• 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.

• Journal of Wetlands Research
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• v.21 no.1
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• pp.57-65
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• 2019

LID(Low Impact Development) facility classified as a social infrastructure can maintain landscape sustainability and functional sustainability through continuous maintenance and management. Since LID is a natural-based solution, the sustainability can be secured through the management of weeds, wastes and vegetation. The LID facility is distributed in the city and is an infrastructure that can be managed through citizen participation because of simple maintenance. Therefore, this study was conducted to investigate the maintenance factors affecting the sustainability of the LID facilities and to suggest measures for maintenance by investigating the participation of the peoples. The factors for landscape sustainability were derived to waste and weed management. Also the factors for functional sustainability were assessed to identification and management of dead bodies and selection of applicable soil and plant species. The citizens showed high agreement of more than 80% in the questionnaires on expanding and managing LID facilities, enacting LID ordinances, and participating in the national movement. The intention to participate in LID management linked to jobs was about 64%, indicating that LID could become a job for the vulnerable. Maintenance of the LID can easily be carried out by non-specialists, which can lead to citizen participation with low cost for each facility. The maintenance cost for citizen participation can be allocated from the social infrastructure management cost reduced by LID application of the local government and the social welfare budget of the central government.

• Journal of Life Science
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• v.28 no.12
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• pp.1529-1535
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• 2018

The number of antibiotic-resistant bacteria is increasing rapidly while the discovery rate of new antibiotics is in decline. A systematic study is therefore necessary to investigate which bacteria are resistant to medically important antibiotics and how high that resistance is. To that end, this study aimed to analyze which bacteria demonstrated resistance to ampicillin, one of the currently most-widely used medical antibiotics. Water samples were collected from the Changwon-Cheon that runs through Changwon City and from the pond in front of the dormitory building at Changwon University. Hundreds of ampicillin-resistant colonies were obtained and 22 morphologically distinct examples were chosen for further study. These bacteria were identified by amplifying their 16S rRNA genes and comparing those sequences with data in GenBank. The bacteria was identified as belonging to 10 families, 12 genera, and 17 species, and all were able to grow in the presence of $50{\mu}g/ml$ ampicillin while seven showed growth at ampicillin concentrations as high as 1.5 mg/ml.

• Particle and aerosol research
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• v.14 no.4
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• pp.135-144
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• 2018

Based on a two-year measurement data, major sources for the ambient carbonaceous aerosols at the Anmyeon Global Atmosphere Watch (GAW) station were identified by using the Positive Matrix Factorization (PMF) model. The particulate matter less than or equal to $2.5{\mu}m$ in aerodynamic diameter (PM2.5) aerosols were sampled between June 2015 to May 2017 and carbonaceous species including ~80 organic compounds were analyzed. When the number of factors was 5 or 6, the performance evaluation parameters showed the best results, With 6 factor case, the characteristics of transported factors were clearer. The 6 factors were identified with various analyses including chemical characteristics and air parcel movement analysis. The 6 factors with their relative contributions were (1) anthropogenic Secondary Organic Aerosols (SOA) (10.3%), (2) biogenic sources (24.8%), (3) local biomass burning (26.4%), (4) transported biomass burning (7.3%), (5) combustion related sources (12.0%), and (6) transported sources (19.2%). The air parcel movement analysis result and seasonal variation of the contribution of these factors also supported the identification of these factors. Thus, the Anmyeon Island GAW station has been affected by both regional and local sources for the carbonaceous aerosols.

