• The Plant Pathology Journal
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• v.38 no.6
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• pp.629-636
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• 2022

Colletotrichum species is known as the major causal pathogen of red pepper anthracnose in Korea and various groups of fungicides are registered for the management of the disease. However, the consistent use of fungicides has resulted in the development of resistance in many red pepper-growing areas of Korea. Effective management of the occurrence of fungicide resistance depends on constant monitoring and early detection. Thus, in this study, various methods such as agar dilution method (ADM), gene sequencing, allele-specific polymerase chain reaction (PCR), and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) were applied for the detection of benzimidazole resistance among 24 isolates of Colletotrichum acutatum s. lat. and Colletotrichum gloeosporioides s. lat. The result of the ADM showed that C. gloeosporioides s. lat. was classified into sensitive and resistant isolates to benomyl while C. acutatum s. lat. was insensitive at ≥1 ㎍/ml of benomyl. The sequence analysis of the β-tubulin gene showed the presence of a single nucleotide mutation at the 198th amino acid position of five isolates (16CACY14, 16CAYY19, 15HN5, 15KJ1, and 16CAYY7) of C. gloeosporioides s. lat. Allele-specific PCR and PCR-RFLP were used to detect point mutation at 198th amino acid position and this was done within a day unlike ADM which usually takes more than one week and thus saving time and resources that are essential in the fungicide resistance management in the field. Therefore, the molecular techniques established in this study can warrant early detection of benzimidazole fungicide resistance for the adoption of management strategies that can prevent yield losses among farmers.

• Journal of Practical Agriculture & Fisheries Research
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• v.24 no.3
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• pp.5-14
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• 2022

Trichoderma is known as pathogen caused serious green mold disease on commercial production. T. pleuroti and T. pleuroticola were common species in various mushroom media. Many strains of T. pleuroti, known as aggressive species causing major economic losses in Korea, showed benomyl resistance. Accurate identification and detection of Trichoderma species associated with oyster mushrooms is very important for disease control. We developed species-specific primers for T. pleuroticola, T. pleuroti, T. harzianum, and T. atroviride based on species-specific fragments isolated from amplified fragment length polymorphism analysis. PCR products corresponding to the predicted fragment of 500bp, 230bp, 180bp, and 410bp were amplified from T. pleuroticola, T. pleuroti, T. harzianum, and T. atroviride, respectively. Multiplex PCR assay using species-specific primers quickly and accurately identified and detected T. pleuroti from mushroom media in which various species co-exist. Our results can be useful for the effective control of mushroom disease.

• Steel and Composite Structures
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• v.48 no.6
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• pp.693-708
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• 2023

Composite beams, two materials joined together, have become more common in structural engineering over the past few decades because they have better mechanical and structural properties. The shear connectors between their layers exhibit some deformability with finite stiffness, resulting in interfacial shear slip, a phenomenon known as partial shear interaction. Such a partial shear interaction contributes significantly to the composite beams. To provide precise predictions of the geometric nonlinear behavior shown by two-layered composite beams with interfacial shear slips, a robust analytical model has been developed that incorporates the influence of significant displacements. The application of a higher-order beam theory to the two material layers results in a third-order adjustment of the longitudinal displacement within each layer along the depth of the beam. Deformable shear connectors are employed at the interface to represent the partial shear interaction by means of a sequence of shear connectors that are evenly distributed throughout the beam's length. The Von-Karman theory of large deflection incorporates geometric nonlinearity into the governing equations, which are then solved analytically using the Navier solution technique. Suggested model exhibits a notable level of agreement with published findings, and numerical outputs derived from finite element (FE) model. Large displacement substantially reduces deflection, interfacial shear slip, and stress values. Geometric nonlinearity has a significant impact on beams with larger span-to-depth ratio and a greater degree of shear connector deformability. Potentially, the analytical model can accurately predict the geometric nonlinear responses of composite beams. The model has a high degree of generality, which might aid in the numerical solution of composite beams with varying configurations and shear criteria.

