• Korean Journal of Environmental Biology
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• v.39 no.3
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• pp.319-328
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• 2021

Tomato spotted wilt virus (TSWV) is one of the most destructive viruses worldwide, which causes severe damage to economically important crops, such as pepper and tomato. In this study, we examined the molecular and biological characterization of a TSWV isolate (SW-TO2) infecting tomato and compared it to the recently reported isolates from boxthorn, butterbur, and angelica plants. The phylogenetic analysis based on the complete genome sequences confirmed that SW-TO2 was clustered with those of isolates from boxthorn and pepper in Korea with the maximum nucleotide identities ranging from 98% to 99%. We developed the bioassay method for screening TSWV resistance and tested some commercial pepper and tomato cultivars for resistance evaluation of four isolates of TSWV. TSWV resistance was evaluated as TSWV resistance when all the following three conditions were satisfied: first, when symptoms of necrotic spots or no symptoms were present in the inoculated leaves; second, when there were no symptoms in the upper leaves; and third, when the upper leaves were negative as a result of RT-PCR diagnosis.

• Journal of the Korea Organic Resources Recycling Association
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• v.29 no.3
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• pp.27-33
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• 2021

CO I gene sequence analysis was applied to earthworms that had been used as test animals in toxicity test in Institute of Kyeongbook Agrochemicals and earthworms used as vermicomposting agents in the farm of Youngdong province to identify their species names. In terms of molecular species, the former was identified as Eisenia fetida and the latter was Eisenia andrei. Cocoons produced from Eisenia fetida was more than those from Eisenia andrei. And No. of adults developed from eggs of Eisenia fetida was more or less higher than those developed from eggs of Eisenia andrei. These results were contradictory to previous reports on two Eisenia spp.. When Eisenia fetida was crossed with Eisenia andrei, hybridized eggs were produced and adults were developed from those eggs, but cocoons and adults were much less than those from non-crossed Eisenia fetida or Eisenia andrei. This indicated that two Eisenia spp. were not distinctly different biological species because there was no complete 'reproductive isolation' between Eisenia fetida and Eisenia andrei. However, this also meant that Eisenia fetida and Eisenia andrei had already been on the tract of speciation.

• Molecules and Cells
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• v.44 no.1
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• pp.26-37
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• 2021

Human papillomaviruses (HPVs) cause cellular hyperproliferation-associated abnormalities including cervical cancer. The HPV genome encodes two major viral oncoproteins, E6 and E7, which recruit various host proteins by direct interaction for proteasomal degradation. Recently, we reported the structure of HPV18 E7 conserved region 3 (CR3) bound to the protein tyrosine phosphatase (PTP) domain of PTPN14, a well-defined tumor suppressor, and found that this intermolecular interaction plays a key role in E7-driven transformation and tumorigenesis. In this study, we carried out a molecular analysis of the interaction between CR3 of HPV18 E7 and the PTP domain of PTPN21, a PTP protein that shares high sequence homology with PTPN14 but is putatively oncogenic rather than tumor-suppressive. Through the combined use of biochemical tools, we verified that HPV18 E7 and PTPN21 form a 2:2 complex, with a dissociation constant of 5 nM and a nearly identical binding manner with the HPV18 E7 and PTPN14 complex. Nevertheless, despite the structural similarities, the biological consequences of the E7 interaction were found to differ between the two PTP proteins. Unlike PTPN14, PTPN21 did not appear to be subjected to proteasomal degradation in HPV18-positive HeLa cervical cancer cells. Moreover, knockdown of PTPN21 led to retardation of the migration/invasion of HeLa cells and HPV18 E7-expressing HaCaT keratinocytes, which reflects its protumor activity. In conclusion, the associations of the viral oncoprotein E7 with PTPN14 and PTPN21 are similar at the molecular level but play different physiological roles.

• Korean Journal of Environment and Ecology
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• v.35 no.1
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• pp.37-47
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• 2021

This study carried out the plant sociological survey of Abies nephrolepis forest in Mt. Seorak, which is in danger of deterioration due to the accelerated climate change. We examined seventy quadrats obtained from the survey and used the TWINSPAN technique to classify communities. We then performed the DCA method for the sequence analysis and analyzed the characteristics of each community. A. nephrolepis forest of Mt. Seorak is composed of four communities (A. nephrolepis-Lonicera caerulea var. edulis community, A. nephrolepis-Acer komarovii community, A. nephrolepis-Ac. pseudosieboldianum community, and A. nephrolepis-Betula costata community). Each community showed a different distribution according to location because different microenvironments are formed depending on location such as altitude and slope direction, resulting in different species composition. Each community showed differences in environmental characteristics such as altitude, rock ratio, soil characteristics, and litter layer thickness. As a result, there were significant differences between communities in the number of species and individuals, coverage, tree size, and species diversity, as well as differences in species composition. The A. nephrolepis-L. caerulea var. edulis and A. nephrolepis-Ac. komarovii communities were located in high altitude with high rock ratios and had little development of tree layer. On the other hand, the A. nephrolepis-Ac. pseudosieboldianum and A. nephrolepis-B. costata communities were relatively in low altitude with high soil ratio and had the development of tree layer with high species diversity.