• Research in Plant Disease
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• v.25 no.3
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• pp.143-148
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• 2019

An outbreak of new disease with leaf and stem blight symptom occurred at bracken-growing fields in Namhae-gun, Gyeongsangnam-do, Korea during the last 4 years. This new disease caused significant yield losses on bracken production in this area. We have collected diseased leaves and stems showing the blight symptom in May, July, and October 2018 to investigate causal pathogens. A total of 92 fungal isolates were obtained from the diseased samples and their pathogenicity was tested on healthy bracken leaves. From the total isolates, 22 isolates were able to produce the leaf blight symptom similar to the original one found in the fields. To identify two fungal pathogens which showed higher virulence levels compared to other pathogenic isolates, we constructed phylogenetic trees using the nucleotide sequences of genes for ribosomal RNA, RNA polymerase beta subunit, beta tubulin, and internal transcribed region. Most phylogenetic trees constructed indicate that both isolates, which are identical to each other, reside in a clade of the genus Didymella and possibly similar to D. rumicicola or D. acetosellae. Nevertheless, the exact identification of these pathogens at the species level needs further investigations. This is the first report of a blight disease on bracken by Didymella sp.

• Journal of odor and indoor environment
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• v.17 no.4
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• pp.355-361
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• 2018

Mold grows more easily when humidity is higher in indoor spaces, and as such is found more often on wetted areas in housing such as walls, toilets, kitchens, and poorly managed spaces. However, there have been few studies that have specifically assessed the level of mold in the indoor spaces of water-damaged housing in the Republic of Korea. We investigated the levels of airborne mold according to the characteristics of water damage types and explored the correlation between the distribution of mold genera and the characteristics of households. Samplings were performed from January 2016 to June 2018 in 97 housing units with water leakage or condensation, or a history of flooding, and in 61 general housing units in the metropolitan and Busan area, respectively. Airborne mold was collected on MEA (Malt extract agar) at flow rate of 100 L/min for 1 min. After collection, the samples were incubated at $25^{\circ}C$ for 120 hours. The cultured samples were counted and corrected using a positive hole conversion table. The samples were then analyzed by single colony culture, DNA extraction, gene amplification, and sequencing. By type of housing, concentrations of airborne mold were highest in flooded housing, followed by water-leaked or highly condensed housings, and then general housing. In more than 50% of water-damaged housing, the level of airborne mold exceeded the guideline of Korea's Ministry of Environment ($500CFU/m^3$). Of particular concern was the fact that the I/O ratio of water-damaged housing was greater than 1, which could indicate that mold damage may occur indoors. The distribution patterns of the fungal species were as follows: Penicillium spp., Cladosporium spp. (14%), Aspergillus spp. (13%) and Alternaria spp. (3%), but significant differences of their levels in indoor spaces were not found. Our findings indicate that high levels of mold damage were found in housing with water damage, and Aspergillus flavus and Penicillium brevicompactum were more dominant in housing with high water activity. Comprehensive management of flooded or water-damaged housing is necessary to reduce fungal exposure.

• Animal Bioscience
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• v.34 no.11
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• pp.1739-1748
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• 2021

Objective: In recent years, long noncoding RNAs (lncRNAs) have been identified in many species, and some of them have been shown to play important roles in muscle development and myogenesis. However, the differences in lncRNAs between Kazakh cattle and Xinjiang brown cattle remain undefined; therefore, we aimed to confirm whether lncRNAs are differentially expressed in the longissimus dorsi between these two types of cattle and whether differentially expressed lncRNAs regulate muscle differentiation. Methods: We used RNA-seq technology to identify lncRNAs in longissimus muscles from these cattle. The expression of lncRNAs were analyzed using StringTie (1.3.1) in terms of the fragments per kilobase of transcript per million mapped reads values of the encoding genes. The differential expression of the transcripts in the two samples were analyzed using the DESeq R software package. The resulting false discovery rate was controlled by the Benjamini and Hochberg's approach. KOBAS software was utilized to measure the expression of different genes in Kyoto encyclopedia of genes and genomes pathways. We randomly selected eight lncRNA genes and validated them by quantitative reverse transcription polymerase chain reaction (RT-qPCR). Results: We found that 182 lncRNA transcripts, including 102 upregulated and 80 downregulated transcripts, were differentially expressed between Kazakh cattle and Xinjiang brown cattle. The results of RT-qPCR were consistent with the sequencing results. Enrichment analysis and functional annotation of the target genes revealed that the differentially expressed lncRNAs were associated with the mitogen-activated protein kinase, Ras, and phosphatidylinositol 3-kinase (PI3k)/Akt signaling pathways. We also constructed a lncRNA/mRNA coexpression network for the PI3k/Akt signaling pathway. Conclusion: Our study provides insights into cattle muscle-associated lncRNAs and will contribute to a more thorough understanding of the molecular mechanism underlying muscle growth and development in cattle.

