• 제목/요약/키워드: ancient DNA (aDNA)

검색결과 44건 처리시간 0.028초

Mitochondrial DNA Variation and Genetic Relationships in Japanese and Korean Cattle

  • Sasazaki, S.;Odahara, S.;Hiura, C.;Mukai, F.;Mannen, H.
    • Asian-Australasian Journal of Animal Sciences
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    • 제19권10호
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    • pp.1394-1398
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    • 2006
  • The complete mtDNA D-loop regions of Japanese and Korean cattle were analyzed for their mtDNA variations and genetic relationships. Sequencing the 30 Higo substrain and 30 Tosa substrain of Japanese Brown, respectively 12 and 17 distinct Bos haplotypes were identified from 77 polymorphic nucleotide sites. In order to focus on the relationships among Japanese and Korean cattle, two types of phylogenetic tree were constructed using individual sequences; first, a neighbor-joining tree with all sequences and second, reduced median networks within each Japanese and Korean cattle group. The trees revealed that two major mtDNA haplotype groups, T3 and T4, were represented in Japanese and Korean cattle. The T4 haplogroup predominated in Japanese Black and Japanese Brown cattle (frequency of 43.3-66.7%), while the T3 haplogroup was predominant (83.3%) and T4 was represented only twice in the Korean cattle. The results suggested that the mitochondrial origins of Japanese Brown were Japanese ancient cattle as well as Japanese Black in despite of the considerable introgression of Korean and European cattle into Japanese Brown.

Maternal lineage of Okinawa indigenous Agu pig inferred from mitochondrial DNA control region

  • Touma, Shihei;Shimabukuro, Hirotoshi;Arakawa, Aisaku;Oikawa, Takuro
    • Asian-Australasian Journal of Animal Sciences
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    • 제32권4호
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    • pp.501-507
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    • 2019
  • Objective: The Agu is the only native pig breed in Japan, which is reared in Okinawa prefecture, the southernmost region in Japan. Its origins are considered to be of Asian lineage; however, the genetic background of the Agu is still unclear. The objective of this study was to elucidate the maternal lineage of the Okinawa indigenous Agu pig with the use of the mitochondrial DNA (mtDNA) control region. Methods: The mtDNA control regions of Agu pigs were sequenced and the phylogenetic relationship among Agu, East Asian and European pigs was investigated with the use of 78 Agu individuals. Results: Twenty-seven polymorphic sites and five different haplotypes (type 1 to type 5) were identified within the Agu population. Phylogenetic analysis indicated that types 1 and 2 were included in East Asian lineages; however, the remaining types 3, 4, and 5 were of European lineages, which showed a gene flow from European pigs in the 20th century. Sixty-seven out of 78 Agu individuals (85.9%) possessed mtDNA haplotypes 1 and 2 of the East Asian lineage, which were identical to two haplotypes of ancient mtDNA (7,200 to 1,700 years before the present) excavated at archaeological sites in Okinawa. Conclusion: This study confirmed that the East Asian lineage is dominant in the maternal genetic background of the Agu population, supporting the hypothesis that the ancestors of the Agu pig were introduced from the Asian continent.

부여 큰독골 유적 출토 인골 조직 및 외부 토양의 세균 군집의 비교연구 (Comparative Study of Soil Bacterial Populations in Human Remains and Soil from Keundokgol Site at Buyeo)

