in Biyuanshu Oral Liquid was 97.50％ and the RSD was 4.43％. The contents of geniposide determined by micellar electrokinetic capillary chromatography were in accordance with the results of HPLC analysis. Conclusion The method is simple, fast, accurate and precise, which can be used for the content determination of geniposide in Biyuanshu Oral Liquid.