• Genomics & Informatics
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• v.14 no.4
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• pp.230-233
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• 2016

Linkage disequilibrium (LD) is the non-random association between the loci and it could give us a preliminary insight into the genetic history of the population. In the present study LD patterns and effective population size (Ne) of three Korean cattle breeds along with Chinese, Japanese and Mongolian cattle were compared using the bovine Illumina SNP50 panel. The effective population size (Ne) is the number of breeding individuals in a population and is particularly important as it determines the rate at which genetic variation is lost. The genotype data in our study comprised a total of 129 samples, varying from 4 to 39 samples. After quality control there were ~29,000 single nucleotide polymorphisms (SNPs) for which $r^2$ value was calculated. Average distance between SNP pairs was 1.14 Mb across all breeds. Average $r^2$ between adjacent SNP pairs ranged between was 0.1 for Yanbian to 0.3 for Qinchuan. Effective population size of the breeds based on $r^2$ varied from 16 in Hainan to 226 in Yanbian. Amongst the Korean native breeds effective population size of Brindle Hanwoo was the least with Ne = 59 and Brown Hanwoo was the highest with Ne = 83. The effective population size of the Korean cattle breeds has been decreasing alarmingly over the past generations. We suggest appropriate measures to be taken to prevent these local breeds in their native tracts.

• Journal of Species Research
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• v.3 no.2
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• pp.127-166
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• 2014

Moniligastrids are an important yet often ignored earthworm group commonly found in cultivated soils, especially paddy, in the tropical East. Seven new taxa are: Drawida koreana austri, D. koreana nanjiro, D. koreana shindo, D. odaesan, D. jeombongsan, D. companio and D. csuzdii Blakemore spp. or sub-spp. nov. from Korea. Drawida csuzdii is the first new species from North Korea since Lumbricidae Eisenia koreana (Zicsi, 1972). Historical East Asian moniligastrids are reviewed chronologically and Drawida barwelli (Beddard, 1886), D. japonica (Michaelsen, 1892) and D. siemsseni Michaelsen, 1910 are compared on their museum types. These three taxa were thought similar and related to D. nepalensis Michaelsen, 1907 and its possible synonym D. burchardi Michaelsen, 1903 (priority!) and both of these to prior D. uniqua (Bourne, 1887). Indian Drawida calebi Gates, 1945 is compared to new material of D. japonica from Japan, and D. willsi Michaelsen, 1907 to the new sub-species of D. koreana Kobayashi, 1938 from Korea. Where available, mtDNA COI gene barcodes are provided to help objective determinations and a phylogram is provided with outgroup Ocnerodrilidae Eukerria saltensis (Beddard, 1895) itself found in rice paddy/irrigation. The challenge now is comparison of all early taxa in their various homelands in order to assess the genetic variability and taxonomic boundaries acceptable, especially for unpigmented D. barwelli and also for pink/grey D. japonica and blue/grey D. koreana. A checklist of moniligastrids is appended showing 22 species from China (including Hainan and Taiwan), 21 from Korea, nine from Japan and the Drawida ghilarovi Gates, 1969 species-complex from far eastern Russian (Siberia). Recent Drawida dandongensis Zhang & Sun, 2014 from Sino-Korean border is misdescribed and cannot be meaningfully compared to any other Drawidas.

• The Plant Pathology Journal
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• v.36 no.5
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• pp.459-467
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• 2020

Areca palm yellow leaf (AYL) disease caused by the 16SrI group phytoplasma is a serious threat to the development of the Areca palm industry in China. The 16S rRNA gene sequence was utilized to establish a rapid and efficient detection system efficient for the 16SrI-B subgroup AYL phytoplasma in China by loop-mediated isothermal amplification (LAMP). The results showed that two sets of LAMP detection primers, 16SrDNA-2 and 16SrDNA-3, were efficient for 16SrI-B subgroup AYL phytoplasma in China, with positive results appearing under reaction conditions of 64℃ for 40 min. The lowest detection limit for the two LAMP detection assays was the same at 200 ag/μl, namely approximately 53 copies/μl of the target fragments. Phytoplasma was detected in all AYL disease samples from Baoting, Tunchang, and Wanning counties in Hainan province using the two sets of LAMP primers 16SrDNA-2 and 16SrDNA-3, whereas no phytoplasma was detected in the negative control. The LAMP method established in this study with comparatively high sensitivity and stability, provides reliable results that could be visually detected, making it suitable for application and research in rapid diagnosis of AYL disease, detection of seedlings with the pathogen and breeding of disease-resistant Areca palm varieties.

