Developing Environmental DNA Marker and Monitoring Application for the Loggerhead Turtle, Green Turtle, and Chinese Sea Snake in Korean Waters

Jaejin Park,Il-Hoon Kim,Min-Woo Park,Il-Kook Park,Jongsun Kim,Daesik Park 한국양서ㆍ파충류학회 2024 한국양서·파충류학회 학술대회 Vol.2024 No.07

Korea is located at the edge of the distribution range of most marine reptiles, so the population density is very low across species. In addition, there are no nesting sites, making the application of various research methods limited and inefficient. To overcome these limitations, we have developed environmental DNA (eDNA) markers for the three most common marine reptiles in Korea (loggerhead turtle, green turtle, and Chinese sea snake), and performed pilot monitoring. The development of species-specific markers was sequentially conducted through program-based marker development and various validation processes using tissue DNA, aquarium eDNA, and foreign marine eDNA. The developed markers were applied for monitoring at 10 (loggerhead turtles), 17 (green turtles) and 10 (Chinese sea snake) sites in the Korea. The three sets of species-specific eDNA markers (Crcr29, Chmy11, Lase_cytb_10) were successfully developed and verified. In the monitoring application of loggerhead turtle marker in 2023, eDNA was detected from two sites in Jeju. Green turtle eDNA was detected from seven sites. . The Chinese sea snake eDNA was detected from six sites and the detection frequency was the highest in November. Considering that monitoring of Korean marine reptiles has been conducted only through passive methods (i.e. sampling bycatch, stranded, or dead individuals) to date, our developed eDNA markers and monitoring methods provide active study methods and can be a very useful in future survey and related research of marine reptiles.

Predation of the Japanese keelback (Hebius vibakari Boie, 1826) by the Slender racer (Orientocoluber spinalis Peters, 1866)

Park, Il-Kook,Park, Jaejin,Park, Jiho,Min, Seong-Hun,Grajal-Puche, Alejandro,Park, Daesik The Ecological Society of Korea 2021 Journal of Ecology and Environment Vol.45 No.1

Background: The Slender racer (Orientocoluber spinalis Peters, 1866) has recently been reclassified to the new genus Orientocoluber from Hierophis. Ecological knowledge of this species is limited due to its highly mobile behavior. On 17 July 2020, we captured a female O. spinalis on Oeyeon Island, Boryeong-si, Republic of Korea, and collected its feces for a diet analysis. We observed snake scales from the collected feces and subsequently determined the prey species through morphological and molecular methods. Results: We initially hypothesized that the extracted fecal sample scales belonged to H. vibakari, due to their thin keel and rhombus shape. We also amplified H. vibakari DNA from the extracted fecal sample using Illumina sequencing methods. Our morphological and molecular results suggest that O. spinalis predates H. vibakari on Oeyeon Island. Conclusion: This is the first report of O. spinalis predating another snake species, ophiophagy, and implies that H. vibakari may be a crucial prey item for O. spinalis on Oeyeon Island.

First detection of ranavirus in a wild population of Dybowski's brown frog (Rana dybowskii) in South Korea

Park, Jaejin,Grajal-Puche, Alejandro,Roh, Nam-Ho,Park, Il-Kook,Ra, Nam-Yong,Park, Daesik The Ecological Society of Korea 2021 Journal of Ecology and Environment Vol.45 No.1

Background: Ranavirus is an emerging infectious disease which has been linked to mass mortality events in various amphibian species. In this study, we document the first mass mortality event of an adult population of Dybowski's brown frogs (Rana dybowskii), in 2017, within a mountain valley in South Korea. Results: We confirmed the presence of ranavirus from all collected frogs (n = 22) via PCR and obtained the 500 bp major capsid protein (MCP) sequence from 13 individuals. The identified MCP sequence highly resembled Frog virus 3 (FV3) and was the same haplotype of a previously identified viral sequence collected from Huanren brown frog (R. huanrenensis) tadpoles in South Korea. Human habitat alteration, by recent erosion control works, may be partially responsible for this mass mortality event. Conclusion: We document the first mass mortality event in a wild Korean population of R. dybowskii. We also suggest, to determine if ranavirus infection is a threat to amphibians, government officials and researchers should develop continuous, country-wide, ranavirus monitoring programs of Korean amphibian populations.

First Report of Epibiont Barnacle Attached to Chinese Sea Krait (Laticauda semifasciata) in the Republic of Korea

Min-Woo Park,Jaejin Park,Il-Kook Park,Jongsun Kim,Il-Hun Kim,Daesik Park 한국양서ㆍ파충류학회 2022 한국양서·파충류학회 학술대회 Vol.2022 No.07

To date, more than 1,000 species of barnacles have been reported, and some barnacles spend most of their life attached to marine vertebrates. As their distribution patterns are as diverse as their species diversity, they can be important data for understanding the behavior or ecology of host organisms as epibiont. However, in Korea, further research is needed because studies on the relationship between barnacles and marine vertebrates are still insufficient. In this study, we report a barnacle attached to a Chinese sea krait (Laticauda semifasciata) caught in the sea of Korea. On September 7, 2016, in the sea near Udo Island, Jeju (33.56°N, 127.02°E), a total of 22 barnacles were found to attach to one L. semifasciata caught. We identified these barnacles as Conchoderma virgatum based on their morphological characteristics such as distinctive feature of the capitulum and peduncle, the number of capitulum with reduced 5 plates, and the number of 2 scutum in Y-shape. There are a total of two types of barnacles (C. virgatum and Platylepas ophiophilus) that have been reported to attach to L. semifasciata in the world. Attached barnacles, including the C. virgatum, may restrict the behavior of sea kraits, cause dysecdysis, or cause the secondary infection through epithelial tissue damage. Therefore, further study on the relationship between barnacles and marine reptiles might be needed.

