• Title/Summary/Keyword: genetic decomposition

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A genome-wide association study for the fatty acid composition of breast meat in an F2 crossbred chicken population

  • Eunjin Cho;Minjun Kim;Sunghyun Cho;Hee-Jin So;Ki-Teak Lee;Jihye Cha;Daehyeok Jin;Jun Heon Lee
    • Journal of Animal Science and Technology
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    • v.65 no.4
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    • pp.735-747
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    • 2023
  • The composition of fatty acids determines the flavor and quality of meat. Flavor compounds are generated during the cooking process by the decomposition of volatile fatty acids via lipid oxidation. A number of research on candidate genes related to fatty acid content in livestock species have been published. The majority of these studies focused on pigs and cattle; the association between fatty acid composition and meat quality in chickens has rarely been reported. Therefore, this study investigated candidate genes associated with fatty acid composition in chickens. A genome-wide association study (GWAS) was performed on 767 individuals from an F2 crossbred population of Yeonsan Ogye and White Leghorn chickens. The Illumina chicken 60K significant single-nucleotide polymorphism (SNP) genotype data and 30 fatty acids (%) in the breast meat of animals slaughtered at 10 weeks of age were analyzed. SNPs were shown to be significant in 15 traits: C10:0, C14:0, C18:0, C18:1n-7, C18:1n-9, C18:2n-6, C20:0, C20:2, C20:3n-6, C20:4n-6, C20:5n-3, C24:0, C24:1n-9, monounsaturated fatty acids (MUFA) and polyunsaturated fatty acids (PUFA). These SNPs were mostly located on chromosome 10 and around the following genes: ACSS3, BTG1, MCEE, PPARGC1A, ACSL4, ELOVL4, CYB5R4, ME1, and TRPM1. Both oleic acid and arachidonic acid contained the candidate genes: MCEE and TRPM1. These two fatty acids are antagonistic to each other and have been identified as traits that contribute to the production of volatile fatty acids. The results of this study improve our understanding of the genetic mechanisms through which fatty acids in chicken affect the meat flavor.

A study on understanding of infinite series (무한급수의 이해에 대한 연구)

  • Oh, Hye-Young
    • Communications of Mathematical Education
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    • v.34 no.3
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    • pp.355-372
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    • 2020
  • The concept of infinite series is an important subject of major mathematics curriculum in college. For several centuries it has provided learners not only counter-intuitive obstacles but also central role of analysis study. As the understanding in concept on infinite series became foundation of development of calculus in history of mathematics, it is essential to present students to study higher mathematics. Most students having concept of infinite sum have no difficulty in mathematical contents such as convergence test of infinite series. But they have difficulty in organizing concept of infinite series of partial sum. Thus, in this study we try to analyze construct the concept of infinite series in terms of APOS theory and genetic decomposition. By checking to construct concept of infinite series, we try to get an useful educational implication on teaching of infinite series.

A Study on Interaction Modes among Populations in Cooperative Coevolutionary Algorithm for Supply Chain Network Design (공급사슬 네트워크 설계를 위한 협력적 공진화 알고리즘에서 집단들간 상호작용방식에 관한 연구)

  • Han, Yongho
    • Korean Management Science Review
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    • v.31 no.3
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    • pp.113-130
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    • 2014
  • Cooperative coevolutionary algorithm (CCEA) has proven to be a very powerful means of solving optimization problems through problem decomposition. CCEA implies the use of several populations, each population having the aim of finding a partial solution for a component of the considered problem. Populations evolve separately and they interact only when individuals are evaluated. Interactions are made to obtain complete solutions by combining partial solutions, or collaborators, from each of the populations. In this respect, we can think of various interaction modes. The goal of this research is to develop a CCEA for a supply chain network design (SCND) problem and identify which interaction mode gives the best performance for this problem. We present general design principle of CCEA for the SCND problem, which require several co-evolving populations. We classify these populations into two groups and classify the collaborator selection scheme into two types, the random-based one and the best fitness-based one. By combining both two groups of population and two types of collaborator selection schemes, we consider four possible interaction modes. We also consider two modes of updating populations, the sequential mode and the parallel mode. Therefore, by combining both four possible interaction modes and two modes of updating populations, we investigate seven possible solution algorithms. Experiments for each of these solution algorithms are conducted on a few test problems. The results show that the mode of the best fitness-based collaborator applied to both groups of populations combined with the sequential update mode outperforms the other modes for all the test problems.

Identification and structural analysis of novel laccase genes in Flammulina elastica genome (Flammulina elastica의 유전체 정보기반 신규 laccase 유전자 동정 및 구조 분석)

  • Yu, Hye-Won;Park, Young-Jin
    • Journal of Mushroom
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    • v.19 no.1
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    • pp.33-40
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    • 2021
  • The genome sequence of various Flammulina species has recently been reported, thereby revealing a diverse genetic repertoire. In this study, we identified laccase genes and analyzed their structural characteristics in Flammulina elastica (F. elastica) genome. Through genome analysis and bioinformatics approaches, three laccase genes (Fe-lac1, -lac2, and -lac3) were identified, ranging from 1,548 to 1,602 bp in length. These genes contained a copper ion-binding region with ten histidine residues and one cysteine residue and a disulfide bond-forming region with four cysteine residues. Full-length cDNA sequencing analysis revealed that laccase genes contain 12 to 16 introns and signal peptides between 17 and 22 bp in the N-terminus. Structural characterization of the laccase genes identified in this study should help in better understanding the biomass decomposition of F. elastica.

