• Journal of Species Research
• /
• v.12 no.4
• /
• pp.341-354
• /
• 2023

This is the third series of catalogs reporting on Korean species discovered through the 'Discovery of Korean Indigenous Species'. This catalog includes 22 species of invertebrates, excluding insects. The catalog includes the scientific name, an abridged list of synonyms, collection sites, distribution, diagnosis, and figures for each species. Additionally, we provide the newly assigned Korean name, specimen voucher, and, if available, mitochondrial CO1 or 16S gene sequences of the species listed. All species identified and documented here will be officially listed on the 'National Species List of Korea', a database maintained by the National Institute of Biological Resources(NIBR).

• BMB Reports
• /
• v.56 no.11
• /
• pp.600-605
• /
• 2023

Intrahepatic cholangiocarcinoma (ICC) is a bile duct cancer and a rare malignant tumor with a poor prognosis owing to the lack of an early diagnosis and resistance to conventional chemotherapy. A combination of gemcitabine and cisplatin is the typically attempted first-line treatment approach. However, the underlying mechanism of resistance to chemotherapy is poorly understood. We addressed this by studying dynamics in the human ICC SCK cell line. Here, we report that the regulation of glucose and glutamine metabolism was a key factor in overcoming cisplatin resistance in SCK cells. RNA sequencing analysis revealed a high enrichment cell cycle-related gene set score in cisplatin-resistant SCK (SCK-R) cells compared to parental SCK (SCK WT) cells. Cell cycle progression correlates with increased nutrient requirement and cancer proliferation or metastasis. Commonly, cancer cells are dependent upon glucose and glutamine availability for survival and proliferation. Indeed, we observed the increased expression of GLUT (glucose transporter), ASCT2 (glutamine transporter), and cancer progression markers in SCK-R cells. Thus, we inhibited enhanced metabolic reprogramming in SCK-R cells through nutrient starvation. SCK-R cells were sensitized to cisplatin, especially under glucose starvation. Glutaminase-1 (GLS1), which is a mitochondrial enzyme involved in tumorigenesis and progression in cancer cells, was upregulated in SCK-R cells. Targeting GLS1 with the GLS1 inhibitor CB-839 (telaglenastat) effectively reduced the expression of cancer progression markers. Taken together, our study results suggest that a combination of GLUT inhibition, which mimics glucose starvation, and GLS1 inhibition could be a therapeutic strategy to increase the chemosensitivity of ICC.

• BMB Reports
• /
• v.57 no.5
• /
• pp.232-237
• /
• 2024

This study investigated how adipose tissue-derived mesenchymal stem cells (AT-MSCs) respond to chondrogenic induction using droplet-based single-cell RNA sequencing (scRNA-seq). We analyzed 37,219 high-quality transcripts from control cells and cells induced for 1 week (1W) and 2 weeks (2W). Four distinct cell clusters (0-3), undetectable by bulk analysis, exhibited varying proportions. Cluster 1 dominated in control and 1W cells, whereas clusters (3, 2, and 0) exclusively dominated in control, 1W, and 2W cells, respectively. Furthermore, heterogeneous chondrogenic markers expression within clusters emerged. Gene ontology (GO) enrichment analysis of differentially expressed genes unveiled cluster-specific variations in key biological processes (BP): (1) Cluster 1 exhibited up-regulation of GO-BP terms related to ribosome biogenesis and translational control, crucial for maintaining stem cell properties and homeostasis; (2) Additionally, cluster 1 showed up-regulation of GO-BP terms associated with mitochondrial oxidative metabolism; (3) Cluster 3 displayed up-regulation of GO-BP terms related to cell proliferation; (4) Clusters 0 and 2 demonstrated similar up-regulation of GO-BP terms linked to collagen fibril organization and supramolecular fiber organization. However, only cluster 0 showed a significant decrease in GO-BP terms related to ribosome production, implying a potential correlation between ribosome regulation and the differentiation stages of AT-MSCs. Overall, our findings highlight heterogeneous cell clusters with varying balances between proliferation and differentiation before, and after, chondrogenic stimulation. This provides enhanced insights into the single-cell dynamics of AT-MSCs during chondrogenic differentiation.