• Maxillofacial Plastic and Reconstructive Surgery
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• v.31 no.4
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• pp.294-305
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• 2009

Purpose: This retrospective study evaluated the changes in hyoid bone and tongue positions as well as oral cavity volume after mandibular setback by BSSRO. Materials and Methods: 18 Koreans who underwent BSSRO to correct mandibular prognathism were studied. Lateral cephalograms were taken and traced preoperatively (T0), immediately (T1) and approximately 6 months postoperatively (T2). Submentovertex radiograghs were taken and traced before surgery (T0) and about 6 months after surgery (T2). The area and volume of oral cavity, the vertical and horizontal dimensions of the hyoid bone and tongue dorsum were measured. Results: Mandibular setback surgery resulted in a significant reduction of lower oral cavity volume. The hyoid bone displaced posteroinferiorly immediately after surgery, and it tended to return to its original vertical position at 6 month after mandibular setback by BSSRO. The retropalatal space around tongue was maintained and the retrolingual space around tongue was reduced immediately postoperatively. The readaptation of tongue was not evident for that the follow up period was not long enough. No significant statistical correlations between the amounts of mandibular setback and the changes of oral cavity volume were observed. Conclusion: Mandibular setback surgery resulted in a significant reduction of lower oral cavity volume, which was most likely attributable to the posterior movement of the mandible. More subjects and long-term observations should be performed to assess the changes of oropharyngeal configuration following mandibular setback surgery.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.6
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• pp.895-902
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• 2012

The Korean native chickens (Woorimotdak$^{TM}$, KNC) and commercial broilers (Ross, CB) show obvious differences in meat flavor after cooking. To understand the contribution of protein and peptide for meat flavor, 2-dimensional (2-D) gel electrophoresis and matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry was performed. A total of 16 protein spots were differentially expressed in the breast and thigh meat between the two breeds. A total of seven protein spots were represented by different levels between KNC and CB for breast meat. Among them three protein spots (TU39149, TU40162 and TU39598) showed increases in their expressions in KNC while other four protein spots (BU40125, BU40119, BU40029 and BU39904) showed increases in CB. All nine protein spots that were represented by different levels between KNC and CB for thigh meat showed increases in their expression in KNC. Phosphoglucomutase 1 (PGM 1), myosin heavy chain (MyHC), heat shock protein B1 (HSP27), cytochrome c reductase (Enzyme Q), Glyoxylase 1, DNA methyltransferase 3B (DNA MTase 3) were identified as the main protein spots by MALDI-TOF mass spectrometry. These results can provide valuable basic information for understanding the molecular mechanism responsible for breed specific differences in meat quality, especially the meat flavour.

• Transactions of the Korean Society for Noise and Vibration Engineering
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• v.17 no.9
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• pp.835-846
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• 2007

This paper deals with the flexural free vibrations of circular strip foundation with the variable breadth on Pasternak soil. The breadth of strip varies with the linear functional fashion, which is symmetric about the mid-arc. Differential equations governing flexural free vibrations of such strip foundation are derived, in which the elastic soil with the shear layer, i.e. Pasternak soil, is considered. Effects of the rotatory and shear deformation are included in the governing equations. Differential equations are numerically solved to calculate the natural frequencies and mode shapes. In the numerical examples, the hinged-hinged, hinged-clamped and clamped-clamped end constraints are considered. Four lowest frequency parameters accompanied with their corresponding mode shapes are reported and parametric studies between frequency parameters and various system parameters are investigated.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.7
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• pp.930-937
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• 2017

Objective: The I pig is a long nurtured longstanding breed in Vietnam, and contains excellent indigenous genetic resources. However, after 1970s, I pig breeds have become a small population because of decreasing farming areas and increasing pressure from foreign breeds with a high growth rate. Thus, there is now the risk of the disappearance of the I pigs breed. The aim of this study was to focus on classifying and identifying the I pig genetic origin and supplying molecular makers for conservation activities. Methods: This study sequenced the complete mitochondrial genome and used the sequencing result to analyze the phylogenetic relationship of I pig with Asian and European domestic pigs and wild boars. The full sequence was annotated and predicted the secondary tRNA. Results: The total length of I pig mitochondrial genome (accession number KX094894) was 16,731 base pairs, comprised two rRNA (12S and 16S), 22 tRNA and 13 mRNA genes. The annotation structures were not different from other pig breeds. Some component indexes as AT content, GC, and AT skew were counted, in which AT content (60.09%) was smaller than other pigs. We built the phylogenetic trees from full sequence and D loop sequence using Bayesian method. The result showed that I pig, Banna mini, wild boar (WB) Vietnam and WB Hainan or WB Korea, WB Japan were a cluster. They were a group within the Asian clade distinct from Chinese pigs and other Asian breeds in both phylogenetic trees (0.0004 and 0.0057, respectively). Conclusion: These results were similar to previous phylogenic study in Vietnamese pig and showed the genetic distinctness of I pig with other Asian domestic pigs.

