Independent component analysis based gene co-expression network inference (ICAnet) to decipher functional modules for better single-cell clustering and batch integration

With the tremendous increase of publicly available single-cell RNA-sequencing (scRNA-seq) datasets, bioinformatics methods based on gene co-expression network are becoming efficient tools for analyzing scRNA-seq data, improving cell type prediction accuracy and in turn facilitating biological discovery. However, the current methods are mainly based on overall co-expression correlation and overlook co-expression that exists in only a subset of cells, thus fail to discover certain rare cell types and sensitive to batch effect. Here, we developed independent component analysis-based gene co-expression network inference (ICAnet) that decomposed scRNA-seq data into a series of independent gene expression components and inferred co-expression modules, which improved cell clustering and rare cell-type discovery. ICAnet showed efficient performance for cell clustering and batch integration using scRNA-seq datasets spanning multiple cells/tissues/donors/library types. It works stably on datasets produced by different library construction strategies and with different sequencing depths and cell numbers. We demonstrated the capability of ICAnet to discover rare cell types in multiple independent scRNA-seq datasets from different sources. Importantly, the identified modules activated in acute myeloid leukemia scRNA-seq datasets have the potential to serve as new diagnostic markers. Thus, ICAnet is a competitive tool for cell clustering and biological interpretations of single-cell RNA-seq data analysis.     

Salidroside Inhibits Reactive Astrogliosis and Glial Scar Formation in Late Cerebral Ischemia via the Akt/GSK-3β Pathway

Neurochemical Research - Cerebral ischemia leads to reactive astrogliosis and glial scar formation. Glial scarring can impede functional restoration during the recovery phase of stroke. Salidroside...     

DNMT3b SUMOylation Mediated MMP-2 Upregulation Contribute to Paclitaxel Induced Neuropathic Pain

Neurochemical Research - Paclitaxel is a common chemotherapeutic agent in cancer treatment, while it often causes chemotherapy-induced peripheral neuropathy (CIPN), which...     

Gibberellin-Induced Alterations to the Expression of Cell Wall-Related Genes in the Xylem of Carrot Root

Journal of Plant Growth Regulation - Gibberellins (GAs) are a group of plant hormones that play important roles in various processes. Previous studies demonstrated that GA can increase the...     

Plant Growth-Promoting Effect of the Chitosanolytic Phosphate-Solubilizing Bacterium Burkholderia gladioli MEL01 After Fermentation with Chitosan and Fertilization with Rock Phosphate

Phosphate-solubilizing bacteria (PSB) are important plant growth-promoting rhizobacteria that can increase soil fertility through the solubilization of insoluble inorganic phosphate and organophosphorus. In this study, a PSB, Burkholderia gladioli MEL01, was isolated and identified from rice–wheat rotation rhizosphere soil. MEL01 had an excellent phosphate-solubilizing capacity (reaching 107.69 mg/L) toward insoluble inorganic phosphate rock phosphate. HPLC analysis revealed that the mechanism of phosphate solubilization of MEL01 was probably due to secreted oxalic acid and gluconic acid transformation of phosphate from insoluble to soluble. MEL01 also exhibited 4030 U/L specific chitosanase activity when cultured with chitosan fermentation medium. Interestingly, the chitosan hydrolysis product chitooligosaccharide could significantly enhance the MEL01 phosphate-solubilizing capacity. Pot experiments showed that MEL01 chitosan medium fermentation liquor (MCMFL) could promote improvement of soil available phosphorus and pakchoi growth when supplemented with phosphate rock phosphate as the phosphate fertilizer. In addition, pot experiments demonstrated that MCMFL could also promote the growth of wheat, which could decrease the amount of compound fertilizer used. Microbial diversity analysis showed that the genera Pseudomonas, Burkholderia, Mycoplana, and Cellvibrio were enriched, which might participate in synergetic phosphate solubilization. Therefore, after fermentation with chitosan and fertilization with rock phosphates, MEL01 has potential as a phosphate biofertilizer in ecological agricultural production.

     

The role of corals on the abundance of a fish ectoparasite in the Great Barrier Reef

Coral Reefs - Gnathiid isopods, common fish ectoparasites, can affect fish physiology, behaviour and survival. Gnathiid juveniles emerge from the benthos to feed on fish blood. In the Caribbean,...     

The Water-Soluble Pool in Biochar Dominates Maize Plant Growth Promotion Under Biochar Amendment

Although amending biochar into agricultural soils has been regarded as an effective measure to improve crop productivity, it remains unclear why biochar increases crop yield. The objective of this study was to compare the relative contribution of different biochar components in crop growth promotion. Three biochar components were separated: (i) water-soluble biochar extract (BE), (ii) mineral nutrients from biochar ash (BA), and (iii) washed biochar residue (WB). Two soils (Anthrosol and Primosol) with distinctly different organic carbon content, soil texture and land use were amended with the three biochar components and their effects on maize (Zea mays L.) growth were tested in a pot experiment. We hypothesized that (1) plant grown in the Anthrosol benefitted more from the water-soluble compounds of biochar than from its mineral nutrients or washed residue, since the soil is already fertile and has a good structure; (2) plant grown in the Primosol benefitted more from the mineral nutrients of biochar and its washed residual, since the soil is nutrient-poor and has a poor structure. The addition of biochar and its three components increased maize aboveground biomass for both soils. In the Anthrosol, BE, BA, and WB increased the aboveground biomass by 41.6%, 32.7%, and 27.1%; in the Primosol, they increased the aboveground biomass by 41.3%, 24.4%, and 18.2%, respectively. BE had the highest plant growth-promoting effect compared to the other two biochar components, which was regardless of soil condition. In addition, the biomass, total volume, surface area, and number of maize root tips under BE amendment were significantly enhanced, particularly the fine roots (< 0.2 mm in diameter). And a strong positive correlation was observed between maize aboveground biomass and the total length of the fine roots. The results demonstrated that the water-soluble compounds present in biochar, in addition to the mineral nutrients and the washed biochar residue, dominate the plant growth promotion under both soil conditions.

     

Inhibition of ER stress attenuates kidney injury and apoptosis induced by 3-MCPD via regulating mitochondrial fission/fusion and Ca2+ homeostasis

Cell Biology and Toxicology - 3-Chloro-1, 2-propanediol (3-MCPD) is a food-borne toxic substance well-known for more than 40 years that is mainly associated with nephrotoxicity. A better...