• Fisheries and Aquatic Sciences
• /
• v.27 no.2
• /
• pp.87-99
• /
• 2024

Global climate change, followed by an increase in anthropogenic activities in aquatic ecosystems, and species invasions, has resulted in a decline in aquatic organism biodiversity. The Batanghari River, Sumatra's longest river, is polluted by mercury-containing illegal gold mining waste (PETI), industrial pollution, and domestic waste. Several studies have provided evidence suggesting a decline in fish biodiversity within the Batanghari River. However, a comprehensive evaluation of the present status of biodiversity in this river is currently lacking. The species under investigation were identified through various molecular-based identification methods, as well as morphological identification, which involved the use of neighbor-joining (NJ) trees. All collected specimens were initially identified using morphological techniques and subsequently confirmed with molecular barcoding analysis. Morphological and DNA barcoding identification categorized all specimens (1,692) into 36 species, 30 genera and 16 families, representing five orders. A total of 36 DNA barcodes were generated from 30 genera using a 650-bp-long fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene. Based on the Kimura two-parameter model (K2P), The minimum and maximum genetic divergences based on K2P distance were 0.003 and 0.331, respectively, and the average genetic divergence within genera, families, and orders was 0.05, 0.12, 0.16 respectively. In addition, the average interspecific distance was approximately 2.17 times higher than the mean intraspecific distance. Our results showed that the COI barcode enabled accurate fish species identification in the Batanghari River. Furthermore, the present work will establish a comprehensive DNA barcode library for freshwater fishes along Batanghari River and be significantly useful in future efforts to monitor, conserve, and manage fisheries in Indonesia.

• Journal of Ecology and Environment
• /
• v.48 no.2
• /
• pp.163-172
• /
• 2024

Background: Fruit bats are natural carriers of Nipah virus (NiV). The primary objective of this study is to identify potential reservoir species in a selected geographic regions. It is necessary to determine an accurate species identification of the associated reservoir bat species distributed in a specific region. Results: In this study, we collected 20 different bat specimens from the NiV-prone area of the Kushtia district. Among these, 14 were tissue samples (BT-1-14) and six were fecal samples (BF-1-6). We used the mitochondrial gene cytochrome b, one of the most abundant and frequently used genetic markers, for polymerase chain reaction amplification and sequencing. Out of the 20 samples, 12 tissue samples and 2 fecal samples were successfully amplified and sequenced. However, two tissue samples and four fecal samples yielded chimeric sequences, rendering them unsuitable for annotation. The sequences of the successfully amplified samples were compared to those deposited in the National Center for Biotechnology Information database using basic local alignment search tool to identify the bat specimen collected. The study identified six different bat species using both morphological and genetic data, which may carriers of the NiV. Conclusions: Our results suggest that additional research should be conducted to gather more information on fruit bats from different localities across the country. The study contributes to the establishment of appropriate measures for NiV carrying disease control and management.

• The Korean Journal of Mycology
• /
• v.52 no.2
• /
• pp.145-153
• /
• 2024

While investigation of the fungal diseases on apples collected from Cheongsong-gun and Bonghwa-gun in Gyeongbuk province, Korea, between August and September 2023 isolated five fungal strains from fruits with sooty blotch and flyspeck (SBFS) disease. The strains were designated as KNUF-23-CS02, KNUF-23-CS-06, KNUF-23-CS12, KNUF-23-BH01, and KNUF-23-BH03. When grown on potato dextrose agar and 2% water agar, the cultural characteristics of the strains were similar to those previously reported characteristics of Peltaster fructicola Pf001. The strains produced monoblastic, hyaline conidiogenous cells; the conidia were hyaline, unicellular, cylindrical to ovoidal, and 3.5-7×1.7-3.9 and 4.0-6.6×1.8-3.2 μm in size on synthetic nutrient-poor agar or water agars, respectively. Secondary conidia production by microcyclic conidiation and budding was observed. The KNUF-23-BH03 strain was shown to cause SBFS symptoms similar to those observed on the apples in the pathogenicity test. Molecular phylogenetic analyses were conducted based on the isolated species sequences of the internal transcribed spacer region, nuclear large ribosomal DNA subunit, and mitochondrial small ribosomal RNA subunit gene. The five strains were clustered with Peltaster fructicola Pf001. Based on the cultural and morphological characteristics and phylogenetic analysis, the five strains were identified as Peltaster fructicola, which has not been previously reported in Korea.

• International Journal of Oncology
• /
• v.57 no.4
• /
• pp.1027-1038
• /
• 2020

Colorectal cancer (CRC) is one of the most commonly diagnosed malignancies and is a leading cause of cancer-related mortality worldwide. Histone deacetylases (HDACs) are a class of enzymes responsible for the epigenetic regulation of gene expression. Some HDAC inhibitors have been shown to be efficient agents for cancer treatment. The aim of the present study was to discover a novel, potent HDAC inhibitor and demonstrate its anticancer effect and molecular mechanisms in CRC cells. A novel fluorinated aminophenyl-benzamide-based compound, CBUD-1001, was designed to specifically target HDAC1, and it was then synthesized and evaluated. CBUD-1001 exerted a potent inhibitory effect on HDAC enzyme activity and exhibited anticancer potency against CRC cell lines. Molecular docking analysis rationalized the high potency of CBUD-1001 by validating its conformation in the HDAC active site. Further investigation using CRC cells demonstrated that CBUD-1001 inhibited HDAC activity by hyper-acetylating histones H3 and H4, and it exerted an apoptotic effect by activating a mitochondrial-dependent pathway. Of note, it was found that CBUD-1001 attenuates the cell motility of CRC cells by downregulating the EMT signaling pathway. Thus, CBUD-1001 may prove to be a promising novel drug candidate for CRC therapy.

