• Journal of the Korea Institute of Information and Communication Engineering
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• v.25 no.11
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• pp.1512-1518
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• 2021

Since single cell RNA sequencing provides the expression profiles of individual cells, it provides higher cellular differential resolution than traditional bulk RNA sequencing. Using these single cell RNA sequencing data, clustering analysis is generally conducted to find cell types and understand high level biological processes. In order to effectively process the high-dimensional single cell RNA sequencing data fir the clustering analysis, this paper uses a variational autoencoder to transform a high dimensional data space into a lower dimensional latent space, expecting to produce a latent space that can give more accurate clustering results. By clustering the features in the transformed latent space, we compare the performance of various classical clustering methods for single cell RNA sequencing data. Experimental results demonstrate that the proposed framework outperforms many state-of-the-art methods under various clustering performance metrics.

• Mycobiology
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• v.50 no.2
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• pp.121-131
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• 2022

The rare edible and medicinal fungus Antrodia cinnamomea has a substantial potential for development. In this study, Illumina HiSeq 2000 was used to sequence its transcriptome. The results were assembled de novo, and 66,589 unigenes with an N50 of 4413 bp were obtained. Compared with public databases, 6,061, 3,257, and 2,807 unigenes were annotated to the Non-Redundant, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes databases, respectively. The genes related to terpene biosynthesis in the mycelia of A. cinnamomea were analyzed, and acetyl CoA synthase (ACS2 and ACS4), hydroxymethylglutaryl CoA reductase (HMGR), farnesyl transferase (FTase), and squalene synthase (SQS) were found to be upregulated in XZJ (twig of C. camphora) and NZJ (twig of C. kanehirae). Moreover, ACS5 and 2,3-oxidized squalene cyclase (OCS) were highly expressed in NZJ, while heme IX farnesyl transferase (IX-FIT) and ACS3 were significantly expressed in XZJ. The differential expression of ACS1, ACS2, HMGR, IX-FIT, SQS, and OCS was confirmed by real-time quantitative reverse transcription PCR. This study provides a new concept for the additional exploration of the molecular regulatory mechanism of terpenoid biosynthesis and data for the biotechnology of terpenoid production.

• Genomics & Informatics
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• v.21 no.2
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• pp.18.1-18.11
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• 2023

Immunologists have activated T cells in vitro using various stimulation methods, including phorbol myristate acetate (PMA)/ionomycin and αCD3/αCD28 agonistic antibodies. PMA stimulates protein kinase C, activating nuclear factor-κB, and ionomycin increases intracellular calcium levels, resulting in activation of nuclear factor of activated T cell. In contrast, αCD3/αCD28 agonistic antibodies activate T cells through ZAP-70, which phosphorylates linker for activation of T cell and SH2-domain-containing leukocyte protein of 76 kD. However, despite the use of these two different in vitro T cell activation methods for decades, the differential effects of chemical-based and antibody-based activation of primary human T cells have not yet been comprehensively described. Using single-cell RNA sequencing (scRNA-seq) technologies to analyze gene expression unbiasedly at the single-cell level, we compared the transcriptomic profiles of the non-physiological and physiological activation methods on human peripheral blood mononuclear cell-derived T cells from four independent donors. Remarkable transcriptomic differences in the expression of cytokines and their respective receptors were identified. We also identified activated CD4 T cell subsets (CD55⁺) enriched specifically by PMA/ionomycin activation. We believe this activated human T cell transcriptome atlas derived from two different activation methods will enhance our understanding, highlight the optimal use of these two in vitro T cell activation assays, and be applied as a reference standard when analyzing activated specific disease-originated T cells through scRNA-seq.

• The Plant Pathology Journal
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• v.40 no.5
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• pp.463-474
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• 2024

Bananas (Musa spp.), which serve millions of people worldwide, face a serious threat from Fusarium wilt (FW) disease caused by Fusarium oxysporum f. sp. cubense (Foc). Developing disease-resistant varieties particularly through breeding is challenging due to banana's seedless nature (parthenocarpic). As an alternative, cold plasma (CP) technology, has the potential to be used for crop improvement. Our study demonstrates a favourable impact of CP on the growth performance of banana (Berangan cultivar, AAA) in terms of height, leaf number and stem diameter. CP-treated plants also displayed delayed disease progression as well as lower disease severity indicated by slightly lower value of leaf symptoms index and rhizome discoloration index compared to the control plants. Additionally, quantitative real-time polymerase chain reaction analysis revealed differential expression of several defence (PR1, WRKY22, PAL, and CEBiP) and growth (Cytochrome P450, NAC68, and CAT) related genes in CP-treated plants, particularly in conjunction with Foc infection. These findings shed light on the potential use of CP in managing FW in banana and offer insights into possible mechanism behind improved traits.

