Plantorganelle Hunter is an effective deep-learning-based method for plant organelle phenotyping in electron microscopy.

Accurate delineation of plant cell organelles from electron microscope images is essential for understanding subcellular behaviour and function. Here we develop a deep-learning pipeline, called the organelle segmentation network (OrgSegNet), for pixel-wise segmentation to identify chloroplasts, mitochondria, nuclei and vacuoles. OrgSegNet was evaluated on a large manually annotated dataset collected from 19 plant species and achieved state-of-the-art segmentation performance. We defined three digital traits (shape complexity, electron density and cross-sectional area) to track the quantitative features of individual organelles in 2D images and released an open-source web tool called Plantorganelle Hunter for quantitatively profiling subcellular morphology. In addition, the automatic segmentation method was successfully applied to a serial-sectioning scanning microscope technique to create a 3D cell model that offers unique views of the morphology and distribution of these organelles. The functionalities of Plantorganelle Hunter can be easily operated, which will increase efficiency and productivity for the plant science community, and enhance understanding of subcellular biology.

Calcium Positively Mediates Blue Light-Induced Anthocyanin Accumulation in Hypocotyl of Soybean Sprouts.

Soybean sprouts are a flavorful microgreen that can be eaten all year round and are widely favored in Southeast Asia. In this study, the regulatory mechanism of calcium on anthocyanin biosynthesis in soybean sprouts under blue light was investigated. The results showed that blue light, with a short wavelength, effectively induced anthocyanin accumulation in the hypocotyl of soybean sprout cultivar "Dongnong 690." Calcium supplementation further enhanced anthocyanin content, which was obviously inhibited by LaCl3 and neomycin treatment. Moreover, exogenous calcium changed the metabolism of anthocyanins, and seven anthocyanin compounds were detected. The trend of calcium fluorescence intensity in hypocotyl cells, as well as that of the inositol 1,4,5-trisphosphate and calmodulin content, was consistent with that of anthocyanins content. Specific spatial distribution patterns of calcium antimonate precipitation were observed in the ultrastructure of hypocotyl cells under different conditions. Furthermore, calcium application upregulated the expression of genes related to anthocyanin biosynthesis, and calcium inhibitors suppressed these genes. Finally, transcriptomics was performed to gain global insights into the molecular regulation mechanism of calcium-associated anthocyanin production. Genes from the flavonoid biosynthesis pathway were distinctly enriched among the differentially expressed genes, and weighted gene co-expression network analysis showed that two MYBs were related to the accumulation of anthocyanins. These results indicated that calcium released from apoplast and intracellular stores in specific spatial-temporal features promote blue light-induced anthocyanin accumulation by upregulation of the expression of genes related to anthocyanin synthesis of "Dongnong 690" hypocotyl. The findings deepen the understanding of the calcium regulation mechanism of blue light-induced anthocyanin accumulation in soybean sprouts, which will help growers produce high-quality foods beneficial for human health.

Cellular Evidence of Exosomes in the Reproductive Tract of Chinese Soft-Shelled Turtle Pelodiscus sinensis.

The oviduct is a location of egg production, fertilization, and sperm storage. While its secretions have broadly attributes toward different physiological functions. We examined the ultrastructure of oviduct epithelium and glands in relation to the secretions, particularly with exosomes origin in Chinese soft-shelled turtle Pelodiscus sinensis using immunohistochemistry and transmission electron microscopy. The ciliated epithelial and gland cells were involved in the release of exosomes and secretions into lumen throughout the year. The exosomes were either released directly from epithelium or in relation with multivesicular body (MVB). The average size of the particles varies between 50 and 130 nm. These exosomes were also widely distributed in the epithelial ciliated cells and pericytoplasm of glands lumen. Intracellular MVB was characterized by membrane-bounded exosomes of different sizes. Exosomes were also found in close contact with the cilia and sperm membrane in the lumen, which is suggestive of their fusogenic properties. Immunohistochemistry results showed strong to moderate positive expression of exosomes, in ciliated and gland cells, during January, September, and December, as it is the time of sperm storage in this turtle, whereas they showed moderate to weak level of expression during breeding season (May). This is first study about identification of the exosomes in female turtles. Epithelial and glandular exosomes, intracellular MVB, secretions, and secretory vesicles give this turtle specie a unique secretory morphology and a potential model for investigating the secretory nature of the oviduct.