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Jeon, J.-H.

Publications and source records attributed to Jeon, J.-H..

2 recordsLinked to original sources

Machine learning analysis reveals the dynamics of mode transition in dendritic cell migration

Dendritic cells (DCs) patrol the body as immunological sentinels and search for pathogens. Upon stimulation, immature DCs (imDCs) become mature DCs (mDCs), which migrate to the lymph nodes and present antigens to T cells. The migratory behavior is crucial for initiating and controlling immune responses; however, the properties of the highly heterogeneous and dynamic motility phenotype are not fully understood. Here, we established an unsupervised machine learning (ML) strategy to investigate spatiotemporal motility patterns in long-term, two-dimensional cell migration trajectories, and determined the number of motility patterns and how these are related to the maturation status. We identified three distinct migratory modes independent of the cell state: slow-diffusive (SD), slow-persistent (SP), and fast-persistent (FP). We found that maturation-dependent motility changes are emergent properties of the distribution and dynamic transitions of these three modes. Remarkably, imDCs changed their migration modes more frequently, and predominantly followed the SD[->]FP[->]SP[->]SD unicyclic transition, indicating that imDCs rapidly increase their speed during the shift from diffusive to persistent motility; however, persistence progressively declines when switching back to diffusive motility. In contrast, mDCs show no transition directionality. Our ML-promoted motility pattern analysis and history-dependent mode transition investigation may provide new insights into the complex process of biological motility.

biophysics↗

Draft Genome of the Korean smelt (Hypomesus nipponensis) and its transcriptomic responses to heat stress in the liver and muscle

Pond smelt (Hypomesus nipponensis) is a cold-freshwater fish species as a winter economic resource of aquaculture in South Korea. Due to its high susceptibility to abnormal water temperature from global warming, a large number of smelt die in hot summer. Here, we present the first draft genome of H. nipponensis and transcriptomic changes in molecular mechanisms or intracellular responses under heat stress. We combined Illumina and PacBio sequencing technologies to generate the draft genome of H. nipponensis. Based on the reference genome, we conducted transcriptome analysis of liver and muscle tissues under normal (NT, 5{degrees}C) versus warm (HT, 23{degrees}C) conditions, to identify heat stress-induced genes and gene categories. We observed a total of 1,987 contigs, with N50 of 0.46 Mbp with a largest contig (3.03 Mbp) in the assembled genome. A total number of 20,644 protein coding genes were predicted, and 19,224 genes were functionally annotated: 15,955 genes for Gene Ontology (GO) terms; and 11,560 genes for KEGG Orthology (KO). We conducted the lost and gained genes analysis compared with three species that human, zebrafish and salmon. In the lost genes analysis, we detected smelt lost 4,461 (22.16%), 2,825 (10.62%), and 1,499 (3.09%) genes compare with above three species, respectively. In the gained genes analysis, we observed smelt gain 1,133 (5.49%), 1,670 (8.09%), and 229 (1.11%) genes compare with above species, respectively. From transcriptome analysis, a total of 297 and 331 differentially expressed genes (DEGs) with False discovery rate (FDR) < 0.05 were identified in the liver and muscle tissues, respectively. Gene enrichment analysis of DEGs indicates that up-regulated genes were significantly enriched for lipid biosynthetic process (GO:0008610, P < 0.001) and regulation of apoptotic process (GO:0042981, P < 0.01), and down-regulated genes by immune responses such as myeloid cell differentiation (GO:0030099, P < 0.001) in the liver under heat stress. In muscle tissue, up-regulated genes were enriched for hypoxia (GO:0001666, P < 0.05), transcription regulator activity (GO:0140110, P < 0.001) and calcium-release channel activity (GO:0015278, P < 0.01), and down-regulated genes for nicotinamide nucleotide biosynthetic process (GO:0019359, P < 0.01). The results of KEGG pathway analysis were similar to that of gene enrichment analysis. The draft genome and transcriptomic of H. nipponensis will be used as a useful genetic resource for functional and evolutionary studies. Our findings will improve understanding of the molecular mechanisms and heat responses and will be useful for predicting survival of the smelt and its closely related species under global warming.

genetics↗