• Animal Bioscience
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• v.37 no.3
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• pp.461-470
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• 2024

Objective: The objective of this study was to investigate the genetic diversity, population structure and whole-genome selection signatures of Luxi cattle to reveal its genomic characteristics in terms of meat and carcass traits, skeletal muscle development, body size, and other traits. Methods: To further analyze the genomic characteristics of Luxi cattle, this study sequenced the whole-genome of 16 individuals from the core conservation farm in Shandong region, and collected 174 published genomes of cattle for conjoint analysis. Furthermore, three different statistics (pi, F_st, and XP-EHH) were used to detect potential positive selection signatures related to selection in Luxi cattle. Moreover, gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed to reveal the potential biological function of candidate genes harbored in selected regions. Results: The results showed that Luxi cattle had high genomic diversity and low inbreeding levels. Using three complementary methods (pi, F_st, and XP-EHH) to detect the signatures of selection in the Luxi cattle genome, there were 2,941, 2,221 and 1,304 potentially selected genes identified, respectively. Furthermore, there were 45 genes annotated in common overlapping genomic regions covered 0.723 Mb, including PLAG1 zinc finger (PLAG1), dedicator of cytokinesis 3 (DOCK3), ephrin A2 (EFNA2), DAZ associated protein 1 (DAZAP1), Ral GTPase activating protein catalytic subunit alpha 1 (RALGAPA1), mediator complex subunit 13 (MED13), and decaprenyl diphosphate synthase subunit 2 (PDSS2), most of which were enriched in pathways related to muscle growth and differentiation and immunity. Conclusion: In this study, we provided a series of genes associated with important economic traits were found in positive selection regions, and a scientific basis for the scientific conservation and genetic improvement of Luxi cattle.

• The Journal of Korean Society of Virology
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• v.30 no.3
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• pp.211-217
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• 2000

Nef is a lentiviral protein involved in pathogenesis of AIDS, but its molecular mechanism of action remains incompletely understood. Here we report the isolation of the interacting protein with the HIV-1 Nef, using the yeast two hybrid system for expression cloning. One of the positive colonies was selected as the final candidate for the interacting protein gene. The nucleotide sequencing revealed that this interacting protein is Human Ikaros/LyF-1. This protein interacted with the C-terminal region of Nef specifically in yeast system, not with the N-terminal region. This interaction was also confirmed by in vitro binding assay.

• Molecules and Cells
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• v.39 no.5
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• pp.382-388
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• 2016

Inherited peripheral neuropathies (IPN), which are a group of clinically and genetically heterogeneous peripheral nerve disorders including Charcot-Marie-Tooth disease (CMT), exhibit progressive degeneration of muscles in the extremities and loss of sensory function. Over 70 genes have been reported as genetic causatives and the number is still growing. We prepared a targeted gene panel for IPN diagnosis based on next generation sequencing (NGS). The gene panel was designed to detect mutations in 73 genes reported to be genetic causes of IPN or related peripheral neuropathies, and to detect duplication of the chromosome 17p12 region, the major genetic cause of CMT1A. We applied the gene panel to 115 samples from 63 non-CMT1A families, and isolated 15 pathogenic or likelypathogenic mutations in eight genes from 25 patients (17 families). Of them, eight mutations were unreported variants. Of particular interest, this study revealed several very rare mutations in the SPTLC2, DCTN1, and MARS genes. In addition, the effectiveness of the detection of CMT1A was confirmed by comparing five 17p12-nonduplicated controls and 15 CMT1A cases. In conclusion, we developed a gene panel for one step genetic diagnosis of IPN. It seems that its time- and cost-effectiveness are superior to previous tiered-genetic diagnosis algorithms, and it could be applied as a genetic diagnostic system for inherited peripheral neuropathies.

• Journal of Korean Society of Rural Planning
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• v.2 no.1
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• pp.79-90
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• 1996

In recent year, construction of national infrastructure, variations of agricultural environment, urbanization of rural life-style, and other things have influenced on rural area. Therefore, its landscapes have been changed rapidly. As a result of it, rural landscape should be controlled with amenity and totality. That is a rural amenity control planning. The purposes of this study is to consider characters of rural settlement area, the directions of landscape control planning as an environmental planning, the structure of rural landscape, the process of rural landscape control planning, and its frameworks. Main viewpoints of landscape control planning in rural settlement are as follows; the using of regional resources, the harmony of surrounding environments, the harmony of natural ecology, locating of facilities, the development of new landscape material, maintenance of sequencing, symbolizing, unificating, and opening, the using of natural/regional materials, the using of waterfront, the making of stories.

• BMB Reports
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• v.33 no.3
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• pp.276-278
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• 2000

The postsynaptic density (PSD), a large protein complex beneath the postsynaptic membrane, is notorious for its 'stickiness'. In order to understand the molecular composition of the PSD fraction, a 17 kDa protein band was isolated by electroelution from SDS-geis, and its partial amino acid sequence was determined from HPLC-purified tryptic peptides of the protein. Surprisingly, the amino acid sequence was identical to that of the previously reported 17 kDa isoform of the myelin basic protein (MBP), an essential protein in CNS myelin formation. Since the protein band represented ~2% of the total proteins in the 1 % n-octyl glucoside-insoluble PSD fraction, these results indicate that a significant amount of the 17 kDa isoform of MBP is tightly associated with the PSD during preparation of the PSD fraction.