• Transactions of the Korean Society for Noise and Vibration Engineering
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• v.15 no.11 s.104
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• pp.1287-1294
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• 2005

The purpose of this paper is to investigate free vibrations and critical loads of the Beck's columns with a tip spring, which carry a tip mass. The ordinary differential equation governing free vibrations of Beck's column subjected to a follower force is derived based on the Bernoulli-Euler beam theory Both the divergence and flutter critical loads are calculated from the load-frequency corves that are obtained by solving the differential equation numerically. The critical loads are presented in the figures as functions of various non-dimensional system parameters such as the subtangential parameter, mass ratio and spring parameter.

• The Plant Pathology Journal
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• v.35 no.1
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• pp.41-50
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• 2019

Sugarcane bacilliform viruses (SCBV), which belong to the genus Badnavirus, family Caulimoviridae, are an important DNA virus complex that infects sugarcane. To explore the genetic diversity of the sugarcane-infecting badnavirus complex in China, we tested 392 sugarcane leaf samples collected from Fujian, Yunnan, and Hainan provinces for the occurrence of SCBV by polymerase chain reaction (PCR) assays using published primers SCBV-F and SCBV-R that target the reverse transcriptase/ribonuclease H (RT/RNase H) regions of the viral genome. A total of 111 PCR-amplified fragments (726 bp) from 63 SCBV-positive samples were cloned and sequenced. A neighbor-joining phylogenetic tree was constructed based on the SCBV sequences from this study and 34 published sequences representing 18 different phylogroups or genotypes (SCBV-A to -R). All SCBV-tested isolates could be classified into 20 SCBV phylogenetic groups from SCBV-A to -T. Of nine SCBV phylogroups reported in this study, two novel phylogroups, SCBV-S and SCBV-T, that share 90.0-93.2% sequence identity and show 0.07-0.11 genetic distance with each other in the RT/RNase H region, are proposed. SCBV-S had 57.6-92.2% sequence identity and 0.09-0.66 genetic distance, while SCBV-T had 58.4-90.0% sequence identity and 0.11-0.63 genetic distance compared with the published SCBV phylogroups. Additionally, two other Badnavirus species, Sugarcane bacilliform MO virus (SCBMOV) and Sugarcane bacilliform IM virus (SCBIMV), which originally clustered in phylogenetic groups SCBV-E and SCBV-F, respectively, are first reported in China. Our findings will help to understand the level of genetic heterogeneity present in the complex of Badnavirus species that infect sugarcane.

• Journal of Microbiology and Biotechnology
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• v.29 no.5
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• pp.794-808
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• 2019

Bacillus velezensis strain WRN014 was isolated from banana fields in Hainan, China. Bacillus velezensis is an important member of the plant growth-promoting rhizobacteria (PGPR) which can enhance plant growth and control soil-borne disease. The complete genome of Bacillus velezensis WRN014 was sequenced by combining Illumina Hiseq 2500 system and Pacific Biosciences SMRT high-throughput sequencing technologies. Then, the genome of Bacillus velezensis WRN014, together with 45 other completed genome sequences of the Bacillus velezensis strains, were comparatively studied. The genome of Bacillus velezensis WRN014 was 4,063,541bp in length and contained 4,062 coding sequences, 9 genomic islands and 13 gene clusters. The results of comparative genomic analysis provide evidence that (i) The 46 Bacillus velezensis strains formed 2 obviously closely related clades in phylogenetic trees. (ii) The pangenome in this study is open and is increasing with the addition of new sequenced genomes. (iii) Analysis of single nucleotide polymorphisms (SNPs) revealed local diversification of the 46 Bacillus velezensis genomes. Surprisingly, SNPs were not evenly distributed throughout the whole genome. (iv) Analysis of gene clusters revealed that rich gene clusters spread over Bacillus velezensis strains and some gene clusters are conserved in different strains. This study reveals that the strain WRN014 and other Bacillus velezensis strains have potential to be used as PGPR and biopesticide.