• Animal Bioscience
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• v.36 no.4
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• pp.671-678
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• 2023

Objective: Previous studies isolated the thermophilic ammonium-tolerant (TAT) bacterium Bacillus sp. TAT105 that grew in composting swine manure with the assimilation of ammonium nitrogen and reduced ammonia emissions during composting. Those studies also investigated the potential for applications of TAT105 to composting. It was observed that the concentration of TAT bacteria, phylogenetically close to TAT105, increased during composting. The objectives of this study were to identify the phylogenetic placement of these TAT bacteria and investigate their distribution in various composts. Methods: The phylogenetic placement of TAT105 was examined based on the sequence of 16S ribosomal RNA gene. The genomic DNA homology between TAT105 and the type strains of bacterial species that were phylogenetically close to TAT105 were examined by DNA-DNA hybridization. Moreover, the tolerances of these strains to NH₄Cl and NaCl were analyzed using a cultivation method. Concentrations of TAT bacteria in various composts were evaluated using an agar medium specific to TAT bacteria and polymerase chain reaction followed by restriction fragment length polymorphism analysis. Results: TAT105 was most closely related to Bacillus thermolactis and Bacillus kokeshiiformis. Many variants of these species have been detected in various environments, including composts. The type strains of these species displayed TAT characteristics that were similar to those of TAT105. Among the composts examined in this study, TAT bacteria were detected at high concentrations (10⁵ to 10⁹ colony forming units per gram of dry matter) in most of the composts made from cattle manure, swine manure, bark, and excess sludge. Conclusion: TAT bacteria comprised B. thermolactis, B. kokeshiiformis, and their phylogenetically close relatives. They were considered to be adaptable to composting of some certain materials, and a favorable target for searching for strains with some useful function that could be applied to composting of these materials.

• Animal Bioscience
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• v.37 no.8
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• pp.1367-1376
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• 2024

Objective: Parathyroid hormone like hormone (PTHLH), as an essential factor for bone growth, is involved in a variety of physiological processes. The aim of this study was to explore the role of PTHLH gene in the growth of antlers. Methods: The coding sequence (CDS) of PTHLH gene cDNA was obtained by cloning in sika deer (Cervus nippon), and the bioinformatics was analyzed. The quantitative real-time polymerase chain reaction (qRT-PCR) was used to analyze the differences expression of PTHLH mRNA in different tissues of the antler tip at different growth periods (early period, EP; middle period, MP; late period, LP). Results: The CDS of PTHLH gene was 534 bp in length and encoded 177 amino acids. Predictive analysis results revealed that the PTHLH protein was a hydrophilic protein without transmembrane structure, with its secondary structure consisting mainly of random coil. The PTHLH protein of sika deer had the identity of 98.31%, 96.82%, 96.05%, and 94.92% with Cervus canadensis, Bos mutus, Oryx dammah and Budorcas taxicolor, which were highly conserved among the artiodactyls. The qRT-PCR results showed that PTHLH mRNA had a unique spatio-temporal expression pattern in antlers. In the dermis, precartilage, and cartilage tissues, the expression of PTHLH mRNA was extremely significantly higher in MP than in EP, LP (p<0.01). In the mesenchyme tissue, the expression of PTHLH mRNA in MP was significantly higher than that of EP (p<0.05), but extremely significantly lower than that of LP (p<0.01). The expression of PTHLH mRNA in antler tip tissues at all growth periods had approximately the same trend, that is, from distal to basal, it was first downregulated from the dermis to the mesenchyme and then continuously up-regulated to the cartilage tissue. Conclusion: PTHLH gene may promote the rapid growth of antler mainly through its extensive regulatory effect on the antler tip tissue.

• Journal of the Korean Society of Fisheries and Ocean Technology
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• v.14 no.1
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• pp.15-36
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• 1978