• Korean Journal of Environmental Biology
• /
• v.38 no.4
• /
• pp.650-657
• /
• 2020

We conducted a phylogeographic analysis of Korean endemic Zacco koreanus populations inhabiting the East-flowing river (Gangneung Yeongokcheon; GY, Yangyang Namdaecheon; YN), the Han River (Seomgang; SG, Soksacheon; SS), and the Nakdong River(Gilancheon; GA) using the mitochondrial DNA cytochrome oxidase I (COI) gene (619 bp). Population genetic analysis was further performed to assess the population connectivity for the GY river where there is a large number of human-made artificial weirs with several fishways. The phylogeographic analysis revealed that while the populations of the East-flowing river and those of the Han River formed a monophyletic lineage, the Nakdong River individuals represented a distinct lineage with 3.7-4.2% (mean=4.0%) genetic distance from the other lineages. The population genetic analysis of the GY showed that a mid-stream population harbored relatively higher mitochondrial diversity relative to up- and down-stream populations, and there was no genetic differentiation between these three populations. The latter findings might suggest high genetic connectivity between the populations via genetic flow along the fishways. However, an analysis using faster-evolving genetic markers, such as microsatellites, is needed to confirm the findings of high population connectivity. Our study suggests the possibility of the presence of cryptic species in Z. koreanus in the Nakdong River basin. However, further study with more individual samples as well as additional markers or even more advanced genomic tools is required to test our hypothesis. Ecological or phenotypic analyses should be conducted to test whether the observed Nakdong River lineage represents a different or cryptic species, or simply hidden, but excessive, intraspecific diversity.

• Food Science of Animal Resources
• /
• v.28 no.3
• /
• pp.276-282
• /
• 2008

It is estimated that over 80% of deer antlers produced in the world are consumed in Korea. However, mislabeling or fraudulent replacement of costly antlers with cheaper ones is one of the most common problems in the domestic antler market. Therefore, there is a great need for the development of technology to identify species of antlers. This study was carried out to develop an accurate and reliable method for the identification and authentication of species or subspecies of antlers using DNA sequence analysis and comparison of mitochondrial cytochrome band D-loop region genes among antlers of five deer species, Cervus elaphus sibericus, Cervus elaphus canadensis, Cervus nippon, Cervus elaphus bactrianus and Rangifer tarandus. A variable region of cytochrome band D-loop genes was amplified using PCR with specifically designed primers and sequenced directly. The cytochrome band D-loop region genes showed different DNA sequences between the species of antlers and thus it is possible to differentiate between species on the basis of sequence variation. To distinguish between reindeer (Rangifer tarandus) antlers and other deer antlers, PCR amplicons of the cytochrome b gene were digested with the restriction enzymes NlaIV and TaqI, respectively, which generates a species-specific DNA profile of the reindeer. In addition, samples of 32 sliced antlers labeled Cervus elaphus sibericus from commercial markets were collected randomly and the mt DNA D-loop region of these antler samples was sequenced. Among the antler samples investigated, only 62.5% were from Cervus elaphus sibericus, and others were from Cervus elaphus bactrianus (25.0%), elk (Cervus elaphus canadensis) and reindeer (Rangifer tarandus). Our results suggest that DNA sequencing of mt DNA and PCR-RFLP methods using NlaIV and TaqI enzymes are useful for the identification and discrimination of deer antler species by routine analysis.

• Korean Journal of Clinical Laboratory Science
• /
• v.49 no.2
• /
• pp.135-140
• /
• 2017

Polymerase chain reaction (PCR) was used to detect cattle material from processed meat products. Seventy-eight different commercial processed meat products were purchased from several big food marts. Among them, 17 products contained cattle material (10 samples contained only cattle, 5 samples mixed with cattle and porcine, 2 samples mixed with cattle, porcine and chicken). The genomic DNA was extracted directly from the processed meat products, and strain-specific primer targeting the 16S ribosomal RNA mitochondrial gene was used. All PCR products were cloned into the pGEM-T easy vector and sequenced. Consequently, the PCR products were amplified from 10 processed meat products, which contained only cattle material in our conditions. Furthermore, PCR reactions showed the same results at mixed samples. The DNA sequence obtained from pGEM-T easy/PCR products showed more than 95% identity with Bos taurus 16S rRNA gene using homology analysis. In conclusion, we suggest that the method using PCR, as performed in this study, could be useful in detecting cattle material in processed meat products. Moreover, our system could be applicable in inspection procedures to improve the verification of correct labeling for import and export processed meat products.