• Journal of Microbiology and Biotechnology
• /
• v.29 no.8
• /
• pp.1324-1334
• /
• 2019

Fish mycobacteriosis is a common bacterial disease in many species of freshwater and marine fish and has caused severe loss of fish production. Mycobacterium marinum has been the most prevalent pathogen observed in several outbreaks of mycobacteriosis of farmed sturgeons in China. However, the immune responses and pathology of sturgeons in mycobacterial infection are rarely studied. Therefore, we used the Illumina RNA-seq method to analyze the transcriptome profile of Acipenser schrenckii challenged with Mycobacterium marinum. To begin, 168,220 non-redundant contigs were acquired from the infection and control groups, and among these, 33,225 contigs have acquired annotations. A total of 4,043 differently expressed (DE) contigs between the two groups were identified, and among these, 2479 were up-regulated and 1564 were down-regulated in the infected fish. A total of 1,340 DE contigs with acquired annotations in KEGG were enriched for 124 pathways including the TNF signaling pathway, and the Toll-like receptor signaling pathway. The roles of DE genes involved in significant pathways and other processes were discussed. The 2,209 DE contigs that have yet to acquire proper annotation may represent candidate genes associated with infection in sturgeons and are expected to serve as immunogenetic resources for further study. To our best knowledge, this is the first transcriptome study on sturgeons under bacterial infection.

• The Korea Journal of Herbology
• /
• v.39 no.3
• /
• pp.37-47
• /
• 2024

Objectives : Because predicting the potential efficacy and mechanisms of Korean medicines is challenging due to their high complexity, employing an approach based on network pharmacology could be effective. In this study, network pharmacological analysis was utilized to anticipate the effects of YunPye-Hwan (YPH) in treating Chronic obstructive pulmonary disease (COPD). Methods : Compounds and their related target genes of YPH were gathered from the TCMSP and PubChem databases. These target genes of YPH were subsequently compared with gene sets associated with COPD to assess correlation. Next, core genes were identified through a two-step screening process, and finally, functional enrichment analysis of these core genes was conducted using both Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways. Results : A total of 15 compounds and 437 target genes were gathered, resulting in a network comprising 473 nodes and 14,137 edges. Among them, 276 genes overlapped with gene sets associated with COPD, indicating a significant correlation between YPH and COPD. Functional enrichment analysis of the 18 core genes revealed biological processes and pathways such as "miRNA Transcription," "Nucleic Acid-Templated Transcription," "DNA-binding Transcription Factor Activity," "MAPK signaling pathway," and "TNF signaling pathway" were implicated. Conclusion : YPH exhibited significant relevance to COPD by modulating cell proliferation, differentiation, inflammation, and cell death pathways. This study could serve as a foundational framework for further research investigating the potential use of YPH in the treatment of COPD.

• The Journal of Korean Medicine
• /
• v.45 no.1
• /
• pp.114-125
• /
• 2024

Objectives: Network pharmacology is an analysis method that explores drug-centered efficacy and mechanism by constructing a compound-target-disease network based on system biology, and is attracting attention as a methodology for studying herbal medicine that has the characteristics for multi-compound therapeutics. Thus, we investigated the potential functions and pathways of Myrrha on Allergic Rhinitis (AR) via network pharmacology analysis and molecular docking. Methods: Using public databases and PubChem database, compounds of Myrrha and their target genes were collected. The putative target genes of Myrrha and known target genes of AR were compared and found the correlation. Then, the network was constructed using STRING database, and functional enrichment analysis was conducted based on the Gene Ontology (GO) Biological process and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways. Binding-Docking stimulation was performed using CB-Dock. Results: The result showed that total 3 compounds and 55 related genes were gathered from Myrrha. 33 genes were interacted with AR gene set, suggesting that the effects of Myrrha are closely related to AR. Target genes of Myrrha are considerably associated with various pathways including 'Fc epsilon RI signaling pathway' and 'JAK-STAT signaling pathway'. As a result of blinding docking, AKT1, which is involved in both mechanisms, had high binding energies for abietic acid and dehydroabietic acid, which are components of Myrrha. Conclusion: Through a network pharmacological method, Myrrha was predicted to have high relevance with AR by regulating AKT1. This study could be used as a basis for studying therapeutic effects of Myrrha on AR.

