• Title/Summary/Keyword: $R^{*}-Tree$

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Whole genome sequencing of Luxi Black Head sheep for screening selection signatures associated with important traits

  • Liu, Zhaohua;Tan, Xiuwen;Wang, Jianying;Jin, Qing;Meng, Xianfeng;Cai, Zhongfeng;Cui, Xukui;Wang, Ke
    • Animal Bioscience
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    • v.35 no.9
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    • pp.1340-1350
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    • 2022
  • Objective: Luxi Black Head sheep (LBH) is the first crossbreed specialized for meat production and was developed by crossbreeding Black Head Dorper sheep (DP) and Small Tailed Han sheep (STH) in the farming areas of northern China. Research on the genomic variations and selection signatures of LBH caused by continuous artificial selection is of great significance for identifying the genetic mechanisms of important traits of sheep and for the continuous breeding of LBH. Methods: We explored the genetic relationships of LBH, DP, and several Mongolian sheep breeds by constructing phylogenetic tree, principal component analysis and linkage disequilibrium analysis. In addition, we analysed 29 whole genomes of sheep. The genome-wide selection signatures have been scanned with four methods: heterozygosity (HP), fixation index (FST), cross-population extended haplotype homozygosity (XP-EHH) and the nucleotide diversity (𝜃π) ratio. Results: The genetic relationships analysis showed that LBH appeared to be an independent cluster closer to DP. The candidate signatures of positive selection in sheep genome revealed candidate genes for developmental process (HoxA gene cluster, BCL2L11, TSHR), immunity (CXCL6, CXCL1, SKAP2, PTK6, MST1R), growth (PDGFD, FGF18, SRF, SOCS2), and reproduction (BCAS3, TRIM24, ASTL, FNDC3A). Moreover, two signalling pathways closely related to reproduction, the thyroid hormone signalling pathway and the oxytocin signalling pathway, were detected. Conclusion: The selective sweep analysis of LBH genome revealed candidate genes and signalling pathways associated with developmental process, immunity, growth, and reproduction. Our findings provide a valuable resource for sheep breeding and insight into the mechanisms of artificial selection.

Verification Test of High-Stability SMEs Using Technology Appraisal Items (기술력 평가항목을 이용한 고안정성 중소기업 판별력 검증)

  • Jun-won Lee
    • Information Systems Review
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    • v.20 no.4
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    • pp.79-96
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    • 2018
  • This study started by focusing on the internalization of the technology appraisal model into the credit rating model to increase the discriminative power of the credit rating model not only for SMEs but also for all companies, reflecting the items related to the financial stability of the enterprises among the technology appraisal items. Therefore, it is aimed to verify whether the technology appraisal model can be applied to identify high-stability SMEs in advance. We classified companies into industries (manufacturing vs. non-manufacturing) and the age of company (initial vs. non-initial), and defined as a high-stability company that has achieved an average debt ratio less than 1/2 of the group for three years. The C5.0 was applied to verify the discriminant power of the model. As a result of the analysis, there is a difference in importance according to the type of industry and the age of company at the sub-item level, but in the mid-item level the R&D capability was a key variable for discriminating high-stability SMEs. In the early stage of establishment, the funding capacity (diversification of funding methods, capital structure and capital cost which taking into account profitability) is an important variable in financial stability. However, we concluded that technology development infrastructure, which enables continuous performance as the age of company increase, becomes an important variable affecting financial stability. The classification accuracy of the model according to the age of company and industry is 71~91%, and it is confirmed that it is possible to identify high-stability SMEs by using technology appraisal items.

Growth-promoting effect of microorganisms from a fairy ring in Yangyang, Korea on Tricholoma matsutake mycelium (국내 양양 송이 자생지 내 균환 유래 토양미생물과 송이균사체 생장촉진 효과)

