• Korean Journal of Microbiology
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• v.54 no.3
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• pp.188-199
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• 2018

Genomic epidemiology exploits various basic microbial research areas. High-throughput sequencing technologies dramatically have been expanding the number of microbial genome sequences available. Abundant genomic data provide an opportunity to perform strain typing more effectively, helping identify microbial species and strains at a higher resolution than ever before. Genomic epidemiology needs to find antimicrobial resistance genes in addition to standard genome annotations. Strain typing and antimicrobial resistance gene finding are static aspects of genomic epidemiology. Finding which hosts infected which other hosts requires the inference of transient transmission routes among infected hosts. The strain typing, antimicrobial resistance gene finding, and transmission tree inference would allow for better surveillance of microbial infectious diseases, which is one of the ultimate goals of genomic epidemiology. Among several high-throughput sequencing technologies, genomic epidemiology will benefit from the more portability and shorter sequencing time of the Oxford Nanopore Technologies's MinION, the third-generation sequencing technology. Here, this study reviewed computational methods for quantifying antimicrobial resistance genes and inferring disease transmission trees. In addition, the MinION's applications to genomic epidemiology were discussed.

• ALGAE
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• v.32 no.1
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• pp.57-66
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• 2017

The red alga Gracilaria vermiculophylla, a species native to the waters of Korea and Japan, has invaded marine coastal areas of Europe and the Americas, thriving in conditions that differ from those of its native habitat. In recent years, G. vermiculophylla has been discovered in the Long Island Sound (LIS) estuary growing alongside the native congener Gracilaria tikvahiae. The goal of this study was to determine whether the two strains of G. vermiculophylla from different regions of the world have evolved genetic differences (i.e., ecotypic differentiation) or if the physiological performance of the strains simply reflects phenotypic plasticity. Two strains of G. vermiculophylla (isolated in Korea and LIS) and a strain of the LIS native G. tikvahiae were grown for four weeks under temperatures ranging from 20 to $34^{\circ}C$ using a temperature gradient table (all other environmental conditions were kept constant). At the end of each week, wet weight of each sample was recorded, and thalli were reduced to the original stocking density of $1gL^{-1}$ (excess biomass was preserved for tissue carbon and nitrogen analysis). Generally, the growth rates of Korean G. vermiculophylla > LIS G. vermiculophylla > G. tikvahiae. After one week of growth G. tikvahiae grew 9.1, 12.0, 9.4, and 0.2% $d^{-1}$, at temperatures of 20, 24, 29, and $34^{\circ}C$, respectively, while G. vermiculophylla (LIS) grew 6.6, 6.2, 5.7, and 3.6% $d^{-1}$. G. vermiculophylla (Korea) grew 15.4, 22.9, 23.2, and 10.1% $d^{-1}$, much higher than the two strains currently inhabiting the LIS. On average, the LIS G. vermiculophylla strain contained 4-5% DW N, while the Korean strain and G. tikvahiae had more modest levels of 2-3% N DW. However, tissue N content declined as temperature increased in LIS and Korean G. vermiculophylla. The non-native haplotype may have evolved genetic differences resulting in lower growth capacity while concentrating significantly more nitrogen, giving the non-native a competitive advantage.

• Journal of Life Science
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• v.18 no.4
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• pp.435-440
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• 2008