• International Journal of Stem Cells
• /
• v.16 no.2
• /
• pp.202-214
• /
• 2023

Background and Objectives: To investigate the role of exosomes from periodontal ligament cells (PDLCs) in bone marrow mesenchymal stem cell (BMSC) migration. Methods and Results: Human PDLCs were applied cyclic tension stretching. Exosomes were extracted from cultured PDLCs by ultracentrifugation, then characterized for their size, morphology and protein markers by NTA, TEM and western blotting. The process that PKH26-labeled exosomes taken up by BMSCs was assessed by confocal microscope. BMSC migration was examined by Transwell assay. Exosomes derived from PDLCs were identified. Cyclic tension stretch application on PDLCs can enhance the migration ability of BMSCs through exosomes. The exosomal miRNA expression profiles of unstretched and stretched PDLCs were tested by miRNA microarray. Four miRNAs (miR-4633-5p, miR-30c-5p, miR-371a-3p and let-7b-3p) were upregulated and six (miR-4689, miR-8485, miR-4655-3p, miR-4672, miR-3180-5p and miR-4476) were downregulated in the exosomes after stretching. Sixteen hub proteins were found in the miRNA-mRNA network. Gene Ontology and KEGG pathway analyses demonstrated that the target genes of differentially expressed exosomal miRNAs closely related to the PI3K pathway and vesicle transmission. Conclusions: The exosomes derived from cyclic tension-stretched PDLCs can promote the migration of BMSCs. Alternation of microRNA profiles provides a basis for further research on the regulatory function of the exosomal miRNAs of PDLCs during orthodontic tooth movement.

• Asian-Australasian Journal of Animal Sciences
• /
• v.28 no.9
• /
• pp.1235-1243
• /
• 2015

The goat Capra hircus is one of several economically important livestock in China. Advances in molecular genetics have led to the identification of several single nucleotide variation markers associated with genes affecting economic traits. Validation of single nucleotide variations in a whole-transcriptome sequencing is critical for understanding the information of molecular genetics. In this paper, we aim to develop a large amount of convinced single nucleotide polymorphisms (SNPs) for Cashmere goat through transcriptome sequencing. In this study, the transcriptomes of Cashmere goat skin at four stages were measured using RNA-sequencing and 90% to 92% unique-mapped-reads were obtained from total-mapped-reads. A total of 56,231 putative SNPs distributed among 10,057 genes were identified. The average minor allele frequency of total SNPs was 18%. GO and KEGG pathway analysis were conducted to analyze the genes containing SNPs. Our follow up biological validation revealed that 64% of SNPs were true SNPs. Our results show that RNA-sequencing is a fast and efficient method for identification of a large number of SNPs. This work provides significant genetic resources for further research on Cashmere goats, especially for the high density linkage map construction and genome-wide association studies.

• Asian Pacific Journal of Cancer Prevention
• /
• v.16 no.6
• /
• pp.2561-2567
• /
• 2015

Pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer death worldwide. Our study aimed to reveal molecular mechanisms. Microarray data of GSE15471 (including 39 matching pairs of pancreatic tumor tissues and patient-matched normal tissues) was downloaded from Gene Expression Omnibus (GEO) database. We identified differentially expressed genes (DEGs) in PDAC tissues compared with normal tissues by limma package in R language. Then GO and KEGG pathway enrichment analyses were conducted with online DAVID. In addition, principal component analysis was performed and a protein-protein interaction network was constructed to study relationships between the DEGs through database STRING. A total of 532 DEGs were identified in the 38 PDAC tissues compared with 33 normal tissues. The results of principal component analysis of the top 20 DEGs could differentiate the PDAC tissues from normal tissues directly. In the PPI network, 8 of the 20 DEGs were all key genes of the collagen family. Additionally, FN1 (fibronectin 1) was also a hub node in the network. The genes of the collagen family as well as FN1 were significantly enriched in complement and coagulation cascades, ECM-receptor interaction and focal adhesion pathways. Our results suggest that genes of collagen family and FN1 may play an important role in PDAC progression. Meanwhile, these DEGs and enriched pathways, such as complement and coagulation cascades, ECM-receptor interaction and focal adhesion may be important molecular mechanisms involved in the development and progression of PDAC.

