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:We found that the number of tumor-infiltrating myofibroblasts was positively correlated to tumor acidification status in hepatocellular carcinoma (HCC). Hepatic stellate cells (HSCs), the predominant precursors of liver myofibroblasts, were activated and transdifferentiated into myofibroblasts under acidic culture condition. To identify the molecular phenotype of LX-2 cells in acidic culture conditions, we further conducted a gene expression profile analysis.
Project description:We found that the number of tumor-infiltrating myofibroblasts was positively correlated to tumor acidification status in hepatocellular carcinoma (HCC). Hepatic stellate cells (HSCs), the predominant precursors of liver myofibroblasts, were activated and transdifferentiated into myofibroblasts under acidic culture condition. To identify the molecular phenotype of LX-2 cells in acidic culture conditions, we further conducted a gene expression profile analysis. LX-2 cells cultured in pH 7.2 or pH 6.2 medium separately for six days was used in gene expression microarray analysis.
Project description:Penicillium citrinum X9-4, which was isolated from infected grapes by our laboratory, produced the highest amount of OTA at pH 5 in culture media, and toxin-production was restrained under acidic environment (pH 3). It revealed the possible mechanism of OTA biosynthesis and metabolic regulation in P. citrinum by transcriptomics, and investigated the reason of OTA biosynthesis was restrained in P. citrinum when cultured under acidic environment.
Project description:Denitrification, a crucial biochemical pathway prevalent among haloarchaea in hypersaline ecosystems, has garnered considerable attention in recent years due to its ecological implications. Nevertheless, the underlying molecular mechanisms and genetic regulation governing this respiration/detoxification process in haloarchaea remain largely unexplored. In this study, RNA-sequencing was used to compare the transcriptomes of the haloarchaeon Haloferax mediterranei under oxic and denitrifying conditions, shedding light on the intricate metabolic alterations occurring within the cell such as the accurate control of the metal homeostasis. Furthermore, the investigation identifies several genes encoding transcriptional regulators and potential accessory proteins with putative roles in denitrification. Among these are bacterioopsin transcriptional activators, proteins harbouring a domain of unknown function (DUF2249), and a cyanoglobin. Additionally, the study delves into the genetic regulation of denitrification, finding a regulatory motif within promoter regions that activates numerous denitrification-related genes. This research serves as a starting point for future molecular biology studies in haloarchaea, offering a promising avenue to unravel the intricate mechanisms governing haloarchaeal denitrification, a pathway of paramount ecological importance.
Project description:Acidic activation domains are intrinsically disordered regions of transcription factors that bind coactivators. The intrinsic disorder and low evolutionary conservation of activation domains have made it difficult to identify the sequence features controlling AD activity. To address this problem, we designed thousands of variants in seven acidic activation domains and measured their activities with a new high-throughput assay in human cell culture. We found that strong activation domain activity required a balance between the number of acidic residues and aromatic and leucine residues. These findings motivated a predictor of activation domains that scans the human proteome for clusters of aromatic and leucine residues embedded in regions of high acidity. This predictor identifies known activation domains and accurately predicts new ones. Our results support a flexible model of activation domains in which acidic residues solubilize hydrophobic motifs so that they can interact with coactivators.
Project description:The H2A variant H2AZ is essential for embryonic development and for proper execution of developmental gene expression programs in embryonic stem cells (ESCs). Divergent regions in H2AZ are likely key for its functional specialization, but we know little about how these differences contribute to chromatin regulation. Here, we show that the extended acidic patch, specifically the three divergent residues in the C-terminal docking domain, is necessary for lineage commitment during ESC differentiation and proper execution of gene expression programs during ESC differentiation. Surprisingly, disruption of the acidic patch domain has a distinct consequence on cellular specification compared to H2AZ depletion. This is consistent with differences in gene expression profiles of H2AZ M-bM-^@M-^Sdepleted and acidic patch (AP) mutant ESCs during early lineage commitment. Interestingly, the distinct consequence of AP mutant expression on gene regulation is coincidence with an altered destabilized chromatin state and high chromatin mobility dependent on active transcription. Collectively, our data shows that the divergent residues within the acidic patch domain are key structural determinants of H2AZ function and links chromatin structure and dynamics with gene regulation and cell fate specification. H2AZ extended acidic patch was mutated, or H2AZ was KD in mouse embryonic stem cells and RNA-Seq analysis was performed on the resulting cultures. Characterization of H2AZ-WT and -AP3-mutant binding specificities were performed by ChIP-Seq.
Project description:We report the application of transcriptome sequencing technology in florfenicol interfering with denitrification by Paracoccus denitrificans. More than 30 billion bases of sequences were obtained by sequencing analysis. We found 433 differentially expressed genes, of which 292 genes were down-regulated and 141 genes were up-regulated, respectively. Importantly, most of the denitrification genes were suppressed, which further led to the enrichment of key metabolic pathways. The weakening of protein synthesis was consistent with the bacteriostatic mechanism of florfenicol. In particular, we found 42 putative differentially expressed sRNAs. After homologous alignment, target gene prediction and functional analysis, it was proved that the sRNAs differential expression profile is likely to be a key transcription factor affected by antibiotics in denitrification. This study provides new ideas for further control of environmental antibiotic pollution.