  • 김윤지;김수훈;권은실;조은민;강소영
    • 헤리티지:역사와 과학
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    • 제47권4호
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    • pp.92-105
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    • 2014
  • 인골과 인골 주변 토양에 분포하는 세균의 군집구조를 비교하기 위해 부여 오수리 큰독골 유적에서 발굴된 조선시대 회곽묘 인골 중 상대적으로 시료 상태가 좋지 않은 4호 인골과 상태가 양호한 5호 인골 및 주변 토양에서 DNA를 추출하였다. 추출한 DNA의 16S rDNA 염기서열 분석을 수행한 결과, 4호 인골에서 구축된 319개 클론은 ${\alpha}$, ${\beta}$, ${\gamma}$-Proteobacteria, Acidobacteria, Actinobacteria, Planctomycetes, Chloroflexi, Chlorobi, Bacteroidetes, Firmicutes 그리고 novel gene group 등 총 11개의 계통군이 확인되었다. 인골 주변 토양에서 구축된 462개 콜론은 ${\alpha}$, ${\beta}$, ${\gamma}$, ${\delta}$-Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, Planctomycetes, Chloroflexi, Chlorobi, Firmicutes, Thermodesulfobacteria, Fibrobacteres, Gemmatimonadetes, Verrucomicrobia 그리고 novel gene group 등 총 16개 계통군이 확인되었다. 5호 인골에서 구축된 271개 클론은 ${\alpha}$, ${\gamma}$-Proteobacteria, Acidobacteria, Actinobacteria, Planctomycetes, Chloroflexi, Bacteroidetes, Firmicutes 그리고 novel gene group 등 총 10개의 계통군이 확인되었으며, 인골 주변 토양에서 구축된 497개 클론은 ${\alpha}$, ${\beta}$, ${\gamma}$-Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Firmicutes, Gemmatimonadetes, Planctomycetes, Bacteroidetes 그리고 Verrucomicrobia 등 총 11개 계통군으로 확인되었다. 4호, 5호의 모든 시료에서 Actinobacteria 계통군이 가장 높은 비율을 차지하고 있으며, ${\alpha}$-Proteobacteria 계통군 또한 높은 비율을 차지하는 것으로 분석되었다. 인골은 주변 토양 세균의 군집에 의해 광범위하게 오염되어 있다는 것이 확인되었으며, 본 결과는 인골의 보존과 관리를 위한 중요 자료로 활용될 것이다.

Application of CRISPR-Cas9 gene editing for congenital heart disease

  • Seok, Heeyoung;Deng, Rui;Cowan, Douglas B.;Wang, Da-Zhi
    • Clinical and Experimental Pediatrics
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    • 제64권6호
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    • pp.269-279
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    • 2021
  • Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR-Cas9) is an ancient prokaryotic defense system that precisely cuts foreign genomic DNA under the control of a small number of guide RNAs. The CRISPR-Cas9 system facilitates efficient double-stranded DNA cleavage that has been recently adopted for genome editing to create or correct inherited genetic mutations causing disease. Congenital heart disease (CHD) is generally caused by genetic mutations such as base substitutions, deletions, and insertions, which result in diverse developmental defects and remains a leading cause of birth defects. Pediatric CHD patients exhibit a spectrum of cardiac abnormalities such as septal defects, valvular defects, and abnormal chamber development. CHD onset occurs during the prenatal period and often results in early lethality during childhood. Because CRISPR-Cas9-based genome editing technology has gained considerable attention for its potential to prevent and treat diseases, we will review the CRISPR-Cas9 system as a genome editing tool and focus on its therapeutic application for CHD.

Comparison of structure, function and regulation of plant cold shock domain proteins to bacterial and animal cold shock domain proteins

  • Chaikam, Vijay;Karlson, Dale T.
    • BMB Reports
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    • 제43권1호
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    • pp.1-8
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    • 2010
  • The cold shock domain (CSD) is among the most ancient and well conserved nucleic acid binding domains from bacteria to higher animals and plants. The CSD facilitates binding to RNA, ssDNA and dsDNA and most functions attributed to cold shock domain proteins are mediated by this nucleic acid binding activity. In prokaryotes, cold shock domain proteins only contain a single CSD and are termed cold shock proteins (Csps). In animal model systems, various auxiliary domains are present in addition to the CSD and are commonly named Y-box proteins. Similar to animal CSPs, plant CSPs contain auxiliary C-terminal domains in addition to their N-terminal CSD. Cold shock domain proteins have been shown to play important roles in development and stress adaptation in wide variety of organisms. In this review, the structure, function and regulation of plant CSPs are compared and contrasted to the characteristics of bacterial and animal CSPs.

