• Molecules and Cells
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• v.23 no.2
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• pp.220-227
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• 2007

The development of suitable genetic markers would be useful for defining species and delineating the species boundaries of morphologically indistinguishable sponges. In this study, genetic variation in the sequences of nuclear rDNA and the mitochondrial cytochrome c oxidase subunit 1 and 3 (CO1 and CO3) regions were compared in morphologically indistinguishable Korean Halichondriidae sponges in order to determine the most suitable species-specific molecular marker region. The maximal congeneric nucleotide divergences of Halichondriidae sponges in CO1 and CO3 are similar to those found among anthozoan cnidarians, but they are 2- to 8-fold lower than those found among genera of other triploblastic metazoans. Ribosomal internal transcribed spacer regions (ITS: ITS1 + ITS2) showed higher congeneric variation (17.28% in ITS1 and 10.29% in ITS2) than those of CO1 and CO3. Use of the guidelines for species thresholds suggested in the recent literature indicates that the mtDNA regions are not appropriate for use as species-specific DNA markers for the Halichondriidae sponges, whereas the rDNA ITS regions are suitable because ITS exhibits a low level of intraspecific variation and a relatively high level of interspecific variation. In addition, to test the reliability of the ITS regions for identifying Halichondriidae sponges by PCR, a species-specific multiplex PCR primer set was developed.

• The Plant Pathology Journal
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• v.25 no.4
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• pp.417-421
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• 2009

The analysis of the full length genome of Korean isolates of Pepper mottle virus (PepMoV) in previous study showed molecular variations and are found to be related to symptom variation and pathogenicity (Kim et al., 2009, Virus Res. 144:83-88). To fully understand the molecular variation of PepMoV in Korea, we further assessed the role of RNA recombination to biological variation and evolution of PepMoV. Full-length genome of a total of 17 Korean-PepMoV and 2 American (CA and FL) isolates were examined for possible detection of genetic recombination using different recombination detections programs and detected 5 and 8 tentative recombination events using RDP3 and Splits Tree4 programs, respectively. Interestingly, tentative recombinants detected such as isolates 57, 134 and 217 were previously identified as severe isolates and 205135 and 205136 as differentiating isolates (Kim et al., 2009, Virus Res. 144:83-88). In addition, recombination was frequently detected in the Vb isolate, the first PepMoV isolate reported in Korea, suggesting significant involvement in the evolution of PepMoV in Korea. These initial results of our recombination analyses among PepMoV isolates in Korea may serve as clues to further investigate the biological variations and evolution of PepMoV brought about by recombination.

• Mycobiology
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• v.49 no.4
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• pp.308-345
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• 2021

Lactifluus (Pers.) Roussel is an ectomycorrhizal genus that was recently recognized to be distinct from the genus Lactarius. To date, 226 Lactifluus species have been reported worldwide. Misidentification of Lactifluus species is common because of intraspecific morphological variation, cryptic diversity, and the limited number of taxonomic keys available. Molecular data are indispensable for species delimitation; a multilocus phylogenetic analysis showed that most Asian Lactifluus species are not conspecific with morphologically similar species present on other continents. In particular, Korea has misused European and North American Lactifluus names. In this study, we evaluated the taxonomy of Lactifluus in Korea using both morphological and multilocus molecular (ITS, nrLSU, rpb1, and rpb2) data. We examined 199 Lactifluus specimens collected between 1980 and 2016, and a total of 24 species across the four Lactifluus subgenera were identified. All Korean species are distinct and clearly separated from European and North American species. Five taxa corresponded to previously described species from Asia and the remaining 19 taxa are confirmed as new species. Herein, we provide keys to the Korean Lactifluus species within their subgenera, molecular phylogenies, a summary of diversity, and detailed description of the new species.

• Molecules and Cells
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• v.42 no.7
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• pp.512-522
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• 2019

Chromosomes located in the nucleus form discrete units of genetic material composed of DNA and protein complexes. The genetic information is encoded in linear DNA sequences, but its interpretation requires an understanding of three-dimensional (3D) structure of the chromosome, in which distant DNA sequences can be juxtaposed by highly condensed chromatin packing in the space of nucleus to precisely control gene expression. Recent technological innovations in exploring higher-order chromatin structure have uncovered organizational principles of the 3D genome and its various biological implications. Very recently, it has been reported that large-scale genomic variations may disrupt higher-order chromatin organization and as a consequence, greatly contribute to disease-specific gene regulation for a range of human diseases. Here, we review recent developments in studying the effect of structural variation in gene regulation, and the detection and the interpretation of structural variations in the context of 3D chromatin structure.

• Molecules and Cells
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• v.25 no.4
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• pp.494-503
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• 2008

Many therapeutic glycoproteins have been successfully generated in plants. Plants have advantages regarding practical and economic concerns, and safety of protein production over other existing systems. However, plants are not ideal expression systems for the production of biopharmaceutical proteins, due to the fact that they are incapable of the authentic human N-glycosylation process. The majority of therapeutic proteins are glycoproteins which harbor N-glycans, which are often essential for their stability, folding, and biological activity. Thus, several glyco-engineering strategies have emerged for the tailor-making of N-glycosylation in plants, including glycoprotein subcellular targeting, the inhibition of plant specific glycosyltranferases, or the addition of human specific glycosyltransferases. This article focuses on plant N-glycosylation structure, glycosylation variation in plant cell, plant expression system of glycoproteins, and impact of glycosylation on immunological function. Furthermore, plant glyco-engineering techniques currently being developed to overcome the limitations of plant expression systems in the production of therapeutic glycoproteins will be discussed in this review.

