• Title/Summary/Keyword: D-loop region

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Evaluating genetic diversity and identifying priority conservation for seven Tibetan pig populations in China based on the mtDNA D-loop

  • Ge, Qianyun;Gao, Caixia;Cai, Yuan;Jiao, Ting;Quan, Jinqiang;Guo, Yongbo;Zheng, Wangshan;Zhao, Shengguo
    • Asian-Australasian Journal of Animal Sciences
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    • v.33 no.12
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    • pp.1905-1911
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    • 2020
  • Objective: Tibetan pigs, an excellent species unique to China, face serious threats, which in turn affects the development and utilization of the outstanding advantages of plateau hypoxia adaptability and reduces their genetic diversity. Therefore, a discussion of measures to conserve this genetic resource is necessary. The method, based on genetic diversity, genetic divergence and total genetic contribution rate of population, reflects the priority conservation order and varies depending on the three different purposes of conservation. Methods: We analyzed mitochondrial DNA control region (D-loop) variation in 1,201 individuals from nine Tibetan pig populations across five provinces and downloaded 564 mtDNA D-loop sequences from three indigenous pig breeds in Qinghai, Sichuan, and Yunnan Provinces distributed near the Tibetan pigs. Results: We analyzed three different aspects: Changdu Tibetan pigs have the highest genetic diversity, and from the perspective of genetic diversity, the priority conservation is Changdu Tibetan pigs. Hezuo Tibetan pigs have the highest genetic contribution, so the priority conservation is Hezuo Tibetan pigs in the genetic contribution aspect. Rkaze Tibetan pigs were severely affected by indigenous pig breeds, so if considering from the perspective of introgression, the priority conservation is Rkaze Tibetan pigs. Conclusion: This study evaluated genetic diversity and comprehensively assessed conservation priority from three different aspects in nine Tibetan pig populations.

Calculations of Load Current of Multi-Stage Cascaded Transmission Lines Excited by a Small Loop in the Near-Field Region (작은 루우프 안테나의 근거리장 영역내에 있는 다단 연쇄 접속 전송선로에 유기되는 부하 전류 계산)

  • 박영태;이상설
    • Journal of the Korean Institute of Telematics and Electronics
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    • v.27 no.6
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    • pp.836-842
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    • 1990
  • The noise currents in the load of cascaded transmission lines excited by a nearly small loop are analyzed and the effective approxiamte method by which we can calculate these currents easily and the computation time can be significantly reduced is developed. Numerical results for n=3 are well agreed with those of Smith by the maximum difference of 3-4dB and show that the length of a segment of line regarded to be illuminated by uniform electric fields should be 1.3 times the distance from the loop to the point midway between the conductors.

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Backbone assignment of HMGB1 A-box and molecular interaction with Hoxc9DBD studied by paramagnetic probe

  • Choi, Ji Woong;Park, Sung Jean
    • Journal of the Korean Magnetic Resonance Society
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    • v.25 no.2
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    • pp.17-23
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    • 2021
  • High mobility group protein B1 (HMGB1) is a highly conserved, non-histone, chromatin associated nuclear protein encoded by HMGB1 gene. HMGB1 proteins may be general co-factors in Hox-mediated transcriptional activation that facilitate the access of Hox proteins to specific DNA targets. It is unclear that the exact binding interface of Hoxc9DBD and HMGB1. To identify the interface and binding affinity of Hoxc9DBD and HMGB1 A-box, the paramagnetic probe, MTSL was used in NMR titration experiment. It is attached to the N-terminal end of HMGB1 A-box by reaction with thiol groups. The backbone assignment of HMGB1 A-box was achieved with 3D NMR techinques. The 15N-labeled HMGB1 A-box was titrated with MTSL-labeled Hoxc9DBD respectively. Based on the chemical shift changes we can identify the interacting residues and further map out the binding sites on the protein structure. The NMR titration result showed that the binding interface of HMGB1 A-box is around loop-1 between helix-1 and helix-2. In addition, the additional contacts were found in N- and C-terminus. The N-terminal arm region of Hoxc9DBD is the major binding region and the loop between helix1 and helix2 is the minor binding region.

