• Korean Journal of Poultry Science
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• v.48 no.3
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• pp.111-122
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• 2021

Recently, interleukin 34 (IL-34) was identified as the second functional ligand for macrophage colony-stimulating factor receptor (M-CSFR). IL-34 functions similarly to M-CSF through its binding to the M-CSFR. There is still insufficient information on IL-34 in chickens, which has until now been reported only through predicted sequences and not through experimental research. Thus, to confirm its expression and to determine its potent biological activity, several chicken lines and cell lines were used. Cloning of recombinant chicken IL-34 and M-CSF genes was performed to investigate their modulatory effects on proinflammatory cytokine expression in vitro. The expression levels of IL-34, M-CSF, and M-CSFR genes were upregulated in broiler chickens with leg dysfunction (cause unknown). However, IL-34 was downregulated in most pathogen-stimulated tissues. M-CSFR expression was enhanced by recombinant IL-34 and M-CSF proteins in vitro. IFN-γ expression was enhanced by recombinant IL-34, but not by M-CSF. However, IL-12 expression was not regulated in any of the treated cells, and IL-1β was decreased in all tissues. These results indicate that IL-34 and M-CSF have roles in both the classical and alternative macrophage activation pathways. Collectively, our findings demonstrate the expression of IL-34 in chickens for pathogenic trials, both in vitro and in vivo. Our results suggest that the IL-34 protein plays a role in both pro- and anti-inflammatory functions in macrophages. Therefore, further research is needed to determine the cytokines or chemokines that can be induced by IL-34 and to further elucidate the functions of IL-34 in the inflammatory pathway.

• Korean Journal of Environment and Ecology
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• v.35 no.5
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• pp.503-524
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• 2021

A largemouth bass (Micropterus salmoides) is an ecosystem disturbance fish species at the highest rank in the aquatic ecosystem, causing a serious imbalance in freshwater ecosystems. Although various attempts have been made to eradicate and control largemouth bass, no effective measures were found. Therefore, it is necessary to find an approach to maximize the effective population reduction based on the unique characteristics of largemouth bass. This study used the transcriptome analysis to derive 182,887 unigene contigs and select 12 types of final target sequences for applying the CRISPR/Cas9 system in the genes of IZUMO1 and Zona pellucida sperm-binding protein, which are proteins involved in sperm-egg recognition. After synthesizing 12 types of sgRNA capable of recognizing each target sequence, 12 types of Cas9-sgRNA ribonucleoprotein (RNP) complexes to be used in subsequent studies were prepared. This study searched the protein-coding gene of sperm-egg through the Next Generation Sequencing (NGS) and edited genes through the CRISPR/Cas9 system to induce infertile individuals that produced reproductive cells but could not form fertilized eggs. Through such a series of processes, it successfully established a composition development process for largemouth bass. It is judged that this study contributed to securing the valuable basic data for follow-up studies to verify its effect for the management of ecological disturbances without affecting the habitat of other endemic species in the same water system with the largemouth bass.

• Genes and Genomics
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• v.40 no.11
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• pp.1169-1180
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• 2018

Cave shrimps from the genera Typhlatya, Stygiocaris and Typhlopatsa (TST complex) comprises twenty cave-adapted taxa, which mainly occur in the anchialine environment. Anchialine habitats may undergo drastic environmental fluctuations, including spatial and temporal changes in salinity, temperature, and dissolved oxygen content. Previous studies of crustaceans from anchialine caves suggest that they have possessed morphological, behavioral, and physiological adaptations to cope with the extreme conditions, similar to other cave-dwelling crustaceans. However, the genetic basis has not been thoroughly explored in crustaceans from anchialine habitats, which can experience hypoxic regimes. To test whether the TST shrimp-complex hypoxia adaptations matched adaptive evolution of mitochondrial OXPHOS genes. The 13 OXPHOS genes from mitochondrial genomes of 98 shrimps and 1 outgroup were examined. For each of these genes was investigated and compared to orthologous sequences using both gene (i.e. branch-site and Datamonkey) and protein (i.e. TreeSAAP) level approaches. Positive selection was detected in 11 of the 13 candidate genes, and the radical amino acid changes sites scattered throughout the entire TST complex phylogeny. Additionally, a series of parallel/convergent amino acid substitutions were identified in mitochondrial OXPHOS genes of TST complex shrimps, which reflect functional convergence or similar genetic mechanisms of cave adaptation. The extensive occurrence of positive selection is suggestive of their essential role in adaptation to hypoxic anchialine environment, and further implying that TST complex shrimps might have acquired a finely capacity for energy metabolism. These results provided some new insights into the genetic basis of anchialine hypoxia adaptation.