가야시대 고분 및 부장품 내에 존재하는 미생물의 다양성 조사 (Microbial Diversity inside Ancient Tombs and Burial Accessories from Gaya Age)

  • 하병석;고선철;조아름;김승락;김상우;노현수
    • 한국균학회지
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    • 제41권2호
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    • pp.67-73
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    • 2013
  • 가야시대(경남 의령, 아라가야) 돌덧널무덤 5호와 6호의 부장품 속에서 채취한 12개의 토양시료에서 곰팡이균 9종과 세균 70종을 순수분리하였다. 분리된 미생물의 16S 및 18S rDNA 염기서열을 분석한 결과, 5호 고분에서 곰팡이 5 균주, 세균 10 속, 22 균주가 발견되었으며, 6호 고분에서는 곰팡이 1 균주, 세균 6 속, 28 균주가 발견되었다. 5호 고분의 높은 미생물다양성으로 미루어 5호 고분이 6호 고분보다는 좀 더 미생물 성장에 좋은 기후조건(여름이나 초가을)에 조성되었을 것으로 추정되었다. 또한 5호 고분에 부장된 대도의 표면에서 동물의 피부에 서식하는 Staphylococcus warneri와 갯벌에서 서식하는 해양성세균 인 Bacillus aquimaris와 같은 독특한 세균이 발견됨에 따라, 매장당시의 의식에 육류와 해산물이 사용되었음을 추정할 수 있다. 결론적으로 본 연구는 미생물학적 연구가 역사학 연구의 도구가 될 수 있음을 보여주었다.

Evolutionary history of the monospecific Compsopogon genus (Compsopogonales, Rhodophyta)

  • Nan, Fangru;Feng, Jia;Lv, Junping;Liu, Qi;Xie, Shulian
    • ALGAE
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    • 제31권4호
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    • pp.303-315
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    • 2016
  • Compsopogon specimens collected in China were examined based on morphology and DNA sequences. Five molecular markers from different genome compartments including rbcL, COI, 18S rDNA, psbA, and UPA were identified and used to construct a phylogenetic relationship. Phylogenetic analyses indicated that two different morphological types from China clustered into an independent clade with Compsopogon specimens when compared to other global samples. The Compsopogon clade exhibited robust support values, revealing the affiliation of the samples to Compsopogon caeruleus. Although the samples were distributed in a close geographical area, unexpected sequence divergences between the Chinese samples implied that they were introduced by different dispersal events and from varied origins. It was speculated that Compsopogon originated in North America, a portion of the Laurentia landmass situated in the Rodinia supercontinent at approximately 573.89-1,701.50 million years ago during the Proterozoic era.Although Compsopogonhad evolved for a rather long time, genetic conservation had limited its variability and rate of evolution, resulting in the current monospecific global distribution. Additional global specimens and sequence information were required to increase our understanding of the evolutionary history of this ancient red algal lineage.

Description of Microscopic Morphology of Leptochiton hakodatensis (Mollusca: Polyplacophora)

  • Park, Jina;Lee, Yucheol;Kim, Yukyung;Park, Joong-Ki
    • Animal Systematics, Evolution and Diversity
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    • 제38권1호
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    • pp.14-19
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    • 2022
  • Leptochiton Gray, 1847 is one of the most ancient chiton groups which includes more than 130 species that occur in cold and deep waters worldwide. Due to their small-sized body, they are often confused as juveniles of other chiton species. Moreover, lack of morphological information makes species identification of this group very challenging. To date, only two Leptochiton species(L. fuliginatus and L. rugatus) have been reported from Korean waters. In this study, we found L. hakodatensis(Thiele, 1909) for the first time in Korea and described microscopic morphological characters of valves (tegmentum sculpture), girdle scale, and radula using a scanning electron microscopy (SEM). Leptochiton hakodatensis is morphologically similar to L. fuliginatus and L. rugatus, but differently characterized by having dorso-ventrally rounded (not carinated) intermediate valves, girdle (perinotum) scales sculptured with 4-7 longitudinal ribs, and bicuspid major lateral teeth of radula. In addition to morphological examination, we determined the partial mitochondrial cytochrome c oxidase subunit I(cox1) as a DNA barcode sequence information. This is the first report that describes microscopic characters (tegmentum of valves, girdle structure, and radula) of L. hakodatensis using a SEM. This study provides a morphological basis for describing Leptochiton species and discovery of a "hidden" species of this genus.