• Asian Pacific Journal of Cancer Prevention
• /
• v.15 no.5
• /
• pp.2309-2312
• /
• 2014

Esophageal squamous cell carcinoma (ESCC) is the most common histologic subtype of esophageal cancer and is characterized by a poor prognosis. Determining gene changes in ESCCs should improve understanding of putative risk factors and provide potential targets for therapy. We sequenced about 55 million pair-end reads from a pair of adjacent normal and ESCC samples to identify the gene expression level and gene fusion. Sanger sequencing was used to verify the result. About 17 thousand genes were expressed in the tissues, of which approximately 2400 demonstrated significant differences between tumor and adjacent non tumor tissue. GO and KEGG pathway analysis revealed that many of these genes were associated with cellular adherence and movement, simulation responses and immune responses. Notably we identified and validated one fusion gene, HLA-E and HLA-B, located 1 MB apart. We also identified thousands of remarkably expressed transcripts. In conclusion, a novel fusion gene HLA-E and HLA-B was identified in ESCC via whole transcriptome sequencing, which would be a biomarker for ESCC diagnosis and target for therapy, shedding new light for better understanding of ESCC tumorigenesis.

• Asian-Australasian Journal of Animal Sciences
• /
• v.26 no.3
• /
• pp.309-315
• /
• 2013

MicroRNAs are a class of endogenous small RNAs that play important roles in post-transcriptional gene regulation by directing degradation of mRNAs or facilitating repression of target gene translation. In this study, three small RNA cDNA libraries from the mammary gland tissues of Laoshan dairy goats (Capra hircus) were constructed and sequenced, individually. Through Solexa high-throughput sequencing and bioinformatics analysis, we obtained 50 presumptive novel miRNAs candidates, and 55,448 putative target genes were predicted. GO annotations and KEGG pathway analyses showed the majority of target genes were involved in various biological processes and metabolic pathways. Our results discovered more information about the regulation network between miRNAs and mRNAs and paved a foundation for the molecular genetics of mammary gland development in goats.

• Proceedings of the Plant Resources Society of Korea Conference
• /
• 2018.04a
• /
• pp.5-5
• /
• 2018

Ginseng (Panax ginseng C.A. Meyer), one of the most widely used medicinal plants in traditional oriental medicine, is used for the treatment of various diseases. It has been classified according to its cultivation environment, such as field cultivated ginseng (FCG) and mountain cultivated ginseng (MCG). However, little is known about differences in gene expression in ginseng roots between field cultivated and mountain cultivated ginseng. In order to investigate the whole transcriptome landscape of ginseng, we employed High-Throughput sequencing technologies using the Illumina HiSeqTM2500 system, and generated a large amount of sequenced transcriptome from ginseng roots. Approximately 77 million and 87 million high-quality reads were produced in the FCG and MCG roots transcriptome analyses, respectively, and we obtained 256,032 assembled unigenes with an average length of 1,171 bp by de novo assembly methods. Functional annotations of the unigenes were performed using sequence similarity comparisons against the following databases: the non-redundant nucleotide database, the InterPro domains database, the Gene Ontology Consortium database, and the Kyoto Encyclopedia of Genes and Genomes pathway database. A total of 4,207 unigenes were assigned to specific metabolic pathways, and all of the known enzymes involved in starch and sucrose metabolism pathways were also identified in the KEGG library. This study indicated that alpha-glucan phosphorylase 1, putative pectinesterase/pectinesterase inhibitor 17, beta-amylase, and alpha-glucan phosphorylase isozyme H might be important factors involved in starch and sucrose metabolism between FCG and MCG in different environments.

• Mycobiology
• /
• v.50 no.5
• /
• pp.357-365
• /
• 2022

Schizophyllum commune has emerged as the most promising model mushroom to study developmental stages (mycelium, primordium), which are two primary processes of fruit body development. Long non-coding RNA (lncRNA) has been proved to participate in fruit development and sex differentiation in fungi. However, potential lncRNAs have not been identified in S. commune from mycelium to primordium developmental stages. In this study, lncRNA-seq was performed in S. commune and 61.56 Gb clean data were generated from mycelium and primordium developmental stages. Furthermore, 191 lncRNAs had been obtained and a total of 49 lncRNAs were classified as differently expressed lncRNAs. Additionally, 26 up-regulated differently expressed lncRNAs and 23 down-regulated between mycelium and primordia libraries were detected. Further, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that differentially expressed lncRNAs target genes from the MAPK pathway, phosphatidylinositol signal, ubiquitin-mediated proteolysis, autophagy, and cell cycle. This study provides a new resource for further research on the relationship between lncRNA and two developmental stages (mycelium, primordium) in S. commune.