Subtype-WGME enables whole-genome-wide multi-omics cancer subtyping.

We present an innovative strategy for integrating whole-genome-wide multi-omics data, which facilitates adaptive amalgamation by leveraging hidden layer features derived from high-dimensional omics data through a multi-task encoder. Empirical evaluations on eight benchmark cancer datasets substantiated that our proposed framework outstripped the comparative algorithms in cancer subtyping, delivering superior subtyping outcomes. Building upon these subtyping results, we establish a robust pipeline for identifying whole-genome-wide biomarkers, unearthing 195 significant biomarkers. Furthermore, we conduct an exhaustive analysis to assess the importance of each omic and non-coding region features at the whole-genome-wide level during cancer subtyping. Our investigation shows that both omics and non-coding region features substantially impact cancer development and survival prognosis. This study emphasizes the potential and practical implications of integrating genome-wide data in cancer research, demonstrating the potency of comprehensive genomic characterization. Additionally, our findings offer insightful perspectives for multi-omics analysis employing deep learning methodologies.

A colorimetric and fluorescent probe of lignocellulose nanofiber composite modified with Rhodamine 6G derivative for reversible, selective and sensitive detection of metal ions in wastewater.

Heavy metal ions have extremely high toxicity. As the top of food chain, human beings certainly will accumulate them by ingesting food and participating other activities, which eventually result in the damage to our health. Therefore, it is very meaningful and necessary to design a simple, portable, stable and efficient material for heavy metal ions detection. Based on the spirolactam Rhodamine 6G (SRh6G) fluorescent probe, we prepared two types of nanocomposite materials (membrane and aerogel) by vacuum filtration and freeze-drying methods with lignocellulose nanofiber (CNF) as a carrier, polyvinyl alcohol (PVA) and glutaraldehyde (GA) as the cross-linkers. Then the microstructure, chemical composition, wetting property, fluorescence intensity and selectivity of as-prepared SRh6G/PVA/CNF would be characterized and analyzed. Results showed that SRh6G/PVA/CNF nanocomposites would turn red in color under strong acidic environment and produced orange fluorescence under ultraviolet light. Besides, they were also to detect Al3+, Cu2+, Hg2+, Fe3+ and Ag+ through color and fluorescence variations. We had further tested its sensitivity, selectivity, adsorption, fluorescence limits of detection (LOD) to Fe3+ and Cu2+. The test towards real water samples (hospital wastewater, Songhua River and tap water) proved that SRh6G/PVA/CNF nanocomposites could detect the polluted water with low concentrations of Fe3+ and Cu2+. In addition, SRh6G/PVA/CNF nanocomposites have excellent mechanical property, repeatability, superhydrophilicity and underwater superoleophobicity, which may offer a theoretical reference for the assembly strategy and detection application of cellulose-based fluorescent probe.

Fabrication of carbon dots-embedded luminescent transparent wood with ultraviolet blocking and thermal insulating capacities towards smart window application.

To expand functions of transparent wood (TW) including fluorescence, ultraviolet blocking, heat preservation and insulation, we adopted carbon quantum dots (CQDs) to prepare luminescent transparent wood. CQDs with yellow/red fluorescence (YCD/RCD) were prepared by chitosan and o-phenylenediamine. Afterwards, Balsa woods were pretreated to obtain wood frameworks (DW/LW), which were further combined with epoxy resin for achieving transparent woods (DW-TW/LW-TW). Results showed LW retained more lignin, the LW-TW blocked more ultraviolet light, displaying the better visible transmission and mechanical strength than DW-TW. After adding YCD and RCD to LW-TW, the yellow and red fluorescence transparent woods with outstanding mechanical and ultraviolet blocking properties were prepared, especially the red fluorescence transparent wood (RTW). Specifically, the tensile strength and elongation at break of RTW reached up to 19.39 MPa and 5.35 %, respectively. Moreover, RTW could block 78.8 % of UV-B light and 78 % of UV-A light, respectively. Besides, RTW possessed excellent visible transmission (70.3 %) and UV blocking (88.87 %). Significantly, both RTW and YTW displayed outstanding water repellency, excellent durability, good thermal stability and insulation. Predictably, luminescent transparent woods certainly will enhance the adaptability of wood, and broaden its applications in green decoration, lighting setup, sensor and other fields.

Physiological and protein profiling analysis provides insight into the underlying molecular mechanism of potato tuber development regulated by jasmonic acid in vitro.

BACKGROUND: Jasmonates (JAs) are one of important phytohormones regulating potato tuber development. It is a complex process and the underlying molecular mechanism regulating tuber development by JAs is still limited. This study attempted to illuminate it through the potential proteomic dynamics information about tuber development in vitro regulated by exogenous JA. RESULTS: A combined analysis of physiological and iTRAQ (isobaric tags for relative and absolute quantification)-based proteomic approach was performed in tuber development in vitro under exogenous JA treatments (0, 0.5, 5 and 50 µΜ). Physiological results indicated that low JA concentration (especially 5 µM) promoted tuber development, whereas higher JA concentration (50 µM) showed inhibition effect. A total of 257 differentially expressed proteins (DEPs) were identified by iTRAQ, which provided a comprehensive overview on the functional protein profile changes of tuber development regulated by JA. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that low JA concentration (especially 5 µM) exhibited the promotion effects on tuber development in various cellular processes. Some cell wall polysaccharide synthesis and cytoskeleton formation-related proteins were up-regulated by JA to promote tuber cell expansion. Some primary carbon metabolism-related enzymes were up-regulated by JA to provide sufficient metabolism intermediates and energy for tuber development. And, a large number of protein biosynthesis, degradation and assembly-related were up-regulated by JA to promote tuber protein biosynthesis and maintain strict protein quality control during tuber development. CONCLUSIONS: This study is the first to integrate physiological and proteomic data to provide useful information about the JA-signaling response mechanism of potato tuber development in vitro. The results revealed that the levels of a number of proteins involved in various cellular processes were regulated by JA during tuber development. The proposed hypothetical model would explain the interaction of these DEPs that associated with tuber development in vitro regulated by JA.