붉은줄지렁이 (Eisenia andrei) 중장에서 발현되는 chitinase 유전자, EaChi의 동정 및 분자생물학적 특성에 관한 연구 (Identification and molecular characterization of the chitinase gene, EaChi, from the midgut of the earthworm, Eisenia andrei)

  • 탁은식;김대환;이명식;안치현;박순철
    • 유기물자원화
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    • 제18권3호
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    • pp.31-37
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    • 2010
  • Chitinase (EC 3.2.1.14)는 곰팡이와 곤충 등에서 세포벽이나 외골격을 형성하는 생물학적 방어기질의 구성 요소인 chitin의 ${\beta}$-1,4-linkages를 가수분해하는 효소이다. 이러한 chitinase를 포함하는 Glycosyl hydrolases 18 family는 Archea, Prokaryotes 그리고 Eukaryotes에 널리 퍼져 있는 Ancient gene으로 알려져 있다. 그 중, 지렁이는 곰팡이와 세균이 많은 환경에서 자라기 때문에 이러한 미생물들의 공격으로부터 스스로를 보호할 수 있는 면역체계를 가지고 있는 것으로 알려져 왔다. 본 연구에서는, 붉은줄지렁이 (Eisenia andrei)의 중장에서 발현되는 Chitinases의 cDNA 서열을 얻기 위해 기존에 알려져 있던 EST 서열을 가지고 RT-PCR 및 RACE-PCR을 수행하였고 이를 통해 E. andrei의 중장에서 발현되는 Chitinase의 특성을 동정 및 규명하였다. 그 결과 309개의 아미노산을 암호화하는 927개의 염기 서열을 얻을 수 있었으며 다른 종들의 Chitinases와 아미노산 서열을 비교 분석한 결과 지렁이의 Chitinase는 Glycosyl hydrolases 18 family에 속하고, 기질 결합과 촉매 작용에 관여하는 2개의 영역이 잘 보존되어 있는 것으로 나타났다.

Genetic Variability of mtDNA Sequences in Chinese Native Chicken Breeds

  • Liu, Z.G.;Lei, C.Z.;Luo, J.;Ding, C.;Chen, G.H.;Chang, H.;Wang, K.H.;Liu, X.X.;Zhang, X.Y.;Xiao, X.J.;Wu, S.L.
    • Asian-Australasian Journal of Animal Sciences
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    • 제17권7호
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    • pp.903-909
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    • 2004
  • The variability of mtDNA hypervariable segment I (HVS I) sequences was investigated in a total of 48 birds belonging to 12 Chinese native chicken breeds. Sixteen haplotypes were identified from 35 polymorphic nucleotide sites which accounted for 6.4% of a sequenced 544 bp fragment. Diversity analysis of the haplotypes showed that Tibetan, Langshan and Henan cockfight chicken had only one haplotype, while ancient haplotypes existed in Taihe silky and Chahua chicken. Phylogenetic analysis of the haplotypes suggested that Chinese native chicken breeds shared 5 maternal lineages and some breeds would share the same maternal lineage, regardless of their external features and ecological types. Both divergent and phylogenetic analysis of the haplotypes indicated the close genetic relationships between the Chinese native chicken breeds and G. g. gallus and G. g. spadiceus from different areas, which implied that G. g. gallus and G. g. spadiceus were the original ancestors of the Chinese native chicken breeds.