Underwater sounds of some fishes and crabs were analyzed in the laboratory. The behavioral responses to the playback sounds of their feeding and croaking sound were investigated. The samples used in the experiment were as follows: Nibea albiflora, seriola quinqueradiata, Navodon modestus, Fugu xanthopterus, chrysophrys major, Scylla serrata, Telmessus acutidens, Charybdis japonica, and Portunus trituberculatus. The feeding and croaking sounds of the samples were recorded by a tape recorder through a hydrophone in an anechoic aquarium. The sound intensity level was measured by means of a sound level meter at an anechoic chamber. The frequency, intensity and wave form of various sounds were analyzed with an analyzing system consisting of a 1/3 octave filter set, a high speed level recorder, an amplifier, an octave band analyzer and an oscilloscope. The most successful recording was edited into a sequence of sound track which repeats sound emitting for 5 to 7 seconds after pausing for 5 to 7 seconds. The sequence was then reproduced into an anechoic aquarium through the under water speaker. The experimental anechoic aquarium used for the sample fishes was divided into the four sections with any three screens selected from 40$\times$40mm, 60$\times$60mm, 80$\times$80mm and 100$\times$100mm mushes according to the species of the fishes, besides that for crabs were not sectioned. The results of the investigation are as follows: 1. Of the feeding sound of fish, the frequency of wave from of the sound produced by Nibea albiflora and seriola quinqucradiata was 125～250Hz, that by Navodon modestus 63～125Hz, and that by Fugu xanthopterus 400～500Hz. The pressure level of the feeding sound produced by Nibea albiflora and Seriola quinqueradiata was 56～62db, that by Navodon modestus 57～59db, and that by Fugu xanthopterus 60～64db. 2. Of the croaking sound of Nibea albiflora, the frequency of the sound was 125～250Hz almost equivalent to that of feeding sound, and the pressure level was 62～63db, slightly higher than that of feeding sound. 3. Of the croaking sounds of crabs, the frequency of the sound produced by scylla serrata was 125～250Hz, that by Charybdis japonica and Telmessus acutidens 500～1,000Hz, and that by Portunus trituberculatus 250～500Hz. The pressure level of the croaking sound by Scylla serrata was 68～70db, and that by Charybdis japonica, Telmessus acutidens and Portuens trituberculatus 50～62db. 4. Phonotactic responses of Nibea albiflora and Seriola quinqueradiata to the feeding sounds produced by their own species, the same body length were conspicuous with the phonotactic index of 56～87%, but that of Navodon modestus, Chrysophrys major and Fugu xanthopterus were hardly recognized. 5. Phonotactic responses of the sample fishes to the sinusoidal sound with the frequency range of 50 to 9,000 Hz were observed not conspicuous. 6. Phonotactic responses of Portunus trituberculatus to the croaking sounds produced by their own species was varied in the range of 40～100%, according to the carapace length and the sex.

• Journal of Animal Science and Technology
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• v.50 no.6
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• pp.753-762
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• 2008

The primers for RT-PCR and RACE-PCR were designed by aligning the pig genomic sequence and the human complement factor B(CFB) coding sequence(CDS) from the GenBank. Each PCR product was amplified in pig cDNA and sequencing was carried out. The CDS length of pig CFB gene was determined to be 2298 bp. In addition, the pig CDS was more longer than human and mouse orthologs because of insertion and deletion. The identities of porcine nucleotide sequences with those of human and mice were 84% and 80%, and the identities of amino acids were 79% to 77%, respectively. Three complement control protein(CCP) domains, one Von Willebrand factor A(VWFA) domain and a serine protease domain, that are revealed typically in mammals, were found in the pig CFB gene. Based on the CDSs determined, the primers were designed in intron regions for amplification of entire length of exons. In amplification and direct sequencing with genomic DNAs of six pig breeds, three cSNPs(coding single nucleotide polymorphisms) were identified and verified as missense mutations. Using the Multiplex-ARMS method, we genotyped and verified the mutations identified from direct sequencing. To demonstrate recrudescence, we performed both direct sequencing and Multiplex-ARMS with two randomly selected DNA samples. The genotype of each sample exhibited the same results using both methods. Therefore, three cSNPs were identified from pig CFB gene and that can be used for haplotype analysis of the swine leukocyte antigen(SLA) class III region. Moreover, the results indicate that the Multiplex-ARMS method should be powerful for genotyping of genes in the SLA region.

• Horticultural Science & Technology
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• v.28 no.4
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• pp.648-655
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• 2010