Multi-environment Trial Analysis for Yield-related Traits of Early Maturing Korean Rice Cultivars

  • Seung Young Lee;Hyun-Sook Lee;Chang-Min Lee;Su-Kyung Ha;Youngjun Mo;Ji-Ung Jeung
    • Proceedings of the Korean Society of Crop Science Conference
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    • 2022.10a
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    • pp.252-252
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    • 2022
  • Genotype-by-environment interaction (GEI) refers to the comparative response of genotypes to different environments conditions. Thus, understanding GEI is a fundamental component for selecting superior genotypes for breeding programs. The significance of utilizing early maturing cultivars not only provides flexibility in planting dates, but also serves as an effective strategy to reduce methane emission from the paddy fields. In this study, we conducted multi-environment trials (METs) to evaluate yield-related traits such as culm length, panicle length, panicle number, spikelet per plant, and thousand grain weight. A total of eighty-one Korean commercial rice cultivars categorized as early maturing cultivars, were cultivated in three regions, two planting seasons for two years. The genotype main effect plus genotype-by-environment interaction (GGE) biplot analysis of yield-related traits and grain yield explained 70.02-91.24% of genotype plus GEI variation, and exhibited various patterns of mega-environment delineation, discriminating ability, representativeness, and genotype rankings across the planting seasons and environments. Moreover, simultaneous selection using weighted average of absolute scores from the singular value decomposition (WAASB) and multi-trait stability index (MTSI) revealed six highly recommended genotypes with high stability and crop productivity. The winning genotypes under specific environment can be utilized as useful genetic materials to develop regional specialty cultivars, and recommended genotypes can be used as elite climate-resilient parents to improve yield-potential and reduce methane emission as part to accomplish carbon-neutrality.

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Analysis of Interactions in Multiple Genes using IFSA(Independent Feature Subspace Analysis) (IFSA 알고리즘을 이용한 유전자 상호 관계 분석)

  • Kim, Hye-Jin;Choi, Seung-Jin;Bang, Sung-Yang
    • Journal of KIISE:Computer Systems and Theory
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    • v.33 no.3
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    • pp.157-165
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    • 2006
  • The change of external/internal factors of the cell rquires specific biological functions to maintain life. Such functions encourage particular genes to jnteract/regulate each other in multiple ways. Accordingly, we applied a linear decomposition model IFSA, which derives hidden variables, called the 'expression mode' that corresponds to the functions. To interpret gene interaction/regulation, we used a cross-correlation method given an expression mode. Linear decomposition models such as principal component analysis (PCA) and independent component analysis (ICA) were shown to be useful in analyzing high dimensional DNA microarray data, compared to clustering methods. These methods assume that gene expression is controlled by a linear combination of uncorrelated/indepdendent latent variables. However these methods have some difficulty in grouping similar patterns which are slightly time-delayed or asymmetric since only exactly matched Patterns are considered. In order to overcome this, we employ the (IFSA) method of [1] to locate phase- and shut-invariant features. Membership scoring functions play an important role to classify genes since linear decomposition models basically aim at data reduction not but at grouping data. We address a new function essential to the IFSA method. In this paper we stress that IFSA is useful in grouping functionally-related genes in the presence of time-shift and expression phase variance. Ultimately, we propose a new approach to investigate the multiple interaction information of genes.

Lithologic and Structural Controls and Geochemistry of Uranium Deposition in the Ogcheon Black-Slate Formation (옥천대(沃川帶) 우라늄광층(鑛層)의 구조규제(構造規制) 및 지구화학적(地球化學的) 특성연구(特性硏究))