• Animal Systematics, Evolution and Diversity
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• v.35 no.4
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• pp.182-185
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• 2019

In this study, cytochrome c oxidase subunit I(COI) sequences of 17 individuals from six Korean diogenid species(i.e., 2 Areopaguristes japonicus, 4 A. nigroapiculus, 3 Paguristes digitalis, 4 P. ortmanni, 3 Diogenes edwardsii, and 1 Ciliopagurus kempfi) were determined and analyzed. The DNA barcoding results of this study were consistent with the morphological identification of these six species. Interspecific variations of COI sequences within six Korean diogenid species exceeded the minimum interspecific variation of diogenid hermit crabs in previous studies. Little intraspecific variation exists except for P. digitalis. This study should facilitate further molecular taxonomy of East Asian diogenids.

• Korean journal of applied entomology
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• v.54 no.4
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• pp.303-310
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• 2015

The diamondback moth, Plutella xylostella, overwinters in some protected areas in Korea. Using a sex pheromone trap, the adults were monitored since the occurrence of the overwintering populations. In Andong, P. xylostella exhibited four adult peaks in a year. Biological characters, such as cold tolerance, insecticide susceptibility, and developmental rate, were analyzed and showed a significant variation among different local overwintering populations. Population genetic variation was assessed with molecular markers, in which the initial high genetic variation among the overwintering populations decreased with the progress of seasons. These results suggests that there may be a significant migration of P. xylostella to decrease the genetic variation among the different local populations that are different in biological characters.

• Journal of Microbiology and Biotechnology
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• v.8 no.5
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• pp.490-496
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• 1998

Random amplified polymorphic DNA (RAPD) markers were used to survey genetic variability among 34 Botrytis cinerea isolates from nine different host plants in Korea. For RAPD analysis, 115 arbitrary decamer primers were initially screened for polymorphic major DNA bands with 11 representative B. cinerea isolates. Eleven primers that initially detected polymorphisms were tested a second time with additional 23 isolates of B. cinerea as well as one isolate of Botrytis squamosa as an outgroup. The RAPD analyses revealed that all isolates except one showed different molecular phenotypes. Dendrograms obtained from dissimilarity matrices using the unweighted paired group method of arithmetic means (UPGMA) showed the 36.4% to 90.0% similarity among all B. cinerea isolates. The B. squamosa isolate showed the least similarity to all B. cinerea isolates. The cluster analyses indicated no correlation among all the characteristics examined including molecular phenotypes, host and geographic origins, year of isolation, or pathogenicity. The RAPD data suggest that a high level of genetic variation exists among Korean populations of B. cinerea and it seems to be caused by heterokaryosis among preexisting molecular phenotypes.

• Journal of Species Research
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• v.10 no.1
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• pp.46-56
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• 2021

Diatoms have been used in examining water quality and environmental change in freshwater systems. Here, we analyzed molecular profiling of seasonal diatoms in the Han River, Korea, using the hypervariable region of 18S V1-V3 rRNA and pyrosequencing. Physicochemical data, such as temperature, DO, pH, and nutrients showed the typical seasonal pattern in a temperate region. In addition, cell counts and chlorophyll-a, were recorded at high levels in spring compared to other seasons, due to the diatom bloom. Metagenomic analysis showed a seasonal variation in the phytoplankton community composition, with diatoms as the most frequently detected in spring (83.8%) and winter (69.7%). Overall, diatom genera such as Stephanodiscus, Navicula, Cyclotella, and Discostella were the most frequent in the samples. However, a large number of unknown Thalassiosirales diatoms were found in spring (35.5%) and winter (36.3%). Our molecular profiling revealed a high number of diatom taxa compared to morphological observation. This is the first study of diatoms in the Han River using molecular approaches, providing a valuable reference for future study on diatoms-basis environmental molecular monitoring and ecology.

• Molecules and Cells
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• v.27 no.1
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• pp.119-123
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• 2009

Porcine endogenous retroviruses (PERVs) gamma1 in the pig genome have the potential to act as harmful factors in xenotransplantation (pig-to-human). Long terminal repeats (LTRs) are known to be strong promoter elements that could control the transcription activity of PERV elements and the adjacent functional genes. To investigate the transcribed PERV gamma1 LTR elements in pig tissues, bioinformatic and experimental approaches were conducted. Using RT-PCR amplification and sequencing approaches, 69 different transcribed LTR elements were identified. And 69 LTR elements could be divided into six groups (15 subgroups) by internal variation including tandem repeated sequences, insertion and deletion (INDEL). Remarkably, all internal variations were indentified in U3 region of LTR elements. Taken together, the identification and characterization of various PERV LTR transcripts allow us to extend our knowledge of PERV and its transcriptional study.