• BMB Reports
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• v.40 no.5
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• pp.801-804
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• 2007

The products of reactions catalyzed by Methanococcus. jannaschii (Mj) aldolase using various substrates were identified by gas chromatography (GC). Although Mj aldolase is considered a fuculose-1-phosphate aldolase based on homology searching after gene sequencing, it has not been proven to be a fuculose-1-phosphate aldolase based on its reaction products. Mj aldolase was found to catalyze reactions between glycoaldehyde or D, L-glyceraldehyde and DHAP (dihydroxyacetone phosphate). Before performing GC the ketoses produced were converted into peracetylated alditol derivatives by sequential reactions, i.e., dephosphorylation, $NaBH_4$ reduction, and acetylation. By comparing the GC data of final products with those of standard alditol samples, it was found that the enzymatic reactions with glycoaldehyde, D-glyceraldehyde, and D, L-glyceraldehyde produced D-ribulose-1-phosphate, D-psicose-1-phosphate, and a mixture of D-psicose and L-tagatose-1-phosphate, respectively. These results provide direct evidence that Mj aldolase is a fuculose-1-phosphate aldolase.

• Journal of Animal Science and Technology
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• v.63 no.6
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• pp.1411-1422
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• 2021

Lactobacillus acidophilus is a gram-positive, microaerophilic, and acidophilic bacterial species. L. acidophilus strains in the gastrointestinal tracts of humans and other animals have been profiled, but strains found in the canine gut have not been studied yet. Our study helps in understanding the genetic features of the L. acidophilus C5 strain found in the canine gut, determining its adaptive features evolved to survive in the canine gut environment, and in elucidating its probiotic functions. To examine the canine L. acidophilus C5 genome, we isolated the C5 strain from a Korean dog and sequenced it using PacBio SMRT sequencing technology. A comparative genomic approach was used to assess genetic relationships between C5 and six other strains and study the distinguishing features related to different hosts. We found that most genes in the C5 strain were related to carbohydrate transport and metabolism. The pan-genome of seven L. acidophilus strains contained 2,254 gene families, and the core genome contained 1,726 gene families. The phylogenetic tree of the core genes in the canine L. acidophilus C5 strain was very close to that of two strains (DSM20079 and NCFM) from humans. We identified 30 evolutionarily accelerated genes in the L. acidophilus C5 strain in the ratio of non-synonymous to synonymous substitutions (dN/dS) analysis. Five of these thirty genes were associated with carbohydrate transport and metabolism. This study provides insights into genetic features and adaptations of the L. acidophilus C5 strain to survive the canine intestinal environment. It also suggests that the evolution of the L. acidophilus genome is closely related to the host's evolutionary adaptation process.

• Parasites, Hosts and Diseases
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• v.55 no.1
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• pp.95-98
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• 2017

Fasciola hepatica is a trematode that causes zoonosis, mainly in cattle and sheep, and occasionally in humans. Few recent studies have determined the infection status of this fluke in Korea. In August 2015, we collected 402 samples of freshwater snails at Hoenggye-ri (upper stream) and Suha-ri (lower stream) of Song-cheon (stream) in Daegwalnyeong-myeon, Pyeongchang-gun in Gangwon-do (Province) near many large cattle or sheep farms. F. hepatica infection was determined using PCR on the nuclear ribosomal internal transcribed spacer 2 (ITS-2). Among the 402 samples, F. hepatica 1TS-2 marker was detected in 6 freshwater snails; thus, the overall prevalence in freshwater snails was 1.5%. The prevalence varied between collection areas, ranging from 0.0% at Hoenggye-ri to 2.9% at Suha-ri. However, F. gigantica ITS-2 was not detected in the 6 F. hepatica-positive samples by PCR. The nucleotide sequences of the 6 F. hepatica ITS-2 PCR-positive samples were 99.4% identical to the F. hepatica ITS-2 sequences in GenBank, whereas they were 98.4% similar to F. gigantica ITS-2 sequences. These results indicated that the prevalence of F. hepatica in snail intermediate hosts was 1.5% in Gangwon-do, Korea; however the prevalence varied between collection areas. These results may help us to understand F. hepatica infection status in natural environments.

• Journal of Genetic Medicine
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• v.15 no.2
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• pp.107-109
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• 2018

X-linked Charcot-Marie-Tooth disease type 1 (CMTX1) is caused by the mutation in GJB1 gene, characterized by the transient central nervous system involvement and long standing peripheral polyneuropathy which does not fulfill the criteria of demyelination or axonopathy. We describe a 37-year-old man with progressive bilateral leg weakness since his early teen. He suffered transient right hemiparesis, followed by quadriparesis at 14 years of age. When we examined him at 37 years of age, he presented a distal muscle weakness on lower extremities with a sensory symptom. The nerve conduction study demonstrated a motor conduction velocity between 26 and 49 m/s. The whole exome sequencing revealed a novel variant c.136 G>A in GJB1. This report will raise awareness in this rare disease, which is frequently misdiagnosed early in its course.

• Microbiology and Biotechnology Letters
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• v.39 no.2
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• pp.97-103
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• 2011

Two Gram positive bacterial strains, designated strain GC-1 and GC-4, were isolated from coastal seawater near Jeju Island in the Republic of Korea. The two strains were identified as members of the genus Bacillus, based on 16S rRNA gene sequencing and data for physiological characteristics analyses. A subtle difference in physiological and genotypical characteristics has led us to designate the strains GC-1 and GC-4. The strain GC-1 showed a 99.91% similarity in 16S rRNA gene sequencing with B. tequiliensis and B. subtilis subsp. inaquosorum and the strain GC-4 showed a 100% similarity in 16S rRNA gene sequencing with those of B. altitudinis, B. stratosphericus, and B. aerophilus. However, both strains exhibited different physiological and genotypical characteristics in many aspects from those of their phylogenetically closest neighbors listed above, which implies that genus Bacillus has diversified into various species during its evolutionary process.