Phylogenetic Analysis using mtDNA D-loop Sequences in Korean Native Ducks (mtDNA D-loop 염기서열 변이를 이용한 토종오리의 계통 분류)

  • Choi, Nu Ri;Seo, Dong Won;Jin, Seon Deok;Sultana, Hasina;Heo, Kang Nyeong;Lee, Jun Heon
    • Korean Journal of Poultry Science
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    • v.41 no.4
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    • pp.235-240
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    • 2014
  • Recently, the consumption of duck meat has been gradually increased in Korea. However, most of the duck breeds in Korea were imported from overseas. Based on the large demands for the breeding stocks of native ducks, a new project for the commercial use of the Korean native ducks has been launched. For the initial investigation of the relationships between Korean native duck (KND) with other duck breeds, the sequences from D-loop control region in mitochondrial DNA (mtDNA) was used. The results from phylogenetic analysis indicated that both KND and White Commercial Duck (WCD) breeds were classified well with wild duck breeds. However, mallard duck was not discriminated well with KND. The haplotype analysis indicated that KND and WCD have eight different haplotypes with eleven SNPs. Three haplotypes (haplotype 1, 3, 4) were shared both in KND and WCD. On the other hand, haplotype 1 was appeared only KND and haplotype 5, 6, 7, 8 were identified only in WCD population. With further verifications, the results presented here can be used for the conservation and commercialization of the Korean native ducks.

Development of OHS System Driven by Linear Motor for Automatic Transfer of LCD Panels (선형전동기를 적용한 LCD 패널 자동반송용 순환궤도차량 시스템 개발)

  • Kim, Won-Gon;Yun, Jong-Bo;Park, Gun-Woo;Hwang, Gye-Ho
    • Journal of the Semiconductor & Display Technology
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    • v.7 no.3
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    • pp.11-16
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    • 2008
  • The authors investigated an overhead shuttle (OHS) system for automatic transferring the liquid crystal display (LCD) panels. The constructed tracks of OHS system include the linear and curve regions and have been installed on the ceiling to transfer the cassette of LCD glass along the closed-loop and open-loop tracks. In this study, the OHS system was implemented by a proposed linear motor to solve encoder installation and the system cost problems of the long distance transfer system. In addition, we utilized a new algorithm of the position detection and a new control algorithm for driving linear motor. The newly developed control algorithm was demonstrated from both a computer simulation and an experimentation, indicating that the highly reliable and speedy transfer system can enhance the LCD panel productivity of commercial OHS system.

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Compact Dual-band CPW-fed Slot Antenna Using Split-Ring Resonator (분할 링 공진기를 이용한 소형 이중 대역 CPW-급전 슬롯 안테나)

  • Yeo, Junho;Park, Jin-Taek;Lee, Jong-Ig
    • Journal of the Korea Institute of Information and Communication Engineering
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    • v.19 no.11
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    • pp.2526-2533
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    • 2015
  • In this paper, a design method for a compact dual-band coplanar waveguide-fed slot antenna using SRR(split-ring resonator) conductor is studied. The SRR conductor is loaded inside a rectangular slot of the proposed antenna for dual-band operation. When the SRR conductor is inserted into the slot, the original rectangular slot is divided into a rectangular loop region and a rectangular slot region, and frequency bands are created by the loop and slot, separately. A prototype of the proposed dual-band slot antenna operating at 2.45 GHz WLAN band and 3.40-5.35 GHz band is fabricated on an FR4 substrate with a dimension of 30 mm by 30 mm. Experiment results show that the antenna has a desired impedance characteristic with a frequency band of 2.38-2.51 GHz and 3.32-5.38 GHz for a voltage standing wave < 2, and measured gain is 1.7 dBi at 2.45 GHz, and it ranges 2.4-3.2 dBi in the second band.

Determination of Regulator Parameters and Transient Analysis of Modified Self-commutating CSI-fed IM Drive

  • Pandey, A.K.;Tripathi, S.M.
    • Journal of Electrical Engineering and Technology
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    • v.6 no.1
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    • pp.48-58
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    • 2011
  • In this paper, an attempt has been made to design the current and speed proportional and integral (PI) regulators of self-commutating current source inverter-fed induction motor drive having capacitors at the machine end and to investigate the transient performance of the same for step changes in reference speed. The mathematical model of the complete drive system is developed in closed loop, and the characteristic equations of the systems are derived using perturbation about steady-state operating point in order to develop the characteristic equations. The D-partition technique is used for finding the stable region in the parametric plane. Frequency scanning technique is used to confirm the stability region. Final selection of the regulator parameters is done by comparing the transient response of the current and speed loops for step variations in reference. The performance of the drive is observed analytically through MATLAB simulation.