• Korean Journal of Plant Taxonomy
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• v.52 no.2
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• pp.85-96
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• 2022

The plant "Hong-do-go-deul-ppae-gi" has been considered as Crepidiastrum × muratagenii, a hybrid between C. denticulatum and C. lanceolatum, based on its morphological traits and geographical distribution. To reveal the hybrid origin of Hong-do-go-deul-ppae-gi, we examined additional morphological traits of this plant and its putative parents (C. denticulatum, C. lanceolatum, C. platyphyllum) and analyzed one nuclear ribosomal internal transcribed spacer (ITS) region and four chloroplast regions (trnT-L, trnL-F, rpl16 intron, and rps16 intron). As a result of examining the morphological traits, putative hybrid individuals were classified into three types based on the habit, cauline leaf, outer phyllary, and achene beak traits. A molecular analysis found that the ITS sequences of Type 1 and Type 2 individuals showed additive species-specific sites of C. denticulatum and C. lanceolatum. Plastid sequences of Type 1 and Type 2 individuals showed C. denticulatum and C. lanceolatum sequences, respectively. However, Type 3 individuals had ITS and plastid sequences corresponding to C. denticulatum. Accordingly, Type 1 and Type 2 individuals not only share morphological traits with C. denticulatum and C. lanceolatum but also show additive species-specific sites for C. denticulatum and C. lanceolatum, and not C. platyphyllum, supporting its origin as a hybrid between C. denticulatum and C. lanceolatum. Type 3 had morphological traits similar to other hybrid types but was distinguished with respect to outer phyllaries and demonstrated some resemblance to C. denticulatum. In a molecular analysis, Type 3 was found to be identical with regard to the sequence of C. denticulatum and was judged to be an ecological variation of C. denticulatum.

• Journal of Mushroom
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• v.20 no.4
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• pp.208-217
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• 2022

Mushrooms in Naejangsan National Park between May and September of 2021 have been surveyed. In this period, a total of 4 divisions, 9 classes, 25 orders, 72 families, 171 genera, and 381 species, including 3 climate-sensitive biological indicator species were found. The order in which the most diverse array of species was observed is Agaricales, which includes 24 families, 64 genera, and 170 species. Among these, the genus Russula was dominant, with 30 species, followed by the genus Amanita with 27 species. Among the 12 grids we investigated, species diversity was greatest in grid F5, in which 56 species of mushrooms were found. In particular, a large number of ectomycorrhizal mushrooms, including Russula spp. and Lactarius spp. were recognized. We presume that the gentle slopes and the low occurrence of Sasa borealis in this area may create a favorable environment for wild mushrooms. In corroboration, some grids (e.g. F6, F8, and F10) covering steep slopes and harboring large numbers of Sasa borealis contained only 19 species. Based on DNA sequence analysis, the NJ21064 was identified as Chlorophyllum hortense, which is newly recorded in Korea.

• Journal of Marine Life Science
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• v.6 no.2
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• pp.47-57
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• 2021

In the fishery industry, global aquaculture production has stagnated due to overfishing of aquatic products, restrictions between countries, and climate change. The aquaculture suggests the possibility of a blue revolution that can be expanded in a new way. The aquaculture industry now accounts for more than half of the fishery products from the sea as a raw material for seafood for human consumption. Various latest biological research methods are being applied for the development of a sustainable aquaculture industry. Genomics has made significant progress in recent years. Since the genome sequence of Atlantic cod was sequenced in 2011, the genomes of more species have been sequenced. The genome information is providing a more robust and productive knowledge base for the aquaculture industry, including breeding and breeding of superior traits, improving disease resistance quality, and optimizing aquaculture feed and feed methods. This review looked at the status of genome analysis technology and the current status of genome research of aquaculture species. The development of genome research technology and massive genomic information is important in solving the challenges of the aquaculture industry and will help sustainable fisheries and aquaculture.