• Genes and Genomics
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• v.40 no.12
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• pp.1319-1329
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• 2018

SSRs were successfully isolated from the Perilla crop in our current study, and used to analyze Perilla accessions from East Asia. Analyses of the clear genetic diversity and relationship for Perilla crop still remain insufficient. In this study, 40 new simple sequence repeat (SSR) primer sets were developed from RNA sequences using transcriptome analysis. These new SSR markers were applied to analyze the diversity, relationships, and population structure among 35 accessions of the two cultivated types of Perilla crop and their weedy types. A total of 220 alleles were identified at all loci, with an average of 5.5 alleles per locus and a range between 2 and 10 alleles per locus. The MAF (major allele frequency) per locus varied from 0.229 to 0.943, with an average of 0.466. The average polymorphic information content (PIC) value was 0.603, ranging from 0.102 to 0.837. The genetic diversity (GD) ranged from 0.108 to 0.854, with an average of 0.654. Based on population structure analysis, all accessions were divided into three groups: Group I, Group II and the admixed group. This study demonstrated the utility of new SSR analysis for the study of genetic diversity and population structure among 35 Perilla accessions. The GD of each locus for accessions of cultivated var. frutescens, weedy var. frutescens, cultivated var. crispa, and weedy var. crispa were 0.415, 0.606, 0.308, and 0.480, respectively. Both weedy accessions exhibited higher GD and PIC values than their cultivated types in East Asia. The new SSR primers of Perilla species reported in this study may provide potential genetic markers for population genetics to enhance our understanding of the genetic diversity, genetic relationship and population structure of the cultivated and weedy types of P. frutescens in East Asia. In addition, new Perilla SSR primers developed from RNA-seq can be used in the future for cultivar identification, conservation of Perilla germplasm resources, genome mapping and tagging of important genes/QTLs for Perilla breeding programs.

• The Plant Pathology Journal
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• v.35 no.4
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• pp.381-388
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• 2019

For several years, temperatures in the Korean peninsula have gradually increased due to climate change, resulting in a changing environment for growth of crops and vegetables. An associated consequence is that emerging species of insect vector have caused increased viral transmission. In Jeju Island, Korea, occurrences of viral disease have increased. Here, we report characterization of five newly collected turnip mosaic virus (TuMV) isolates named KBJ1, KBJ2, KBJ3, KBJ4 and KBJ5 from a survey on Jeju Island in 2017. Full-length cDNAs of each isolate were cloned into the pJY vector downstream of cauliflower mosaic virus 35S and bacteriophage T7 RNA polymerase promoters. Their fulllength sequences share 98.9-99.9% nucleotide sequence identity and were most closely related to previously reported Korean TuMV isolates. All isolates belonged to the BR group and infected both Chinese cabbage and radish. Four isolates induced very mild symptoms in Nicotiana benthamiana but KBJ5 induced a hypersensitive response. Symptom differences may result from three amino acid differences uniquely present in KBJ5; Gly(382)Asp, Ile(891)Val, and Lys(2522)Glu in P1, P3, and NIb, respectively.

• Journal of Animal Science and Technology
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• v.60 no.12
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• pp.32.1-32.10
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• 2018

Background: Necdin (NDN), a member of the melanoma antigen family showing imprinted pattern of expression, has been implicated as causing Prader-Willi symptoms, and known to participate in cellular growth, cellular migration and differentiation. The region where NDN is located has been associated to QTLs affecting reproduction and early growth in cattle, but location and functional analysis of the molecular mechanisms have not been established. Methods: Here we report the sequence variation of the entire coding sequence from 72 samples of cattle, yak, buffalo, goat and sheep, and discuss its variation in Bovidae. Median-joining network analysis was used to analyze the variation found in the species. Synonymous and non-synonymous substitution rates were determined for the analysis of all the polymorphic sites. Phylogenetic analysis were carried out among the species of Bovidae to reconstruct their relationships. Results: From the phylogenetic analysis with the consensus sequences of the studied Bovidae species, we found that only 11 of the 26 nucleotide changes that differentiate them produced amino acid changes. All the SNPs found in the cattle breeds were novel and showed similar percentages of nucleotides with non-synonymous substitutions at the N-terminal, MHD and C-terminal (12.3, 12.8 and 12.5%, respectively), and were much higher than the percentage of synonymous substitutions (2.5, 2.6 and 4.9%, respectively). Three mutations in cattle and one in sheep, detected in heterozygous individuals were predicted to be deleterious. Additionally, the analysis of the biochemical characteristics in the most common form of the proteins in each species show very little difference in molecular weight, pI, net charge, instability index, aliphatic index and GRAVY (Table 4) in the Bovidae species, except for sheep, which had a higher molecular weight, instability index and GRAVY. Conclusions: There is sufficient variation in this gene within and among the studied species, and because NDN carry key functions in the organism, it can have effects in economically important traits in the production of these species. NDN sequence is phylogenetically informative in this group, thus we propose this gene as a phylogenetic marker to study the evolution and conservation in Bovidae.