Identifying the Source Rookery of Green Turtles (Chelonia mydas) Found in Feeding Grounds around the Korea Peninsula

Min-Woo Park,Il-Hun Kim,Jaejin Park,Changho Yi,Min-Seop Kim,In-Young Cho,Il-Kook Park,Hee-Jin Noh,Sang Hee Hong,Daesik Park 한국양서ㆍ파충류학회 2024 한국양서·파충류학회 학술대회 Vol.2024 No.07

Assessing the genetic composition and origin of green turtle populations, which are migratory marine species, is known to be an effective way to increase their conservation efficiency. This study showed the genetic composition and origin of the green turtle population found in Korea and evaluated the genetic composition, diversity, and origin of the Korean feeding population. Genetic analysis was performed using partial mitochondrial control region (CR) sequences, and mixed stock analysis (MSA) was performed to confirm the origin. A total of 10 CR haplotypes were identified in Korean feeding population and all of them previously reported in the green turtle breeding population in Japan. In the haplotype network analysis, six haplotypes were grouped with the Japan clade, three haplotypes were grouped with the Indo-Pacific clade, and one haplotype was grouped with the Central South Pacific clade. In the MSA results, the Korean feeding population is largely contributed by the rookeries in Ogasawara Island (OGA) and Central Ryukyu Island (CRI). In regard to season, maturity, and specific feeding region groups, individuals found in summer and the Jeju feeding region had the highest contribution of OGA, and found in fall and the East Sea feeding region had the highest contribution of CRI. The results of analysis by maturity group showed no significant differences. Our results showed that the origin of Korean green sea turtle feeding population is mainly from Japan's MU, and have genetic orgin from Japan, Indo-Pacific, and Central South Pacific clades. Population conservation efforts in Korea will not only affect the nearby Japanese breeding population, but also affect Indo-Pacific region. International collaboration with Japan as well as the countries in Northeast Asia and Southeast Asia must develop for green turtle conservation.

FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors.

Park, Jongsun,Park, Jaejin,Jang, Suwang,Kim, Seryun,Kong, Sunghyung,Choi, Jaeyoung,Ahn, Kyohun,Kim, Juhyeon,Lee, Seungmin,Kim, Sunggon,Park, Bongsoo,Jung, Kyongyong,Kim, Soonok,Kang, Seogchan,Lee, Yon Oxford University Press 2008 Bioinformatics Vol.24 No.7

<P>Genomes of more than 60 fungal species have been sequenced to date, yet there has been no systematic approach to analyze fungal transcription factors (TFs) kingdom widely. We developed a standardized pipeline for annotating TFs in fungal genomes. Resulting data have been archived in a new database termed the Fungal Transcription Factor Database (FTFD). In FTFD, 31,832 putative fungal TFs, identified from 62 fungal and 3 Oomycete species, were classified into 61 families and phylogenetically analyzed. The FTFD will serve as a community resource supporting comparative analyses of the distribution and domain structure of TFs within and across species.</P>

First Record of Laticauda semifasciata (Reptilia: Squamata: Elapidae: Laticaudinae) from Korea

Jaejin Park,Il-Hun Kim,Kyo-Sung Koo,Daesik Park 한국동물분류학회 2016 Animal Systematics, Evolution and Diversity Vol.32 No.2

The Chinese sea snake Laticauda semifasciata (Reinwardt in Schlegel, 1837) is newly reported from Korean waters based on three specimens collected from Jeju Island, Korea, in August, September, and November 2015. This is the first time that the genus Laticauda and subfamily Laticaudinae has been reported from Korean waters. The subfamily Laticaudinae has ventrals that are four to five times wider than the adjacent dorsals, which are unlike the ventrals that are similar or up to two times wider than adjacent dorsals in the subfamily Hydrophiinae. Laticauda semifasciata is distinct from other species because it has three prefrontals and its rostrals are horizontally divided into two. As the result of this report, four species (L. semifasciata, Hydrophis (Pelamis) platurus, Hydrophis cyanocinctus, and H. melanocephalus) of sea snakes have been reported in Korean waters.