Random amplified polymorphic DNA (RAPD) markers were used to identify the genetic diversities among and within varieties and landraces of Rehmannia glutinosa. Polymorphic and reproducible bands were produced by 10 primers out of total 20 primers used in the experiment. In RAPD analysis of the 11 genotypes, 64 fragments out of 73 amplified genomic DNA fragments were polymorphic which represented an average 6.4 polymorphic fragments per primer. Number of amplified fragments with random primers ranged from 2 (OPA-1) to 13 (OPA-11) and varied in size from 200 bp to 1,400 bp. Especially, OPA-10, OPA-11 and OPA-19 primers showed specific bands for varieties of Korea Jiwhang and Jiwhang il ho, which could be useful for discriminating from other varieties and landraces of R. glutinosa. Percentage polymorphism ranged from a minimum of 50% (OPA-1) to a maximum of 100% (OPA-11), with an average of 87.7%. Similarity coefficients were higher in the genotypes of Korea Jiwhang and Jiwhang il ho than in other populations. In cluster analysis, genotypes of Korea Jiwhang, Jiwhang il ho, and Japanese accession were separated from those of other varieties and landraces. Average of genetic diversity within the population $(H_S)$ was 0.110, while average of total genetic diversity $(H_T)$ was 0.229. Across all RAPD makers the $G_{ST}$ value was 0.517, indicating that about 52% of the total genetic variation could be explained by RAPDs differences while the remaining 48% might be attributable to differences among samples. Consequently, RAPD analysis was useful method to discriminate different populations such as domestic varieties and other landraces. The results of the present study will be used to understand the population and evolutionary genetics of R. gllutinosa.

• Korean Journal of Poultry Science
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• v.46 no.3
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• pp.185-191
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• 2019

Nucleoporin 210 (Nup210) is associated with several physiological processes including muscle and neural cell differentiation, autoimmune diseases, and peripheral T cell homeostasis. Chicken Nup210 (chNup210) gene was originally identified as one of the differentially expressed genes (DEGs) in the kidney tissues of chicken. To elucidate the role of Nup210 in metabolic disease of chicken, we studied the molecular characteristics of chNup210 and analyzed its gene expression under the stimulation of Toll-like receptor 3 (TLR3) ligands. The Nup210 genomic DNA and amino acid sequences of various species including fowls, fishes, and mammals were retrieved from the Ensemble database and subjected to bioinformatics analyses. The expression of Nup210 from several chicken tissues was probed through qRT-PCR, and chicken fibroblast DF-1 cell line was used to determine the change in expression of chNup210 after stimulation with TLR3 ligand, polyinosinic-polycytidylic acid (poly (I:C)). The chNup210 gene was highly expressed in chicken lung and spleen tissues. Although highly conserved among the species, chNup210 was evolutionary clustered in the same clade as that of duck compared to other mammals. Furthermore, this study revealed that chNup210 is expressed in TLR3 signaling pathway and provides fundamental information on Nup210 expression in chicken. Future studies that offer insight into the involvement of chNup210 in the chicken innate immune response against viral infection are recommended.

• Korean journal of applied entomology
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• v.61 no.1
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• pp.91-100
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• 2022

Ticks are the arthropod vector capable of transmitting diverse pathogens, which include bacteria, viruses, protozoan and fungi. Ticks are able to survive under stressful environmental conditions. One of evolutionary outcomes of these obligatory hematophagous arthropods is the survival for extended periods of time without a blood meal during off-host periods. Water conservation biology and heat tolerance have allowed ticks to thrive even under high temperatures and low relative humidity, thus they have become highly successful arthropods as they are distributed globally. Tick osmoregulatory physiology is a complex mechanism, which involves multiple osmoregulatory organs (salivary glands, Malpighian tubules, hindgut and synganglion) for the acquisition and excretion of water and ions. Blood feeding and water vapor uptake have been early reported as the primary passages for ixodid tick to acquire water. Recently, we have learned that ticks can actively drink environmental water allowing hydration. The acquired water can be traced to the salivary glands (type I acini) and the midgut diverticula. This opens new avenues for tick management through the delivery of toxic agents into their drinking water, in addition to an alternative strategy for the study of tick physiology. Here we address the osmoregulatory physiology in the ixodid ticks as a potential target physiological mechanism for tick control. We discuss the implications of water drinking behavior for tick control through the delivery of toxic agents and discuss the dermal excretion physiology as an additional pathway to induce tick dehydration and tick death.