  • Lee, Dai Sung;Yun, Suckew;Lee, Jong Hyeog;Kim, Jeong Taeg
    • Economic and Environmental Geology
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    • v.19 no.spc
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    • pp.19-41
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    • 1986
  • Structural, radioactive, petrological, petrochemical, mineralogical and stable isotopic study as well as the review of previous studies of the uranium-bearing slates in the Ogcheon sequence were carried out to examine the lithological and structural controls, and geochemical environment in the uranium deposition in the sequence. And the study was extended to the coal-bearing formation (Jangseong Series-Permian) to compare the geochemical and sedimentologic aspects of uranium chemistry between Ogcheon and Hambaegsan areas. The results obtained are as follows: 1. The uranium mineralization occurs in the carbonaceous black slates of the middle to lower Guryongsan formation and its equivalents in the Ogcheon sequence. In general, two or three uranium-bearing carbonaceous beds are found with about 1 to 1.5km stratigraphic interval and they extend from Chungju to Jinsan for 90km in distance, with intermittent igneous intrusions and structural Jisturbances. Average thickness of the beds ranges from 20 to 1,500m. 2. These carbonaceous slate beds were folded by a strong $F_1$-fold and were refolded by subsequent $F_1$-fold, nearly co-axial with the $F_1$, resulting in a repeated occurrence of similar slate. The carbonaceous beds were swelled in hing zones and were shrinked or thined out in limb by the these foldings. Minor faulting and brecciation of the carbonaceous beds were followed causing metamorphism of these beds and secondary migration and alteration of uranium minerals and their close associations. 3. Uranium-rich zones with high radioactive anomalies are found in Chungju, Deogpyong-Yongyuri, MiwonBoun, Daejeon-Geumsan areas in the range of 500~3,700 cps (corresponds to 0.017~0.087%U). These zones continue along strike of the beds for several tens to a few hundred meters but also discontinue with swelling and pinches at places that should be analogously developed toward underground in their vertical extentions. The drilling surveyings in those area, more than 120 holes, indicate that the depth-frequency to uranium rich bed ranging 40~160 meter is greater. 4. The features that higher radioactive anomalies occur particularly from the carbonaceous beds among the argillaceous lithologic units, are well demonstrated on the cross sections of the lithology and radioactive values of the major uranium deposits in the Ogcheon zone. However, one anomalous radioactive zone is found in a l:ornfels bed in Samgoe, near Daejeon city. This is interpreted as a thermal metamorphic effect by which original uranium contents in the underlying black slate were migrated into the hornfels bed. 5. Principal minerals of the uranium-bearing black slates are quartz, sericite, biotite and chlorite, and as to chemical composition of the black slates, $Al_2O_3$ contents appear to be much lower than the average values by its clarke suggesting that the Changri basin has rather proximal to its source area. 6. The uranium-bearing carbonaceous beds contain minor amounts of phosphorite minerals, pyrite, pyrrhotite and other sulfides but not contain iron oxides. Vanadium. Molybdenum, Barium, Nickel, Zirconium, Lead, Cromium and fixed Carbon, and some other heavy metals appear to be positive by correlative with uranium in their concentrations, suggesting a possibility of their genetic relationships. The estimated pH and Eh of the slate suggests an euxenic marine to organic-rich saline water environment during uranium was deposited in the middle part of Ogcheon zone. 7. The Carboniferous shale of Jangseong Series(Sadong Series) of Permian in Hambaegsan area having low radioactivity and in fluvial to beach deposits is entirely different in geochemical property and depositional environment from the middle part of Ogcheon zone, so-called "Pibanryong-Type Ogcheon Zone". 8. Synthesizing various data obtained by several aspects of research on uranium mineralization in the studied sequence, it is concluded that the processes of uranium deposition were incorporated with rich organic precipitation by which soluble uranyl ions, $U{_2}^{+{+}}$ were organochemically complexed and carried down to the pre-Ogcheon sea bottoms formed in transitional environment, from Red Sea type basin to Black Sea type basin. Decomposition of the organic matter under reducing conditions to hydrogen sulfide, which reduced the $UO{_2}^{+2}$ ions to the insoluble uranium dioxide($UO_2$), on the other side the heavy metals are precipitated as sulfides. 9. The EPMA study on the identification of uraninite and others and the genetic interpretation of uranium bearing slates by isotopic values of this work are given separately by Yun, S. in 1984.

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Development of a Molecular Selection Marker for Bacillus licheniformis K12 (Bacillus licheniformis K12 균주 분자 선발 마커 개발)

  • Young Jin Kim;Sam Woong Kim;Tae Wok Lee;Won-Jae Chi;Woo Young Bang;Ki Hwan Moon;Tae Wan Kim;Kyu Ho Bang;Sang Wan Gal
    • Journal of Life Science
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    • v.33 no.10
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    • pp.808-819
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    • 2023
  • This study was conducted to develop a selection marker for the identification of the Bacillus licheniformis K12 strain in microbial communities. The strain not only demonstrates good growth at moderate temperatures but also contains enzymes that catalyze the decomposition of various polymer materials, such as proteases, amylases, cellulases, lipases, and xylanases. To identify molecular markers appropriate for use in a microbial community, a search was conducted to identify variable gene regions that show considerable genetic mutations, such as recombinase, integration, and transposase sites, as well as phase-related genes. As a result, five areas were identified that have potential as selection markers. The candidate markers were two recombinase sites (BLK1 and BLK2), two integration sites (BLK3 and BLK4), and one phase-related site (BLK5). A PCR analysis performed with different Bacillus species (e.g., B. licheniformis, Bacillus velezensis, Bacillus subtilis, and Bacillus cereus) confirmed that PCR products appeared at specific locations in B. licheniformis: BLK1 in recombinase, BLK2 in recombinase family protein, and BLK3 and BLK4 as site-specific integrations. In addition, BLK1 and BLK3 were identified as good candidate markers via a PCR analysis performed on subspecies of standard B. licheniformis strains. Therefore, the findings suggest that BLK1 can be used as a selection marker for B. licheniformis species and subspecies in the microbiome.