Roles of Forkhead-box Transcription Factors in Controlling Development, Pathogenicity, and Stress Response in Magnaporthe oryzae

Park, Jaejin,Kong, Sunghyung,Kim, Seryun,Kang, Seogchan,Lee, Yong-Hwan The Korean Society of Plant Pathology 2014 Plant Pathology Journal Vol.30 No.2

Although multiple transcription factors (TFs) have been characterized via mutagenesis to understand their roles in controlling pathogenicity and infection-related development in Magnaporthe oryzae, the causal agent of rice blast, if and how forkhead-box (FOX) TFs contribute to these processes remain to be characterized. Four putative FOX TF genes were identified in the genome of M. oryzae, and phylogenetic analysis suggested that two of them (MoFKH1 and MoHCM1) correspond to Ascomycota-specific members of the FOX TF family while the others (MoFOX1 and MoFOX2) are Pezizomycotina-specific members. Deletion of MoFKH1 (${\Delta}Mofkh1$) resulted in reduced mycelial growth and conidial germination, abnormal septation and stress response, and reduced virulence. Similarly, ${\Delta}Mohcm1$ exhibited reduced mycelial growth and conidial germination. Conidia of ${\Delta}Mofkh1$ and ${\Delta}Mohcm1$ were more sensitive to one or both of the cell cycle inhibitors hydroxyurea and benomyl, suggesting their role in cell cycle control. On the other hand, loss of MoFOX1 (${\Delta}Mofox1$) did not show any noticeable changes in development, pathogenicity, and stress response. Deletion of MoFOX2 was not successful even after repeated attempts. Taken together, these results suggested that MoFKH1 and MoHCM1 are important in fungal development and that MoFKH1 is further implicated in pathogenicity and stress response in M. oryzae.

Chondrogenesis of human umbilical cord-derived mesenchymal stem cells in vitro by TGFβ3 and BMP6

Jaejin Cho, Eu Gene Park, TaeJun Cho, Soon-Keun Kwon, Dong-Sup Lee 충북대학교 동물의학연구소 2012 Journal of Biomedical and Translational Research Vol.13 No.4

Human umbilical cord is easy to obtain because it is discarded after birth, so that ethical issues can be avoided. Chondrogenesis studies using MSCs from bone marrow, cord blood, and adipose have indicated that TGFβ3 and BMP6 stimulate chondrogenesis. Therefore, we investigated chondrogenesis of hUC-MSCs on TGFβ3, BMP6, and combination of the two growth factors. We initiated chondrogenesis of cells by application of physical forces to form 3D cell clusters. After initiation, we designated four experimental groups for differentiation of cells, as follows: control, 10 ng/mL TGFβ3, 100 ng/mL BMP6, and the combination of 5 ng/mL TGFβ3 and 50 ng/mL BMP6. For analysis of chondrogenesis, GAG contents, mRNA expression, histological analysis and immunohistochemistry (IHC) were performed. For analysis of GAG contents, GAG assay was performed and RT-PCR was performed for determination of chondrogenic markers. Histological analysis was performed through safranin O, alcian blue, and IHC was performed using collagen type I and II. GAG contents were increased 184% by TGFβ3, 147% by BMP6, and 189% by the combination of TGFβ3 and BMP6, compared to control. The growth factors improved collagen II and aggrecan expression; in particular, TGFβ3 and BMP6 showed a synergistic effect, compared to only TGFβ3 or BMP6 treated. The results of histological and IHC analysis indicated that chondrogenic differentiation in TGFβ3 and the combination of TGFβ3 and BMP6 showed more cartilage deposition. In conclusion, TGFβ3 and BMP6 differentiated hUC-MSCs into chondrogenic clusters of the combination treatment of the two growth factors showed more efficient chondrogenic ability.

Bidirectional-Genetics Platform, a Dual-Purpose Mutagenesis Strategy for Filamentous Fungi

Park, Jaejin,Lee, Yong-Hwan American Society for Microbiology 2013 EUKARYOTIC CELL Vol.12 No.11

<P>Rapidly increasing fungal genome sequences call for efficient ways of generating mutants to translate quickly gene sequences into their functions. A reverse genetic strategy via targeted gene replacement (TGR) has been inefficient for many filamentous fungi due to dominant production of undesirable ectopic transformants. Although large-scale random insertional mutagenesis via transformation (i.e., forward genetics) facilitates high-throughput uncovering of novel genes of interest, generating a huge number of transformants, which is necessary to ensure the likelihood of mutagenizing most genes, is time-consuming. We propose a new strategy, entitled the <U>Bi</U>directional-<U>G</U>enetics (BiG) platform, which combines both forward and reverse genetic strategies by recycling ectopic transformants derived from TGR as a source for random insertional mutants. The BiG platform was evaluated using the rice blast fungus <I>Magnaporthe oryzae</I> as a model. Over 10% of >1,000 <I>M. oryzae</I> ectopic transformants, generated during disruption of specific genes, displayed abnormality in vegetative growth, pigmentation, and/or asexual reproduction. In this pool of putative mutants, we isolated insertional mutants with mutations in three genes involved in histidine biosynthesis (<I>MoHIS5</I>), vegetative growth (<I>MoVPS74</I>), or conidiophore formation (<I>MoFRQ</I>) (where “<I>Mo</I>” indicates “<I>M. oryzae</I>”), supporting the utility of this platform for systematic gene function studies.</P>