  • Doo-Ho Choi;Eunji Lee;Kang-Hyo Lee;Gi-Hong An
    • Journal of Mushroom
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    • v.22 no.1
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    • pp.22-26
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    • 2024
  • Tricholoma matsutake is a traditional favorite food in East Asia, cultivated in fairy rings called "shiro," which are found near Pinus densiflora. For effective artificial cultivation of Tri. matsutake, microorganisms from symbiotic fairy rings are co-cultivated. In this study, one bacterial isolate (Y22_B35) and two fungal isolates (Y22_F64 and Y22_F68) displayed growth-promoting effects on Tri. matsutake mycelium (158.47, 125.00, and 122.26% enhanced growth, respectively). For identification, 16S rRNA or ITS regions from the microorganisms¡¯ genomes were sequenced. Other sequences, including BenA, CaM, and RPB2 were sequenced in the fungal isolates. The bacterial isolate Y22_B35 was identified as Bacillus cereus. Y22_F64 and Y22_F68 were identified as Umbelopsis nana and Aspergillus parvulus, respectively. To identify the effects of the dominant microorganisms on Tri. Matsutake cultivation, metagenomic analyses were performed. Discovery of these Tri. matsutake mycelium growth-promoting microorganisms and metagenomics analyses are expected to contribute to our understanding of Tri. matsutake fruiting body growth and construction of biomimicry.

Varietal and Locational Variation of Grain Quality Components of Rice Produced in Hilly and High Altitude Areas in Korea (중산간지와 고냉지산 쌀 형태 및 이화학적특성의 품종 및 산지간 변이)

  • Choi, Hae-Chune;Chi, Jeong-Hyun;Lee, Chong-Seob;Kim, Young-Bae;Cho, Soo-Yeon
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.39 no.1
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    • pp.27-37
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    • 1994
  • To catch the relative importance of varietal and environmental variation in various grain quality components associated with palatability of cooked rice, grain appearance, milling recovery, several physicochemical properties of milled rice and texture or eating quality of cooked rice for rice materials of five japonica cultivars, produced at four locations of the mid-mountainous and alpine area of Korea in 1989, were evaluated and analyzed the obtained data. Highly significant varietal and locational variations were detected in 1000-grain weight, amylose content, K/Mg ratio, gelatinization temperature, peak viscosity, breakdown and setback viscosities as compared with variety x location interaction variation. Also, marked locational variations were recongnized in milling recovery from rough to brwon rice, alkali digestibility and protein content, and significant varietal variation was caught in stickiness /hardness ratio of cooked rice. The variety x location interaction variation was especially large in quality components of grain appearance and ripening, palatability of cooked rice and consistency viscosity. One thousand kernel weight was heaviest in Jinbuolbyeo and Odaebyeo, and the unfilled grain ratio was lowest in Jinbuolbyeo. Odaebyeo showed slightly' lower ratio of intact and clear milled rice because of more chalky rice kernels compared with other cultivars. Amylose content of Jinbuolbyeo and Sobaegbyeo was about 1% lower than that of others and K/Mg ratio of Odaebyeo was the lowest one among rice materials. Odaebyeo, Sobaegbyeo and Jinbuolbyeo revealed significantly low gelatinization temperature and setback viscosity while high peak and breakdown viscosities. Cholwon rice showed the greatest kernel weight, good grain filling but lowest ratio of intact and clear milled rice while Jinbu rices exhibited the highest milling recovery from rough to brown rice and ratio of sound milled rice. Amylose content of milled rice in Jinbu rices was about 2-3% lower than those in other locations. Protein content of polished rice was about 1% lower in rice materials of middle zone than those of southern part of Korea. K/Mg ratio of milled rice was highest in Jinbu rice and potassium content was slightly higher in the rice materials of middle region than in those of southern region. Alkali digestion value and gelatinization temperature of polished rice was markedly high in Jinbu rices as compared with other locations. Breakdown viscosity was hightest in Chlown rices and next higher with the order of Hwaso>Unbong>Jinbu rices, and setback viscosity was the quite contrary tendency with breakdown. The stickiness /hardness ratio of cooked rice was relatively higher value in Cholwon rices than in the others and the palatability of cooked rice was a little better in Unbong and Cholwon rices than in Jinbu and Hwaso rices, although variety x location interaction variation was large. The rice materials can be classified largely into two groups of Jinbu and the others by the distribution on the plane of 1st and 2nd principal components (about 60% of total informations) contracted from twelve grain quality properties closely associated with eating quality of cooked rice. Also, Jinbu and the other rices were divided into two and three rice groups respectively. Varietal variation of overall rice quality was smallest in Hwaso. The most superior rice group in overall quality evaluation included Odaebyeo produced at Cholwon, Unbong and Hwaso, and Sobaegbyeo grown at Unbong