• Korean Journal of Plant Taxonomy
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• v.53 no.1
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• pp.32-37
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• 2023

Spiraea prunifolia f. simpliciflora Nakai is a perennial shrub widely used for horticultural and medicinal purposes. We simultaneously obtained the complete plastid genome (plastome) and nuclear ribosomal gene transcription units, 45S nuclear ribosomal DNA (nrDNA) and 5S nrDNA of S. prunifolia f. simpliciflora, using Illumina short-read data. The plastome is 155,984 bp in length with a canonical quadripartite structure consisting of 84,417 bp of a large single-copy region, 18,887 bp of a short single-copy region, and 26,340 bp of two inverted repeat regions. Overall, a total of 113 genes (79 protein-coding genes, 30 tRNAs, and four rRNAs) were annotated in the plastome. The 45S nrDNA transcription unit is 5,848 bp in length: 1,809 bp, 161 bp, and 3,397 bp for 18S, 5.8S, and 26S, respectively, and 261 bp and 220 bp for internal transcribed spacer (ITS) 1 and ITS 2 regions, respectively. The 5S nrDNA unit is 512 bp, including 121 bp of 5S rRNA and 391 bp of intergenic spacer regions. Phylogenetic analyses showed that the genus Spiraea was monophyletic and sister to the clade of Sibiraea angustata, Petrophytum caespitosum and Kelseya uniflora. Within the genus Spiraea, the sections Calospira and Spiraea were monophyletic, but the sect. Glomerati was nested within the sect. Chamaedryon. In the sect. Glomerati, S. prunifolia f. simpliciflora formed a subclade with S. media, and the subclade was sister to S. thunbergii and S. mongolica. The close relationship between S. prunifolia f. simpliciflora and S. media was also supported by the nrDNA phylogeny, indicating that the plastome and nrDNA sequences assembled in this study belong to the genus Spiraea. The newly reported complete plastome and nrDNA transcription unit sequences of S. prunifolia f. simpliciflora provide useful information for further phylogenetic and evolutionary studies of the genus Spiraea, as well as the family Rosaceae.

• Journal of Microbiology and Biotechnology
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• v.34 no.2
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• pp.457-466
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• 2024

Cellobiose dehydrogenases (CDHs) are a group of enzymes belonging to the hemoflavoenzyme group, which are mostly found in fungi. They play an important role in the production of acid sugar. In this research, CDH annotated from the actinobacterium Cellulomonas palmilytica EW123 (CpCDH) was cloned and characterized. The CpCDH exhibited a domain architecture resembling class-I CDH found in Basidiomycota. The cytochrome c and flavin-containing dehydrogenase domains in CpCDH showed an extra-long evolutionary distance compared to fungal CDH. The amino acid sequence of CpCDH revealed conservative catalytic amino acids and a distinct flavin adenine dinucleotide region specific to CDH, setting it apart from closely related sequences. The physicochemical properties of CpCDH displayed optimal pH conditions similar to those of CDHs but differed in terms of optimal temperature. The CpCDH displayed excellent enzymatic activity at low temperatures (below 30℃), unlike other CDHs. Moreover, CpCDH showed the highest substrate specificity for disaccharides such as cellobiose and lactose, which contain a glucose molecule at the non-reducing end. The catalytic efficiency of CpCDH for cellobiose and lactose were 2.05 × 10⁵ and 9.06 × 10⁴ (M^-1 s^-1), respectively. The result from the Fourier-transform infrared spectroscopy (FT-IR) spectra confirmed the presence of cellobionic and lactobionic acids as the oxidative products of CpCDH. This study establishes CpCDH as a novel and attractive bacterial CDH, representing the first report of its kind in the Cellulomonas genus.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.19 no.3
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• pp.601-613
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• 2018

