Xylooligosaccharides Enhance Lettuce Root Morphogenesis and Growth Dynamics.

Enhancing root development is pivotal for boosting crop yield and augmenting stress resilience. In this study, we explored the regulatory effects of xylooligosaccharides (XOSs) on lettuce root growth, comparing their impact with that of indole-3-butyric acid potassium salt (IBAP). Treatment with XOS led to a substantial increase in root dry weight (30.77%), total root length (29.40%), volume (21.58%), and surface area (25.44%) compared to the water-treated control. These enhancements were on par with those induced by IBAP. Comprehensive phytohormone profiling disclosed marked increases in indole-3-acetic acid (IAA), zeatin riboside (ZR), methyl jasmonate (JA-ME), and brassinosteroids (BRs) following XOS application. Through RNA sequencing, we identified 3807 differentially expressed genes (DEGs) in the roots of XOS-treated plants, which were significantly enriched in pathways associated with manganese ion homeostasis, microtubule motor activity, and carbohydrate metabolism. Intriguingly, approximately 62.7% of the DEGs responsive to XOS also responded to IBAP, underscoring common regulatory mechanisms. However, XOS uniquely influenced genes related to cutin, suberine, and wax biosynthesis, as well as plant hormone signal transduction, hinting at novel mechanisms of stress tolerance. Prominent up-regulation of genes encoding beta-glucosidase and beta-fructofuranosidase highlights enhanced carbohydrate metabolism as a key driver of XOS-induced root enhancement. Collectively, these results position XOS as a promising, sustainable option for agricultural biostimulation.

A microencapsulation approach to design microbial seed coatings to boost wheat seed germination and seedling growth under salt stress.

Introduction: Salt stress in seed germination and early seedling growth is the greatest cause of crop loss in saline-alkali soils. Microbial seed coating is an effective way to promote plant growth and salt resistance, but these coatings suffer from poor seed adhesion and low survival rates under typical storage conditions. Methods: In this study, the marine bacterium Pontibacter actiniarum DSM 19842 from kelp was isolated and microencapsulated with calcium alginate using the emulsion and internal gelation method. Results: Compared to unencapsulated seeds, the spherical microcapsules demonstrated a bacterial encapsulation rate of 65.4% and survival rate increased by 22.4% at 25°C for 60 days. Under salt stress conditions, the seed germination percentage of microcapsule-embedded bacteria (M-Embed) was 90%, which was significantly increased by 17% compared to the germination percentage (73%) of no coating treatment (CK). Root growth was also significantly increased by coating with M-Embed. Chlorophyll, peroxidase, superoxide dismutase, catalase, proline, hydrogen peroxide and malondialdehyde levels indicated that the M-Embed had the best positive effects under salt stress conditions. Discussion: Therefore, embedding microorganisms in suitable capsule materials provides effective protection for the survival of the microorganism and this seed coating can alleviate salt stress in wheat. This process will benefit the development of sustainable agriculture in coastal regions with saline soils.

Cell type identification from single-cell transcriptomes in melanoma.

BACKGROUND: Single-cell sequencing approaches allow gene expression to be measured at the single-cell level, providing opportunities and challenges to study the aetiology of complex diseases, including cancer. METHODS: Based on single-cell gene and lncRNA expression levels, we proposed a computational framework for cell type identification that fully considers cell dropout characteristics. First, we defined the dropout features of the cells and identified the dropout clusters. Second, we constructed a differential co-expression network and identified differential modules. Finally, we identified cell types based on the differential modules. RESULTS: The method was applied to single-cell melanoma data, and eight cell types were identified. Enrichment analysis of the candidate cell marker genes for the two key cell types showed that both key cell types were closely related to the physiological activities of the major histocompatibility complex (MHC); one key cell type was associated with mitosis-related activities, and the other with pathways related to ten diseases. CONCLUSIONS: Through identification and analysis of key melanoma-related cell types, we explored the molecular mechanism of melanoma, providing insight into melanoma research. Moreover, the candidate cell markers for the two key cell types are potential therapeutic targets for melanoma.

The exploration of disease-specific gene regulatory networks in esophageal carcinoma and stomach adenocarcinoma.

BACKGROUND: Feed-forward loops (FFLs), consisting of miRNAs, transcription factors (TFs) and their common target genes, have been validated to be important for the initialization and development of complex diseases, including cancer. Esophageal Carcinoma (ESCA) and Stomach Adenocarcinoma (STAD) are two types of malignant tumors in the digestive tract. Understanding common and distinct molecular mechanisms of ESCA and STAD is extremely crucial. RESULTS: In this paper, we presented a computational framework to explore common and distinct FFLs, and molecular biomarkers for ESCA and STAD. We identified FFLs by combining regulation pairs and RNA-seq data. Then we constructed disease-specific co-expression networks based on the FFLs identified. We also used random walk with restart (RWR) on disease-specific co-expression networks to prioritize candidate molecules. We identified 148 and 242 FFLs for these two types of cancer, respectively. And we found that one TF, E2F3 was related to ESCA, two genes, DTNA and KCNMA1 were related to STAD, while one TF ESR1 and one gene KIT were associated with both of the two types of cancer. CONCLUSIONS: This proposed computational framework predicted disease-related biomolecules effectively and discovered the correlation between two types of cancers, which helped develop the diagnostic and therapeutic strategies of Esophageal Carcinoma and Stomach Adenocarcinoma.