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Varietal and Locational Variation of Grain Quality Components of Rice Produced n Middle and Southern Plain Areas in Korea (중ㆍ남부 평야지산 발 형태 및 이화학적 특성의 품종 및 산지간 변이)

  • Choi, Hae-Chune;Chi, Jeong-Hyun;Lee, Chong-Seob;Kim, Young-Bae;Cho, Soo-Yeon
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.39 no.1
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    • pp.15-26
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    • 1994
  • To understand the relative contribution of varietal and environmental variation on various grain quality components in rice, grain appearance, milling recovery, several physicochemical properties of rice grain and texture or palatability of cooked rice for milled rice materials of seven cultivars(five japonica & two Tongil-type), produced at six locations of the middle and southern plain area of Korea in 1989, were evaluated and analyzed the obtained data. Highly significant varietal variations were detected in all grain quality components of the rice materials and marked locational variations with about 14-54% portion of total variation were recognized in grain appearance, milling recovery, alkali digestibility, protein content, K /Mg ratio, gelatinization temperature, breakdown and setback viscosities. Variations of variety x location interaction were especially large in overall palatability score of cooked rice and consistency or set- back viscosities of amylograph. Tongil-type cultivars showed poor marketing quality, lower milling recovery, slightly lower alkali digestibility and amylose content, a little higher protein content and K /Mg ratio, relatively higher peak, breakdown and consistency viscosities, significantly lower setback viscosity, and more undesirable palatability of cooked rice compared with japonica rices. The japonica rice varieties possessing good palatability of cooked rice were slightly low in protein content and a little high in K /Mg ratio and stickiness /hardness ratio of cooked rice. Rice 1000-kernel weight was significantly heavier in rice materials produced in Iri lowland compared with other locations. Milling recovery from rough to brown rice and ripening quality were lowest in Milyang late-planted rice while highest in Iri lowland and Gyehwa reclaimed-land rice. Amylose content of milled rice was about 1% lower in Gyehwa rice compared with other locations. Protein content of polished rice was about 1% lower in rice materials of middle plain area than those of southern plain regions. K/Mg ratio of milled rice was lowest in Iri rice while highest in Milyang rice. Alkali digestibility was highest in Milyang rice while lowest in Honam plain rice, but the temperature of gelatinization initiation of rice flour in amylograph was lowest in Suwon and Iri rices while highest in Milyang rice. Breakdown viscosity was lowest in Milyang rice and next lower in Ichon lowland rice while highest in Gyehwa and Iri rices, and setback viscosity was the contrary tendency. The stickiness/hardness ratio of cooked rice was slightly lower in southern-plain rices than in middle-plain ones, and the palatability of cooked rice was best in Namyang reclaimed-land rice and next better with the order of Suwon$\geq$Iri$\geq$Ichon$\geq$Gyehwa$\geq$Milyang rices. The rice materials can be classified genotypically into two ecotypes of japonica and Tongil-type rice groups, and environmentally into three regions of Milyang, middle and Honam lowland by the distribution on the plane of 1st and 2nd principal components contracted from eleven grain quality properties closely associated with palatability of cooked rice by principal component analysis.

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Studies of Eri-Silk Cultring in Korea (한국피마잠사개발에 대한 연구)

  • 최병희;김재두;박창준
    • Journal of Sericultural and Entomological Science
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    • v.9
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    • pp.49-66
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    • 1969
  • Eri-silkworm is known as a tropical insect where as poly-voltine type in that area. It eats caster oil plant leaves which are cultivated as an every year cultivatable seed oil use in this country, even though it grows for many years in tropical countries. That is why, farmers have freedom for its cultivation in any year if they want. Therefore, eri-silkworm rearing service is flexible for its diet procurment as wish of farmer. The eri-cocoon price or economical fluctuation may be reactable for the rearing work not like as mulberry cocoon. Fortunately, it also eats cynthia tree leaves. Standing from such a easy condition, the authors have studied about this problem since 1963 to develope a culturing method of eri-silkworm rearing in this country and the authors brought out the matters to be produced as an industry scale. Here, the authors summarized their works of the results covering with thirty three work tables. The obtained results are as follows.

