Project description:Analysis of gene expression in SKOv3ip1 cells with and without co-culture of human primary adipocytes. Hypothesis is that adipocyte co-culure changes lipid metabolism pathways in ovarian cancer cells.
Project description:Primary human omental adipocytes were isolated from patients with non-cancer conditions. Subsequently, gene expression profiled in adipocytes and ovarian cancer cell line (SKOV3ip1) alone (control) or under co-culture conditions. Following co-culture cells were separated and total RNA isolated for microarray analysis.
Project description:Gene regulatory interactions that shape developmental processes can often can be inferred from microarray analysis of gene expression, but most computational methods used require extensive datasets that can be difficult to generate. Here, we show that maximumentropy network analysis allows extraction of genetic interactions from limited microarray datasets. Maximum-entropy networks indicated that the inflammatory cytokine TNF-_ plays a pivotal role in Schwann cell–axon interactions, and these data suggested that TNF mediates its effects by orchestrating cytoplasmic movement and axon guidance. In vivo and in vitro experiments confirmed these predictions, showing that Schwann cells in TNF_/_ peripheral sensory bundles fail to envelop axons efficiently, and that recombinant TNF can partially correct these defects. These data demonstrate the power of maximum-entropy network-based methods for analysis of microarray data, and they indicate that TNF-_ plays a direct role in Schwann cell–axon communication.
Project description:Candida spp. are commensal opportunistic fungal pathogens that often colonize and infect mucosal surfaces of the human body. Candida, along with other microbes in the microbiota, generally grow as biofilms in a polymicrobial environment. Due to the nature of cellular growth in a biofilm (such as production of a protective extracellular matrix) and the recalcitrance of biofilms, infections involving biofilms are very difficult to treat with antibiotics and perpetuate the cycle of infection. The two most commonly isolated Candida spp. from Candida infections are Candida albicans and Candida glabrata, and the presence of both of these species results in increased patient inflammation and overall biofilm formation. This work aims to investigate the interspecies interactions between C. albicans (Ca) and C. glabrata (Cg) in co-culture through transcriptome analysis over the course of biofilm growth. We report that during co-culture, lipid biosynthesis and transporter genes were significantly modulated in both Ca and Cg. Differentially expressed genes in Ca during co-culture growth included putative transporter genes (C2_02180W_A and C1_09210C_B; up-regulated), amino acid biosynthesis (ARO7; up-regulated most in Ca:Cg 1:3), and lipid-related genes (LIP3 and IPT1; down-regulated). Differentially expressed genes in Cg in co-culture included putative transmembrane transporters (CAGL0H03399g and CAGL0K04609g; up-regulated), an oxidative stress response gene (CAGL0E04114g; down-regulated most in Ca:Cg 1:3), genes involved in the TCA cycle (LYS12 and CAGL0J06402g; down-regulated), and several genes involved in cell wall/membrane biosynthesis (SEC53, GAS2, VIG9; down-regulated). Additionally, confocal microscopy was utilized for membrane lipid analysis between monoculture and co-culture biofilms. Through filipin-stained lipid analysis, we found that there was a significant increase in cell membrane lipid content in Ca:Cg 1:3 biofilms compared to Ca and Ca:Cg 3:1 biofilms. These results suggest substantial modifications of both cell wall, cell membrane, and transporters in both Ca and Cg during the time course of co-culture growth, which allows for increased biofilm formation and virulence in Candida co-culture biofilms.
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:CO-culture of Microglia and Neurons. The NC/ APOE knocked down/ CD74 knocked down BV2 was stimulated by the ACP cystic fluid for 48 hours.
Project description:Organotypic three dimensional cultures of epithelial cells are grown at the air–liquid interface (ALI) and resemble the in vivo counterparts. Although the complexity of in vivo cellular responses could be better manifested in co-culture models in which additional cell-types such as fibroblasts were incorporated, the presence of another cell-type could mask the response of the other. This study reports the impact of whole combustible cigarette smoke (CS) on organotypic mono- and co-culture models to evaluate the relevancy of organotypic models for toxicological assessment of aerosols. Two organotypic bronchial models were directly exposed to low and high concentrations of CS of the reference research cigarette 3R4F: mono-culture of bronchial epithelial cells without fibroblasts (BR) and co-culture with fibroblasts (BRF) models. Adenylate kinase-based cytotoxicity, cytochrome P450 (CYP) 1A1/1B1 activity, tissue histology, and concentrations of secreted mediators in the basolateral media, as well as transcriptomes were evaluated following the CS exposure. The results demonstrated similar impact of CS on the AK-based cytotoxicity, CYP1A1/1B1 activity, and tissue histology in both models. However, a greater number of secreted mediators were found in the basolateral media of the mono-culture than in the co-culture models. Furthermore, annotation analysis and network-based systems biology analysis of the transcriptomic profiles indicated a more prominent cellular stress and tissue damage following CS in the mono-culture epithelium model without fibroblasts. Finally, our results indicated that the in vivo smoking-induced xenobiotic metabolism response in the bronchial epithelial cells was better reflected on the in vitro co-culture model upon CS exposure.
Project description:Purpose: Determine the function of lncBATE10 in brown and white adipocyte differentiation Methods: primary brown and white apreadipocytes were isolated by cell culture. We infected brown preadipocytes with retroviral shRNA targeting lncBATE10 or with retrovirus overexpressing lncBATE10. Cells were induced to differetinate for 5 days. Total RNA were harvested for RNA-seq Conclusions: Our study shows that lncBATE10 is required for BAT-selective program expression. Overexpression of lncBATE10 is not sufficient to promote BAT marker expression.