• Korean Journal of Poultry Science
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• v.41 no.4
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• pp.287-296
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• 2014

Chicken eggs undergo various physiological changes during egg maturation. To study genes associated with the egg maturation in pre-ovulation (immature) and post-ovulation (mature), we compared gene expression patterns between in the immature egg and mature egg using RNA sequencing data. Mature and immature eggs were obtained from a Heuksaek Jaerae-jong of Korean native chicken. Total RNAs obtained from the eggs were sequenced by Illumina HiSeq 2000 platform, and the generated sequence reads were mapped to Galgal4 reference sequence assembly using Tuxedo Protocol. From the comparison of the RNA sequencing data, 315 genes were differentially expressed between mature and immature eggs, and 46 genes were only detected in immature egg. Further gene ontology (GO) analysis was performed for the differentially expressed genes using DAVID, showing that 29 and 28 GO terms were independently clustered from mature and immature, respectively. From those clustered GO terms, genes related to germ cell development, sex differentiation and defense response to bacterium were mainly expressed in the immature egg, while genes related to regulation of apoptosis, steroid metabolic process and lipid homeostasis were mainly detected in the mature egg. Our results could contribute to understand egg maturation before and after ovulation, and develop genetic markers for improving egg quality and productivity.

• Molecules and Cells
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• v.39 no.11
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• pp.790-796
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• 2016

Dental pulp is a highly vascularized tissue requiring adequate blood supply for successful regeneration. In this study, we investigated the functional role of stem cells from human exfoliated deciduous teeth (SHEDs) as a perivascular source for in vivo formation of vessel-like structures. Primarily isolated SHEDs showed mesenchymal stem cell (MSC)-like characteristics including the expression of surface antigens and in vitro osteogenic and adipogenic differentiation potentials. Moreover, SHEDs were positive for NG2, ${\alpha}$-smooth muscle actin (SMA), platelet-derived growth factor receptor beta ($PDGFR{\beta}$), and CD146 as pericyte markers. To prove feasibility of SHEDs as perivascular source, SHEDs were transplanted into immunodeficient mouse using Matrigel with or without human umbilical vein endothelial cells (HUVECs). Transplantation of SHEDs alone or HUVECs alone resulted in no formation of vessel-like structures with enough red blood cells. However, when SHEDs and HUVECs were transplanted together, extensive vessel-like structures were formed. The presence of murine erythrocytes within lumens suggested the formation of anastomoses between newly formed vessel-like structures in Matrigel plug and the host circulatory system. To understand underlying mechanisms of in vivo angiogenesis, the expression of angiogenic cytokine and chemokine, their receptors, and MMPs was compared between SHEDs and HUVECs. SHEDs showed higher expression of1VEGF, SDF-$1{\alpha}$, and $PDGFR{\beta}$ than HUVECs. On the contrary, HUVECs showed higher expression of VEGF receptors, CXCR4, and PDGF-BB than SHEDs. This differential expression pattern suggested reciprocal interactions between SHEDs and HUVECs and their involvement during in vivo angiogenesis. In conclusion, SHEDs could be a feasible source of perivascular cells for in vivo angiogenesis.

• Journal of Animal Science and Technology
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• v.50 no.6
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• pp.783-792
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• 2008

The present study was performed to determine expression of cytochrome P450 aromatase(Cyp19) in the efferent ductules(EDs) and the epididymis of male rat reproductive tract at different postnatal ages. Total RNAs isolated were reverse-transcribed, and cDNAs were utilized for real-time PCR analysis. In the EDs, the Cyp19 transcript was expressed at all prepubertal ages with the highest level at 14 days of age, but not at 90 days of age. Expression of Cyp19 mRNA in the epididymis was found at all age groups, except 7 days of age. Distinct expression patterns of Cyp19 transcript were shown in each segment of the epididymis. These results indicate that expression of Cyp19 gene in the excurrent duct of male reproductive tract is differentially regulated in age-dependent and segment-specific manners.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.1
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• pp.19-24
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• 2008