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Evaluation of CO2 Emission to Changes of Soil Water Content, Soil Temperature and Mineral N with Different Soil Texture in Pepper Cultivation (고추재배에서 토성별 토양수분, 토양온도, 무기태질소 변화에 따른 CO2 배출량 평가)

  • Kim, Gun-Yeob;Song, Beom-Heon;Hong, Suk-Young;Ko, Byong-Gu;Roh, Kee-An;Shim, Kyo-Moon;Zhang, Yong-Seon
    • Korean Journal of Soil Science and Fertilizer
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    • v.41 no.6
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    • pp.393-398
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    • 2008
  • Several researchers have proposed models or equations to predict soil $CO_2$ flux from more readily available biotic and abiotic measurement. Tree commonly used abiotic variables were N mineral and soil temperature and soil water content. This study was conducted to determine $CO_2$ emission to mineral N, soil water content and soil temperature with clay loam and sandy loam in pepper cultivation in 2004~2005. $CO_2$ flux in the upland with different levels of soil water potential was measured at least once in two weeks during the cropping period in the pepper cultivation plots. Soil water potential in the clay loam and sandy loam soils was established at -30kPa and -50kPa by measuring the soil gravimetric water content with two replications. $CO_2$ emission rate from the differently managed plots was highly correlation coefficient to between the mineral N ($R=0.830^{**}$, $0.876^{**}$) and soil temperature ($r^2=0.793^{**}$, $0.804^{**}$) in the clay loam and sandy loam, respectively. However, the relationships between $CO_2$ emission and soil water content were non-significant. $CO_2$ emissions at sandy loam soils was lower to 21~37% than at clay loam soils for both soil water conditions without differences in yield. At difference levels of soil water conditions, $CO_2$ emission at -50kPa decreased to 37.5% in comparison with that at -30kPa. From the path analysis as to contribution factors of GHGs, it appeared that contribution rate was in the order of soil temperature (54.9%), mineral N (32.7%), and soil moisture content (12.4%).

The Association of Intra-Annual Cambial Activities of Pinus koraiensis and Chamaecyparis pisifera planted in Mt. Worak with Climatic Factors (월악산에 식재된 잣나무와 화백나무의 형성층 활동과 기후인자와의 관계)

  • Seo, Jeong-Wook;Choi, En-Bi;Ju, Jeong-Deok;Shin, Chang-Seop
    • Journal of the Korean Wood Science and Technology
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    • v.45 no.1
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    • pp.43-52
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    • 2017
  • This study was fulfilled to verify the durations of cambial activity and analyze the associations of degree days and precipitation with the initiation of cambial activity and intra-annual wood formation for Pinus koraiensis and Chamaecyparis pisifera planted at Mt. Worak, respectively, by monitoring of their intra-annual cambial activities. And more, the reason was also analyzed why the DBH of Chamaecyparis pisifera known as planted in the same year could be classified as two groups (CPL: ${\phi}30cm$, CPS: ${\phi}15cm$). The intra-annual cambial activity was monitored using mini-cores (${\phi}2mm$) and they were collected in 2-week interval between April and October. However, between April and May and between middle September and October expected as the initiation and cessation of the cambial activity, respectively, it was fulfilled in 1-week interval. The average number of tree rings for PK (30) was less than CPS (37) and CPL (38), whereas the average ring width of PK (4.12 mm) was wider than CPS (1.84 mm) and CPL (3.97 mm). In the comparison of ring widths between CPL and CPS, CPL was 2.13 mm wider than CPS, however, excepting CPS 1 (0.83 mm), the average ring widths of CPS 2 (2.42 mm) and CPS 3 (2.73 mm) in the last 3 years were close to the average of CPL (2.71 mm). The initiation of cambial activity for PK was between 1 and 21 April, which was 1 week earlier than CPL and CPS (excepting CPS 1) and the cessation was between 1 and 22 September. The longest growing season therefore was 157.3 days (${\pm}3.3$) and it was longer than CPL ($145.7{\pm}6.6days$) and CPS ($148.0{\pm}15.1days$). In CP groups there were wide variations for the cessation of cambial activity and also there were the meaningful linear relationship between the growing seasons and the ring widths (r = 0.69, p < 0.064). The cambial activity in PK was initiated when degree days were between 99 and 134 and in CPS (excepting PCS 1) and CPL between 134 and 200. Excepting CPS 3, the false ring was observed in all samples collected on 21 July when drought stress was high due to low precipitation from June to the beginning of July.