• Korean Journal of Microbiology
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• v.55 no.1
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• pp.69-73
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• 2019

During screening of microbes for compounds having cosmetic benefits, we isolated Marinobacter salarius HL2708#2 from lava seawater on Jeju Island, Republic of Korea. The complete genome sequence was determined. Strain HL27080#2 features a circular chromosome of 4,304,603 bp with 57.21% G+C content and a 244,163 bp plasmid with 53.14% G+C. There were 4,180 protein coding sequences identified, along with 49 transfer RNA and 18 ribosomal RNA noncoding genes. The genome harbored genes for the utilization of alcohol, maltose/starch, and monosaccharide as sole carbon sources. Genes responsible for halophilic characteristics and heavy metal resistance could be annotated, as well as aromatic and alkane hydrocarbons. Contrary to the prior report that M. salarius is negative for nitrate and nitrite reduction, nitrate/nitrite reductase along with nitrate/nitrate transporters and nitronate monooxygenase were evident, suggesting that strain HL2708#2 may be able to denitrify extracellular nitroalkenes to ammonia.

• Journal of Navigation and Port Research
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• v.42 no.6
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• pp.421-426
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• 2018

With regard to LED lighting devices which have currently been commercialized, LED operating sequences are being sold in a fixed state. In such a state, the external environmental factors are not taken into consideration as only the illumination environment application is considered. Currently, it is difficult to create an optimal lighting environment which can adapt to changes in external environmental factors in the ship. Therefore, it was concluded that there is a need to input the external environment value so that the optimal illumination value can be reflected in real time in order to adapt more organically and actively to the change of external environmental factors. In this paper, we used a microprocessor as an integrated management system for environmental data that changes in real time according to existing external environmental factors. In addition, a controller capable of lighting control of RGB LED module by combining fuzzy inference system. For this, a fuzzy control algorithm is designed and a fuzzy control system is constructed. The distance and the illuminance value from the external environment element are input to the sensor, and these values are converted to the optimum illumination value through the fuzzy control algorithm, and are expressed through the dimming control of the RGB LED module and the practical effectiveness of the fuzzy control system is confirmed.

• Composites Research
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• v.32 no.5
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• pp.216-221
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• 2019

Piecewise integrated composite (PIC) beam has different stacking sequences for several regions with respect to their superior load-resisting capabilities. On the interest of current research is to improve bending characteristics of PIC beam, with assigning specific stacking sequence to a specific region with the help of machine learning techniques. 240 elements of from the FE model were chosen to be reference points. Preliminary FE analysis revealed triaxialities at those regularly distributed reference points to obtain learning data creation of machine learning. Triaxiality values catagorise the type of loading i.e. tension, compression or shear. Machine learning model was formulated by learning data as well as hyperparameters and proper load fidelity was suggested by tuned values of hyperparameters, however, comparatively higher nonlinearity intensive region, such as side face of the beam showed poor load fidelity. Therefore, irregular distribution of reference points, i.e., dense reference points were distributed in the severe changes of loading, on the contrary, coarse distribution for rare changes of loading, was prepared for machine learning model. FE model with irregularly distributed reference points showed better load fidelity compared to the results from the model with regular distribution of reference points.

• Journal of Korean Tunnelling and Underground Space Association
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• v.21 no.1
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• pp.137-153
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• 2019

Estimating tunnel construction time and costs are the most fundamental part of a tunnel project planning, which has been generally assessed on a deterministic basis until now. In this paper, excavation cycle time was investigated for two road tunnels and one subway tunnel, and the results were compared with the Standard of Construction Estimate (SE), which is made for the estimation of construction time and cost in a design stage. The results show that the difference in cycle time between SE and actual cycle time is 50%, 7% and 31% respectively for the three tunnels, which means that SE does not reflect practical operation time. The major reasons of the difference are skilled level of tunneling workers, the change of operation sequences for more effective operations, much more complicated working atmosphere in a tunnel than the assumption of SE etc. Finally, even though the results can not be generalized since investigated tunnels are only 3, but it is thought that SE needs to be upgraded into the model able to consider quite common situations through additional tunnel investigation and studies in the future.