This study aims to find out the types of convergence types between devices/technology and artifact in smart city space. The main contents of the research are in-depth analysis on the convergence change of ET, IT, and ET+IT in a smart city. First, the devices/technology and artifacts through 31 cases study are found out below. There are 92 artifacts and 134 devices/technologies (ET:83, IT:51). Second, the convergence change between devices/technology and artifacts is evolved by 7 types. Type 1, the Evolutionary ET type of ET-centric, is Period 1 (Separation fusion between ET and IT), Period 2 (ET-centric fusion), and Period 3 (Growth IT and ET+IT fusion of ET-centric). Type 2, the Advanced ET type of ET+IT-centric, is Period 1 (ET+IT fusion), Period 2 (Advanced ET of ET+IT-centric), and Period 3 (Hyper-advanced ET of ET+IT-centric). Type 3, the All-in-One type of ET+IT, is Period 1 (Separation fusion between ET and IT), Period 2 (Mixed fusion between ET and IT), and Period 3 (All-in-One fusion of ET and IT). Type 4, the Advanced type of IT-centric, is Period 1 (Development of IT-centric), Period 2 (Advanced IT-centric), and Period 3 (Hyper-advanced IT-centric). Types 5 and 6, the Advanced together type of ET+IT, is Period 1 (Developed IT of ET+IT-centric), Period 2 (Advanced IT of ET+IT-centric), and Period 3 (Hyper-advanced IT of ET+IT-centric). Type 7, the Advanced IT type of ET+IT-centric, is Period 1 (ET+IT fusion), Period 2 (Sub-fusion of ET, Advanced IT), and Period 3 (Sub-fusion of ET, Hyper-advanced IT). This study results are going to expect making new types of convergence through further study.

• Korean Journal of Environment and Ecology
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• v.31 no.4
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• pp.381-396
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• 2017

Understanding species distribution plays an important role in conservation as well as evolutionary biology. In this study, we applied a species distribution model to predict hotspot areas and habitat characteristics for endangered herpetofauna species in South Korea: the Korean Crevice Salamander (Karsenia koreana), Suweon-tree frog (Hyla suweonensis), Gold-spotted pond frog (Pelophylax chosenicus), Narrow-mouthed toad (Kaloula borealis), Korean ratsnake (Elaphe schrenckii), Mongolian racerunner (Eremias argus), Reeve's turtle (Mauremys reevesii) and Soft-shelled turtle (Pelodiscus sinensis). The Kori salamander (Hynobius yangi) and Black-headed snake (Sibynophis chinensis) were excluded from the analysis due to insufficient sample size. The results showed that the altitude was the most important environmental variable for their distribution, and the altitude at which these species were distributed correlated with the climate of that region. The predicted distribution area derived from the species distribution modelling adequately reflected the observation site used in this study as well as those reported in preceding studies. The average AUC value of the eigh species was relatively high ($0.845{\pm}0.08$), while the average omission rate value was relatively low ($0.087{\pm}0.01$). Therefore, the species overlaying model created for the endangered species is considered successful. When merging the distribution models, it was shown that five species shared their habitats in the coastal areas of Gyeonggi-do and Chungcheongnam-do, which are the western regions of the Korean Peninsula. Therefore, we suggest that protection should be a high priority in these area, and our overall results may serve as essential and fundamental data for the conservation of endangered amphibian and reptiles in Korea.

• Horticultural Science & Technology
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• v.34 no.2
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• pp.305-313
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• 2016

Brassica juncea (2n = 4x = 36, AABB genome, 1,068 Mb) is a U's triangle species and an amphidiploid derivative of B. rapa and B. nigra. Fifteen varieties were used to study the ITS (internal transcribed spacer) regions of ribosomal DNA and MITEs (miniature inverted-repeat transposable elements) with a view of developing specific molecular markers. ITSs and MITEs are an excellent resource for developing DNA markers for genomics and evolutionary studies because most of them are stably inherited and present in high copy numbers. The ITS (ITS1 and ITS2) sequence was compared with the consensus sequence of B. rapa and B. nigra. Variation in ITS1 created two separate groups among 15 varieties, with 10 varieties in one group and 5 in the other. Phylogenetic analysis revealed two major clusters for those 10 and 5 varieties. Among the 160 different MITE primers used to evaluate the selected 15 varieties of B. juncea, 70 were related to the Stowaway, 79 to the Tourist, 6 to the hAT, and 5 to the Mutator super-families of MITEs. Of 160 markers examined, 32 were found to be polymorphic when fifteen different varieties of B. juncea were evaluated. The variety 'Blackgat' was different from the other mustard varieties with respect to both phenotype and genotype. The diversity of 47 additional accessions could be verified using eight selected molecular markers derived from MITE family sequences. The polymorphic markers identified in this study can be used for varietal classification, variety protection, and other breeding purposes.