Enhanced Production of Carboxymethylcellulase by a Newly Isolated Marine Microorganism Bacillus atrophaeus LBH-18 Using Rice Bran, a Byproduct from the Rice Processing Industry (미강을 이용한 해양미생물 Bacillus atrophaeus LBH-18 유래의 carboxymethylcellulase 생산의 최적화)

  • Kim, Yi-Joon;Cao, Wa;Lee, Yu-Jeong;Lee, Sang-Un;Jeong, Jeong-Han;Lee, Jin-Woo
    • Journal of Life Science
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    • v.22 no.10
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    • pp.1295-1306
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    • 2012
  • A microorganism producing carboxymethylcellulase (CMCase) was isolated from seawater and identified as Bacillus atrophaeus. This species was designated as B. atrophaeus LBH-18 based on its evolutionary distance and the phylogenetic tree resulting from 16S rDNA sequencing and the neighbor-joining method. The optimal conditions for rice bran (68.1 g/l), peptone (9.1 g/l), and initial pH (7.0) of the medium for cell growth was determined by Design Expert Software based on the response surface method; conditions for production of CMCase were 55.2 g/l, 6.6 g/l, and 7.1, respectively. The optimal temperature for cell growth and the production of CMCase by B. atrophaeus LBH-18 was $30^{\circ}C$. The optimal conditions of agitation speed and aeration rate for cell growth in a 7-l bioreactor were 324 rpm and 0.9 vvm, respectively, whereas those for production of CMCase were 343 rpm and 0.6 vvm, respectively. The optimal inner pressure for cell growth and production of CMCase in a 100-l bioreactor was 0.06 MPa. Maximal production of CMCase under optimal conditions in a 100-l bioreactor was 127.5 U/ml, which was 1.32 times higher than that without an inner pressure. In this study, rice bran was developed as a carbon source for industrial scale production of CMCase by B. atrophaeus LBH-18. Reduced time for the production of CMCase from 7 to 10 days to 3 days by using a bacterial strain with submerged fermentation also resulted in increased productivity of CMCase and a decrease in its production cost.

Development of Species-Specific PCR to Determine the Animal Raw Material (종 특이 프라이머를 이용한 동물성 식품원료의 진위 판별법 개발)

  • Kim, Kyu-Heon;Lee, Ho-Yeon;Kim, Yong-Sang;Kim, Mi-Ra;Jung, Yoo Kyung;Lee, Jae-Hwang;Chang, Hye-Sook;Park, Yong-Chjun;Kim, Sang Yub;Choi, Jang Duck;Jang, Young-Mi
    • Journal of Food Hygiene and Safety
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    • v.29 no.4
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    • pp.347-355
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    • 2014
  • In this study, the detection method was developed using molecular biological technique to distinguish authenticity of animal raw materials. The genes for distinction of species about animals targeted at Cytochrome c oxidase subunit I (COI), Cytochrome b (Cytb), and 16S ribosomal RNA (16S rRNA) genes in mitochondrial DNA. The species-specific primers were designed by that Polymerase Chain Reaction (PCR) product size was around 200 bp for applying to processed products. The target 24 raw materials were 2 species of domestic animals, 6 species of poultry, 2 species of freshwater fishes, 13 species of marine fishes and 1 species of crustaceans. The results of PCR for Rabbit, Fox, Pheasant, Domestic Pigeon, Rufous Turtle Dove, Quail, Tree Sparrow, Barn Swallow, Catfish, Mandarin Fish, Flying Fish, Mallotus villosus, Pacific Herring, Sand Lance, Japanese Anchovy, Small Yellow Croaker, Halibut, Jacopever, Skate Ray, Ray, File Fish, Sea Bass, Sea Urchin, and Lobster raw materials were confirmed 113 bp ~ 218 bp, respectively. Also, non-specific PCR products were not detected in compare species by species-specific primers. The method using primers developed in this study may be applied to distinguish an authenticity of food materials included animal raw materials for various processed products.