The yellow catfish, Pelteobagrus fulvidraco (Siluriformes: Bagridae) is an economically important fish in China. However, genomic research and resources on this species are largely unavailable and still in infancy. In the present study, we constructed a cDNA library following poly I:C injection to screen for immune response genes in the spleens of P. fulvidraco using suppression subtractive hybridization (SSH). A total of 420 putative expressed sequence tag (EST) clones were identified at 24 h post-injection, which contain 103 genes consisting of 25 immune response genes, 12 cytoskeleton genes, 7 cell cycle and apoptosis genes, 7 respiration and energy metabolism genes, 7 transport genes, 26 metabolism genes, 10 stress response genes, 9 translational regulation genes, and 71 unknown genes. Real-time quantitative reverse transcription-PCR (qRT-PCR) results revealed that a set of randomly selected immune response genes were identified to be up-regulated after 24 h of poly I:C stimulation compared to controls. Our study provides an annotation of immune genes in detail and insight into fish immunity.
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http://dx.doi.org/10.1016/j.fsi.2016.06.041 | DOI Listing |
Brief Bioinform
November 2024
Department of Automation, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.
Studying the changes in cellular transcriptional profiles induced by small molecules can significantly advance our understanding of cellular state alterations and response mechanisms under chemical perturbations, which plays a crucial role in drug discovery and screening processes. Considering that experimental measurements need substantial time and cost, we developed a deep learning-based method called Molecule-induced Transcriptional Change Predictor (MiTCP) to predict changes in transcriptional profiles (CTPs) of 978 landmark genes induced by molecules. MiTCP utilizes graph neural network-based approaches to simultaneously model molecular structure representation and gene co-expression relationships, and integrates them for CTP prediction.
View Article and Find Full Text PDFTransl Vis Sci Technol
January 2025
Department of Ophthalmology, Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
Purpose: Regulating intraocular pressure (IOP), mainly via the trabecular meshwork (TM), is critical in developing glaucoma. Whereas current treatments aim to lower IOP, directly targeting the dysfunctional TM tissue for therapeutic intervention has proven challenging. In our study, we utilized Dexamethasone (Dex)-treated TM cells as a model to investigate how extracellular vesicles (EVs) from immortalized corneal stromal stem cells (imCSSCs) could influence ANGPTL7 and MYOC genes expression within TM cells.
View Article and Find Full Text PDFDokl Biochem Biophys
January 2025
Institute of Bioengineering, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia.
The expression profile of the key genes of biosynthesis (VTC2, GPP, GalDH, and GalLDH) and recycling (MDHAR1, MDHAR4, and MDHAR5) of ascorbate in response to infection with the fungal pathogen Fusarium proliferatum in garlic cultivars resistant (Podnebesny) and sensitive (Dubkovsky) to Fusarium rot was determined. It was found that differences in resistance to Fusarium lead to discrepancies in the dynamics and expression of individual genes of the ascorbate pathway, as well as in the ascorbate content. It was shown that, in response to infection, the expression level of the MDHAR4 gene increases in the resistant cultivar and decreases in the Fusarium-sensitive accession.
View Article and Find Full Text PDFDokl Biochem Biophys
January 2025
State Research Center-Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, 123098, Moscow, Russia.
Background: The effects of ionizing radiation (IR) involve a highly orchestrated series of events in cells, including DNA damage and repair, cell death, and changes in the level of proliferation associated with the stage of the cell cycle. A large number of existing studies in literature have examined the activity of genes and their regulators in mammalian cells in response to high doses of ionizing radiation. Although there are many studies, the research in effect of low doses of ionizing radiation remains limited.
View Article and Find Full Text PDFDiscov Oncol
January 2025
Department of General Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou, 350001, People's Republic of China.
Background: Pancreatic ductal adenocarcinoma (PDAC) has a heterogeneous make-up of myeloid cells that influences the therapeutic response and prognosis. However, understanding the myeloid cell at both a genetic and cellular level remains a significant challenge.
Methods: Single-cell RNA sequencing (scRNA-seq) data were downloaded from t the Tumor Immune Single-cell Hub and gene expression data were retrieved from The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database.
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