This study is the first comprehensive report on the molecular cloning, structural characterization, sequence comparison between wild and mutant types, copy number in the genome, expression features and activities of a gene encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) in Korean lawn grass ($Zoysia$ $japonica$). The full length cDNA of the EPSPS from Korean lawn grass ($zj$EPSPS) obtained from a 3' and 5' RACE method was 1540 bp, containing a 1176 bp ORF, a 144 bp leader sequence (5' UTR) and a 220 bp 3' UTR, which was eventually decoded 391 amino acid residues with a molecular mass of 41.74 kDa. The Southern blot detection of the $zj$EPSPS showed that the gene exists as a single copy in the Korean lawn grass genome. Sequence comparison of the $zj$EPSPS gene demonstrated that the glyphosate-tolerant mutant (GT) having a Pro-53 to Ser substitution in the gene seems to have a preferred binding activity of the enzyme to phosphoenol pyruvate(PEP) over glyphosate, which allows the continuous synthesis of aromatic amino acids in the shikimate pathway. From the Northern blotting analysis, the $zj$EPSPS was found to be highly expressed, with continuous increase until 36 hours after 0.5% glyphosate treatment in both wild and mutant samples, but 1.5-fold higher EPSP synthase activity was observed in the tolerant mutant when exposed to the glyphosate treatment. The molecular information of the $zj$EPSPS gene obtained from this study needs to be further dissected to be more effectively applied to the development of gene-specific DNA markers and zoysiagrass cultivars; nevertheless, the glyphosate-tolerant mutant having the featured $zj$EPSPS gene can be provided to turfgrass managers for weed problems with timely adoptable management options.

• Journal of Plant Biotechnology
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• v.42 no.1
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• pp.25-33
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• 2015

A PyrcpPR-10 gene with differentially expressed was isolated by using the suppression subtractive hybridization assay between '93-3-98' (highly resistant against scab caused by Venturia nashicola) and 'Sweat Skin'(highly susceptible) and analyzed the expression pattern according to organs and cultivars. The full length of PyrcpPR-10 was cloned as 743bp with 480bp's ORP, and was determined to encode a protein of 159 amino acid residues. On analyzing PyrcpPR-10 gene sequence compared with resistant and susceptible cultivars, 'Hwangsilri' (resistant), 'Gamcheonbae' (moderately resistant), 'Wonhwang' (moderately susceptible), 'Niitaka' (highly susceptible), and 'Sweat Skin' (highly susceptible) had identical gene sequence but 'Bartlett' (highly resistant) showed partly different sequences. The deduced amino acid sequence showed 64 ~ 98% homology and had the GXGGXG motif to known amino acid of other plants PR-10 by the BLAST X analysis. Among several organs or tissues, petal was showed highest expression level of PyrcpPR-10 gene followed by leaf, floral axis, bud, and bark. The expression level of PyrcpPR-10 gene was dramatically increased at 24 hr after inoculation in all cultivars and also up-regulated in accordance with resistant degree of cultivars. While resistant cultivars ('Bartlett', '93-3-98', and 'Hwangsilri') induced relatively high expression level of PyrcpPR-10 gene, susceptible cultivars ('Niitaka', and 'Sweat Skin') showed low expression level. PyrcpPR-10 gene is assumed that it is directly connected with defense mechanisms to pear scab.

• The Korean Journal of Mycology
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• v.24 no.2 s.77
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• pp.155-165
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• 1996

This study was carried out to identify the phylogenetic relationship among several isolates of Pleurotus species by comparing ITS II region of ribosomal DNA(rDNA) repeat unit. Two primers from ribosomal DNA sequences were chosen to amplify the specific internal transcribed spacer (ITS) II region of Pleurotus spp. The exact ITS II region with an unique band from six species of Pleurotus genus could be amplified using the two primers taken from at the 3'-end of 5.8S rDNA and 5'-end of 28S rDNA. Six representative species of the Pleurotus genus were easily characterized according to the length differences of ITS II region. Furthermore, within P. ostreatus species, different sizes of ITS II region could be observed in the isolates of ASI 2025 and ASI 2095 although they were classified as P. ostreatus by the conventional observation. The nucleotide sequence analyses of PCR-amplified ITS II region indicated that the isolates ASI 2025 and ASI 2095 were different from other Pleurotus spp. When the nucleotide sequences of six Pleurotus species were compared, three typical ITS II regions were highly variable especially at both ends of this region. The phylogenetic tree obtained by the Neighbor program of Felsenstein PHYLIP package with all the nucleotide sequence of Pleurotus spp. indicated that P. ostreatus, P. florida, P. sajor-caju and P. eryngii were closely related to one phylogenetic branch and P. cystidious was related to other branch with P. cornucopiae. The isolates ASI 2025 and 2038, however, were not closely related to any other Pleurotus spp. and formed their own individual branches.