Project description:We conducted a culture experiment by deeply submerging plants in swine wastewater in culturing Iris tectorum and co-culturing Iris tectorum and Dictyosphaerium sp., and found that the plants grew sub-normal in the plant-microalgae co-culture while the plants were dead after 21 days in the plant culture. We generated a comprehensive RNA-seq dataset from the submerged Iris tectorum leaves in both the plant culture and the plant-microalgae co-culture, aiming at providing information on the response mechanisms of the plants to waterlogging stress. Besides raw reads of the RNA-seq dataset, we used DEseq2 algorithms to detect the differently expressed genes in the plants between the different cultures. Additionally, we performed the plant disease resistance gene analysis for all the differentially expressed genes.
Project description:To investigate the mechanism by which the microalgae-yeast co-culture system promotes wastewater denitrification. We concluded that microalgae and yeast exhibit a mutually beneficial relationship in the co-culture system. Microalgae nitrogen metabolism can be influenced by both miRNA and mRNA, and the presence of yeast stimulates gene expression in microalgae.
Project description:A three-dimensional culture system of keratinocytes is able to mimic the formation of stratified epidermis. Air-exposure treatment is essential to promote keratinocyte differentiation. During the culture, we compared the transcripts in the cells with (Air) and without (Liq; submerged) air-exposure. Then, since rocking (shaking) the culture dish enabled to recover the keratinocyte differentiation despite the submerged culture (Liq), a comparative study between with and without rocking was also carried out to investigate the characteristics of the restored differentiation by RNA-seq. Transcriptome analyses revealed the expected similar pattern of the transcripts between air-exposure and rocking culture, which differed from those in Liq culture.
Project description:Global climate changes cause severe floods that hinder plant development and breeding. The phenomenon in which a single plant can significantly alter its leaf shape structure and physiology based on surrounding environments is known as heterophylly, a trait commonly observed in amphibious plants. Heterophylly is a special survival strategy that enables adaptation to both submerged and terrestrial conditions, aiding in response to environmental changes. Molecular mechanisms of heterophylly are not well understood due to a lack of models. Hygrophila difformis, also known as Water wisteria, shows typical heterophylly in terrestrial and submerged environments, and is an emerging model plant to explore heterophylly. In this study, we conducted single-cell RNA sequencing (scRNA-seq) analysis of isolated protoplasts from both terrestrial and submerged shoots of H. difformis to obtain data on the gene expression patterns of tissue-specific cells. These scRNA-seq data enabled the identification of gene expression patterns by cell types, providing a foundation to elucidate the molecular mechanisms of heterophylly and plant environmental adaptations at a single-cell level.
Project description:Tuberculosis Immune Reconstitution Inflammatory Syndrome (TB-IRIS) frequently complicates combined anti-retroviral therapy (ART) and anti-tubercular therapy in HIV-1 co-infected tuberculosis (TB) patients. The immunopathological mechanism underlying TB-IRIS is incompletely defined. Differential transcript abundance in PBMC from IRIS and control patients stimulated with heat killed H37Rv was determined by microarray Blood samples were collected during longitudinal observational studies of TB-IRIS patients and controls (both groups HIV-infected patients placed on antiretroviral treatment). PBMC were stimulated with heat killed H37Rv and RNA extracted.