Mitochondrial DNA Polymorphism, Maternal Lineage and Correlations with Postnatal Growth of Japanese Black Beef Cattle to Yearling Age

  • Malau-Aduli, A.E.O.;Nishimura-Abe, A.;Niibayas, T.;Yasuda, Y.;Kojima, T.;Abe, S.;Oshima, K;Hasegawa, K.;Komatsu, M.
    • Asian-Australasian Journal of Animal Sciences
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    • v.17 no.11
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    • pp.1484-1490
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    • 2004
  • Mitochondrial DNA haplotypes from the displacement-loop (D-loop) region (436 bp) were genotyped and sequenced in Japanese Black beef cattle raised in the same herd. Correlation coefficients between mitochondrial DNA haplotypes, maternal lineage, birth weight, preweaning average daily gain, weaning weight, post weaning average daily gain and yearling weight were computed. The objective was to study the relationship between maternal and postnatal growth traits and to investigate if postnatal growth of calves to yearling age could be accurately predicted from mitochondrial DNA haplotypes. Results of the phylogenetic analysis revealed 17 maternal lineages and four mitochondrial DNA haplotypes. There were strong, positive and highly significant (p<0.001) correlations among maternal traits ranging from 0.52 to 0.98. Similarly, among postnatal growth traits, most of the correlations were also strong, positive and highly significant (p<0.001); the highest correlation of 0.94 was between preweaning average daily gain and weaning weight. However, correlations between mitochondrial DNA haplotypes and postnatal growth traits were very low, mostly negative and non-significant (p>0.05) ranging from -0.05 to 0.1. Prediction of postnatal growth from mitochondrial DNA yielded very low $R^{2}$ values ranging from 0.002 to 0.019. It was concluded that mitochondrial DNA polymorphism has no significant association with postnatal growth from birth to yearling age, and by implication, nuclear rather than cytoplasmic DNA, accounts for most of the genetic variation observed in postnatal growth of Japanese Black cattle. Therefore, mitochondrial DNA genotyping at an early age has no bearing on the accurate prediction of the future growth performance of calves.

Some Tertiary Interactions in 5S rRNA from Xanthomonas celebensis (Xanthomonas celebensis 5S rRNA의 몇 가지 삼차상호작용)

  • Bongrae Cho;Yeonghoon Lee;Myung-Un Choi;Inwon Park
    • Journal of the Korean Chemical Society
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    • v.37 no.2
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    • pp.237-243
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    • 1993
  • The primary and secondary structure of the 5S rRNA isolated from Xanthomonas celebensis were determined by enzymatic and chemical degradation methods. It consists of 119 nucleotides and contains no modified nucleosides. As with the 5S rRNAs of X. maltophilia and X. citri, it contains an additional uridine residue on the 5'-terminus. Its secondary structure was almost identical to the models previously proposed by us for the 5S rRNA of two Xanthomonas species. Its secondary structure consists of five helices, five loops and two bulges. The tertiary interactions in the 5S rRNA molecule were analyzed by Fe(II)-EDTA treatment and hybridization method using deoxyhexamer. From the fact that some adenine residues in loop M, region $I_1-C$, loop $H_1$, and loop $H_2$ become susceptible to diethylpyrocarbonate when the 5S rRNA was hybridized with deoxyhexamer complementary to the sequence $U_{35}CCCAU_{40}$ and that some nucleotide residues in loop M, loop $H_1$ and region $D-I_2$ become resistant Fe(II)-EDTA cleavage in the presence of $Mg^{2+}$, it is presumed that loops $H_1$ and $H_2$ interact with loop M in some way. In the tertiary interaction, the regions $I_1-C$ and $D-I_2$ seem to act as hinges in folding the stems $B-I_1-C$ and $D-I_2-E.$ It was found that loop $H_1$ changes into a smaller loop of three bases by forming noncanonical A : C base-pairs ih acidic environment.

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Genetic Diversity of mtDNA D-loop Polymorphisms in Laotian Native Fowl Populations

  • Kawabe, K.;Worawut, R.;Taura, S.;Shimogiri, T.;Nishida, T.;Okamoto, S.
    • Asian-Australasian Journal of Animal Sciences
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    • v.27 no.1
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    • pp.19-23
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    • 2014
  • Here, we studied the genetic diversity of native fowls in Laos by analyzing a mitochondrial DNA (mtDNA) sequence polymorphism. A 546-bp fragment of the mtDNA D-loop region was sequenced in 129 chickens from the areas of Vientiane, Luang Prabang and Pakse. In total, 29 haplotypes were identified and formed five clades. Haplotype diversity and nucleotide diversity of the native fowls in Laos were $0.85536{\pm}0.0172$ and $0.010158{\pm}0.005555$, respectively. Although the Laotian native fowls were distributed across five clades, most of them were clustered in two main clades (A and B), which were originated in China. The other haplotypes were contained in clades D, F, and I, which originated from continental southeast Asia. These results suggest that multiple maternal lineages were involved in the origin of domestic chicken in Laos. Moreover, there appear to be at least two maternal lineages, one from China and the other from the southeast Asian continent.