The purpose of this study was to detect expression of genes related to egg production in Taiwan Country chickens by suppression subtractive hybridization. Liver samples of mRNA extraction from two Taiwan Country chicken strains (L2 and B), originated from the same population but with very distinct egg production rates after long-term selection for egg and meat production respectively. Two-way subtraction was performed. The hepatic cDNA from the low egg production chickens (B) was subtracted from the hepatic cDNA from the high egg production strain (L2). The reversed subtraction (L2 from B) was also performed. The resulting differentially expressed gene fragments were cloned and sequenced. We sequenced 288 clones from the forward subtraction and 96 clones from the reverse subtraction. These genes were subjected to further screening to confirm the differential expression between the two genetic breeds of chickens. The apolipoprotein B (apoB) was expressed to a greater extent in the liver of the L2 than in the B line chickens. The 5-aminoimidazole- 4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (PURH) was expressed to a greater extent in the liver of the B than in the L2 strain chickens. We demonstrated that both apoB and PURH were more highly expressed in the liver than that in other tissues (muscle, ovary, and oviduct) in laying Taiwan Country chickens. Taken together, these data suggest that after the selection for egg production, expression of apoB and PURH genes were also changed. Whether the changed expression of these genes is directly related to egg production is not known, but these two genes may be useful markers for egg laying performance in Taiwan Country chickens.

• Journal of Sericultural and Entomological Science
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• v.53 no.1
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• pp.44-49
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• 2015

We characterized tissue specific-expressed genes in the posterior silk gland of Bombyx mori using by the Annealing Control Primer based differential display-PCR manner. In this study, we isolated 34 differentially expressed PCR amplicons, which one of these was identified as a novel transcript named as ACP-16 (366 bp), its expression was observed only in the posterior silk glands by Northern blot analysis. To determine promoter region of the ACP-16, we isolated and analyzed a phage DNA having 1.7 kb-long genome DNA including the open reading flame and 5'- upstream untranslated region of the ACP-16 gene from a genomic DNA library. We have estimated a promoter region of the ACP-16 gene by a web promoter prediction engine, which locates -750 ~ -165 from translation initiation site (ATG, +1). ACP-16 gene is necessary to more studies about critical biological role in order to apply the silkworm's transgenic system.

• Animal Bioscience
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• v.37 no.8
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• pp.1345-1354
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• 2024

Objective: The objective of this study was to identify candidate genes that play important roles in skeletal muscle development in ducks. Methods: In this study, we investigated the transcriptional sequencing of embryonic pectoral muscles from two specialized lines: Liancheng white ducks (female) and Cherry valley ducks (male) hybrid Line A (LCA) and Line C (LCC) ducks. In addition, prediction of target genes for the differentially expressed mRNAs was conducted and the enriched gene ontology (GO) terms and Kyoto encyclopedia of genes and genomes signaling pathways were further analyzed. Finally, a protein-to-protein interaction network was analyzed by using the target genes to gain insights into their potential functional association. Results: A total of 1,428 differentially expressed genes (DEGs) with 762 being up-regulated genes and 666 being down-regulated genes in pectoral muscle of LCA and LCC ducks identified by RNA-seq (p<0.05). Meanwhile, 23 GO terms in the down-regulated genes and 75 GO terms in up-regulated genes were significantly enriched (p<0.05). Furthermore, the top 5 most enriched pathways were ECM-receptor interaction, fatty acid degradation, pyruvate degradation, PPAR signaling pathway, and glycolysis/gluconeogenesis. Finally, the candidate genes including integrin b3 (Itgb3), pyruvate kinase M1/2 (Pkm), insulin-like growth factor 1 (Igf1), glucose-6-phosphate isomerase (Gpi), GABA type A receptor-associated protein-like 1 (Gabarapl1), and thyroid hormone receptor beta (Thrb) showed the most expression difference, and then were selected to verification by quantitative real-time polymerase chain reaction (qRT-PCR). The result of qRT-PCR was consistent with that of transcriptome sequencing. Conclusion: This study provided information of molecular mechanisms underlying the developmental differences in skeletal muscles between specialized duck lines.