• Journal of The Korean Society of Grassland and Forage Science
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• v.40 no.4
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• pp.259-264
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• 2020

The aim of this study was to investigate the feasibility of discrimination 12 different cultivar of sorghum × sudangrass hybrid (Sorghum genus) seed through near infrared spectroscopy (NIRS). The amount of samples for develop to the best discriminant equation was 360. Whole samples were applied different three spectra range (visible, NIR and full range) within 680-2500 nm wavelength and the spectrastar 2500 Near near infrared was used to measure spectra. The calibration equation for discriminant analysis was developed partial least square (PLS) regression and discrimination equation (DE) analysis. The PLS discriminant analysis model for three spectra range developed with mathematic pretreatment 1,8,8,1 successfully discriminated 12 different sorghum genus. External validation indicated that all samples were discriminated correctly. The whole discriminant accuracy shown 82 ~ 100 % in NIR full range spectra. The results demonstrated the usefulness of NIRS combined with chemometrics as a rapid method for discrimination of sorghum × sudangrass hybrid cultivar through seed.

• Mycobiology
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• v.50 no.1
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• pp.66-78
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• 2022

The identification of oleaginous yeast species capable of simultaneously utilizing xylose and glucose as substrates to generate value-added biological products is an area of key economic interest. We have previously demonstrated that the Cutaneotrichosporon dermatis NICC30027 yeast strain is capable of simultaneously assimilating both xylose and glucose, resulting in considerable lipid accumulation. However, as no high-quality genome sequencing data or associated annotations for this strain are available at present, it remains challenging to study the metabolic mechanisms underlying this phenotype. Herein, we report a 39,305,439 bp draft genome assembly for C. dermatis NICC30027 comprised of 37 scaffolds, with 60.15% GC content. Within this genome, we identified 524 tRNAs, 142 sRNAs, 53 miRNAs, 28 snRNAs, and eight rRNA clusters. Moreover, repeat sequences totaling 1,032,129 bp in length were identified (2.63% of the genome), as were 14,238 unigenes that were 1,789.35 bp in length on average (64.82% of the genome). The NCBI non-redundant protein sequences (NR) database was employed to successfully annotate 11,795 of these unigenes, while 3,621 and 11,902 were annotated with the Swiss-Prot and TrEMBL databases, respectively. Unigenes were additionally subjected to pathway enrichment analyses using the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG), Clusters of orthologous groups for eukaryotic complete genomes (KOG), and Non-supervised Orthologous Groups (eggNOG) databases. Together, these results provide a foundation for future studies aimed at clarifying the mechanistic basis for the ability of C. dermatis NICC30027 to simultaneously utilize glucose and xylose to synthesize lipids.

• Journal of Life Science
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• v.31 no.7
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• pp.671-676
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• 2021

A cDNA encoding the protein lethal (2) essential for life [l(2)efl] was cloned from Gryllus bimaculatus and named GBl(2)efl. This protein is composed of 189 amino acids, including an N-glycosylation site and 15 phosphorylation sites. Its predicted molecular mass is 21.19 kDa, with a theoretical isoelectric point of 6.2. The secondary structure of GBl(2)efl was predicted from the identification of random coils (56.08%), alpha helices (22.22%), extended strands (17.99%), and beta turns (3.7%) through sequence analyses. A homology analysis revealed that GBl(2)efl exhibited a high similarity with other species at the amino acid level, ranging from 52% to 69%. While GBl(2)efl mRNA expression was higher in the dorsal longitudinal flight muscle following a three-day starvation and in the Malpighian tubules following a one-day starvation, no changes in expression were detected in other tissues. Furthermore, tunicamycin-induced endoplasmic reticulum (ER) stress resulted in an approximately 1.8-fold higher expression in the fat body compared with the wild type.