• Animal Bioscience
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• v.35 no.3
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• pp.399-409
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• 2022

Objective: Follicle-stimulating hormone (FSH) is the central hormone involved in mammalian reproduction, maturation at puberty, and gamete production that mediates its function by control of follicle growth and function. The present study investigated the mutations involved in the regulation of FSH receptor (FSHR) activation. Methods: We analyzed seven naturally-occurring mutations that were previously reported in human FSHR (hFSHR), in the context of equine FSHR (eFSHR); these include one constitutively activation variant, one allelic variant, and five inactivating variants. These mutations were introduced into wild-type eFSHR (eFSHR-wt) sequence to generate mutants that were designated as eFSHR-D566G, -A306T, -A189V, -N191I, -R572C, -A574V, and -R633H. Mutants were transfected into PathHunter EA-parental CHO-K1 cells expressing β-arrestin. The biological function of mutants was analyzed by quantitating cAMP accumulation in cells incubated with increasing concentrations of FSH. Results: Cells expressing eFSHR-D566G exhibited an 8.6-fold increase in basal cAMP response, as compared to that in eFSHR-wt. The allelic variation mutant eFSHR-A306T was not found to affect the basal cAMP response or half maximal effective concentration (EC₅₀) levels. On the other hand, eFSHR-D566G and eFSHR-A306T displayed a 1.5- and 1.4-fold increase in the maximal response, respectively. Signal transduction was found to be completely impaired in case of the inactivating mutants eFSHR-A189V, -R572C, and -A574V. When compared with eFSHR-wt, eFSHR-N191I displayed a 5.4-fold decrease in the EC₅₀ levels (3,910 ng/mL) and a 2.3-fold decrease in the maximal response. In contrast, cells expressing eFSHR-R633H displayed in a similar manner to that of the cells expressing the eFSHR-wt on signal transduction and maximal response. Conclusion: The activating mutant eFSHR-D566G greatly enhanced the signal transduction in response to FSH, in the absence of agonist treatment. We suggest that the state of activation of the eFSHR can modulate its basal cAMP accumulation.

• Korean Journal of Environmental Biology
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• v.40 no.4
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• pp.387-397
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• 2022

The germination characteristics of the resting cysts of Pheopolykrikos hartmannii collected from the southern coastal sediments of Korea were studied at different temperature conditions, and the morphology and phylogeny of the germlings were examined. The resting cysts of Ph. hartmannii were round and characterized by a red accumulation body and many arrow-like spines and could germinate at temperature of 10 to 30℃. High germination rates (>90%) were observed at 15 and 20℃, indicating that the resting cysts could act as seed populations for the bloom initiation of Ph. hartmannii in Korean coastal waters in early summer or early fall. The morphology of the germlings was generally consistent with the previous description, and an apical groove characterized by a fully enclosed loop was observed. Phylogenetic analysis based on large SubUnit (LSU) rRNA gene sequences revealed that the germlings shared an identical sequence with the Korean and American isolates of Ph. hartmannii and was a sister clade of Polykrikos species.

• Journal of the Korea Institute of Military Science and Technology
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• v.27 no.4
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• pp.507-515
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• 2024

Microbial forensics is a scientific discipline for analyzing evidence related to biological crimes by identifying the origin of microorganisms. Multiple locus variable number tandem repeat analysis(MLVA) is one of the microbiological analysis methods used to specify subtypes within a species based on the number of tandem repeat in the genome, and advances in next generation sequencing(NGS) technology have enabled in silico anlysis of full-length whole genome sequences. In this paper, we analyzed unknown samples provided by Robert Koch Institute(RKI) through The United Nations Secretary-General's Mechanism(UNSGM)'s external quality assessment exercise(EQAE) project, which we officially participated in 2023. We confirmed that the 3 unknown samples were B. anthracis through nucleic acid isolation and genetic sequence analysis studies. MLVA results on 32 loci of B. anthracis were analysed by using genome sequences obtained from NGS(NextSeq and MinION) and Sanger sequencing. The MLVA typing using short-reads based NGS platform(NextSeq) showed a high probability of causing assembly error when a size of the tandem repeats was grater than 200 bp, while long-reads based NGS platform(MinION) showed higher accuracy than NextSeq, although insertion and deletion was observed. We also showed hybrid assembly can correct most indel error caused by MinION. Based on the MLVA results, genetic identification was performed compared to the 2,975 published MLVA databases of B. anthracis, and MLVA results of 10 strains were identical with 3 unkonwn samples. As a result of whole genome alignment of the 10 strains and 3 unknown samples, all samples were identified as B. anthracis strain A4564 which is associated with injectional anthrax isolates in heroin users.