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Many physiological retinal processes, such as outer segment disk shedding and visual sensitivity, exhibit a daily rhythm. However, the detailed transcriptome dynamics and related biological processes of the retina are not fully understood. Retinal tissues were collected from C57BL/6J male mice housed in a 12h light/12h dark (LD) cycle for 4 weeks, at Zeitgeber time (ZT) 0, 4, 8, 12, 16, and 20. Total RNA was extracted from the tissues and used for unique identifier RNA sequencing experiments. The rhythmicity of gene expression was determined using the MetaCycle R package. We found that 1741 genes (10.26%) were rhythmically expressed in the retina. According to the expression patterns, the rhythmically expressed genes were assigned to four clusters, each with about 361-492 genes, using the Mfuzz R package. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were conducted to identify pathways and biological processes of the profiled genes. Genes in Clusters 1 and 4 were associated with glycolysis and energy production, showed higher activity at night (from ZT16 to ZT20), and were enriched in the Hif-1α signaling pathway and low-oxygen-related terms. Genes in Cluster 2 were predominantly involved in cilium assembly and organization and were relatively upregulated during the day. Genes in Cluster 3 were associated with ribosome biosynthesis and were highly expressed during the day-night transition period. Taken together, these results demonstrate that a large proportion of retinal genes are expressed rhythmically. Genes involved in energy production and glycolysis are highly expressed at night, leading to relative hypoxia and activation of the Hif-1α signaling pathway. Genes associated with the formation of photoreceptor cilia are expressed during the day.
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http://dx.doi.org/10.1016/j.exer.2021.108565 | DOI Listing |
Zhonghua Er Ke Za Zhi
March 2025
Department of Pediatrics, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China.
To analyze a novel intronic variant in the SPTB gene and explore its effect on SPTB mRNA splicing. Clinical data of a child diagnosed with hereditary spherocytosis (HS) and admitted to the First Affiliated Hospital of Xi'an Jiaotong University in February 2022 were analyzed retrospectively. Whole genome sequencing was used to identify disease-causing mutations and the results were validated with Sanger sequencing, mRNA sequencing was used to determine the SPTB gene's mRNA expression level, and bioinformatics tools were used for splicing site prediction and analysis.
View Article and Find Full Text PDFJ Neuroendocrinol
March 2025
Department of Zoology, University of Allahabad, Prayagraj, India.
Extra-retinal photoreception is common across fish and avian species. In birds, the hypothalamus contains non-visual photoreceptors that detect light and regulate multiple endocrine systems. To date, light-dependent control of seasonal reproduction is one of the most well-studied systems that require deep brain photoreception.
View Article and Find Full Text PDFCNS Neurosci Ther
March 2025
Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China.
Background: Gliomas represent the most aggressive malignancies of the central nervous system, with posttranslational modifications (PTMs) emerging as critical regulators of oncogenic processes through dynamic protein functional modulation. Despite their established role in tumor biology, the systematic characterization of PTM-mediated molecular mechanisms driving glioma progression remains unexplored. This study aims to uncover the molecular mechanisms of glioma, with a focus on the role of PTMs.
View Article and Find Full Text PDFMicrobes Environ
March 2025
Department of Marine Science and Technology, Faculty of Marine Science and Technology, Fukui Prefecture University.
Ascetosporeans are parasitic protists of invertebrates. A deep sequencing ana-lysis of species within the orders Mikrocytida, Paramyxida, and Haplosporida using metagenomic approaches revealed that their mitochondria were functionally reduced and their organellar genomes were lacking. Ascetosporeans belonging to the order Paradinida have not been sequenced, and the nature of their mitochondria remains unclear.
View Article and Find Full Text PDFJ Gen Appl Microbiol
March 2025
Program of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University.
Ralstonia pseudosolanacearum is a plant-pathogenic bacterium that causes bacterial wilt in economically important crops. Chemotaxis is required for full virulence in R. pseudosolanacearum.
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