• Title/Summary/Keyword: Sequence Analyses

검색결과 936건 처리시간 0.029초

Molecular Characterization of Extracellular Medium-chain-length Poly(3-hydroxyalkanoate) Depolymerase Genes from Pseudomonas alcaligenes Strains

  • Kim Do Young;Kim Hyun Chul;Kim Sun Young;Rhee Young Ha
    • Journal of Microbiology
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    • 제43권3호
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    • pp.285-294
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    • 2005
  • A bacterial strain M4-7 capable of degrading various polyesters, such as poly$(\varepsilon-caprolactone)$, poly(3-hydroxybutyrate-co-3-hydroxyvalerate), poly(3-hydroxyoctanoate), and poly(3-hydroxy-5-phenylvalerate), was isolated from a marine environment and identified as Pseudomonas alcaligenes. The relative molecular mass of a purified extracellular medium-chain-length poly(3-hydroxyalkanoate) (MCL-PHA) depolymerase $(PhaZ_{palM4-7})$ from P. alcaligenes M4-7 was 28.0 kDa, as determined by SDS-PAGE. The $PhaZ_{palM4-7}$ was most active in 50 mM glycine-NaOH buffer (pH 9.0) at $35^{\circ}C$. It was insensitive to dithiothreitol, sodium azide, and iodoacetamide, but susceptible to p-hydroxymercuribenzoic acid, N-bromosuccinimide, acetic anhydride, EDTA, diisopropyl fluorophosphate, phenylmethylsulfonyl fluoride, Tween 80, and Triton X-100. In this study, the genes encoding MCL-PHA depolymerase were cloned, sequenced, and characterized from a soil bacterium, P. alcaligenes LB19 (Kim et al., 2002, Biomacro-molecules 3, 291-296) as well as P. alcaligenes M4-7. The structural gene $(phaZ_{palLB19})$ of MCL-PHA depolymerase of P. alcaligenes LB19 consisted of an 837 bp open reading frame (ORF) encoding a protein of 278 amino acids with a deduced $M_r$ of 30,188 Da. However, the MCL-PHA depolymerase gene $(phaZ_{palM4-7})$ of P. alcaligenes M4-7 was composed of an 834 bp ORF encoding a protein of 277 amino acids with a deduced Mr of 30,323 Da. Amino acid sequence analyses showed that, in the two different polypeptides, a substrate-binding domain and a catalytic domain are located in the N-terminus and in the C-terminus, respectively. The $PhaZ_{palLB19}$ and the $PhaZ_{palM4-7}$ commonly share the lipase box, GISSG, in their catalytic domains, and utilize $^{111}Asn$ and $^{110}Ser$ residues, respectively, as oxyanions that play an important role in transition-state stabilization of hydrolytic reactions.

Sedimentary Facies and Architecture of a Gigantic Gravelly Submarine Channel System in a Cretaceous Foredeep Trough (the Magallanes Basin, Southern Chile)

  • Sohn, Young Kwan;Jo, Hyung Rae;Woo, Jusun;Kim, Young-Hwan G.;Choe, Moon Young
    • Ocean and Polar Research
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    • 제39권2호
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    • pp.85-106
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    • 2017
  • The Lago Sofia conglomerate in southern Chile is a deep-marine gravelly deposit, which is hundreds of meters thick and kilometers wide and extends laterally for more than 100 km, filling the foredeep trough of the Cretaceous Magallanes Basin. For understanding the depositional processes and environments of this gigantic deep-sea conglomerate, detailed analyses on sedimentary facies, architecture and paleoflow patterns were carried out, highlighting the differences between the northern (Lago Pehoe and Lago Goic areas) and southern (Lago Sofia area) parts of the study area. The conglomerate bodies in the northern part occur as relatively thin (< 100 m thick), multiple units intervened by thick mudstone-dominated sequences. They show paleoflows toward ENE and S to SW, displaying a converging drainage pattern. In the southern part, the conglomerate bodies are vertically interconnected and form a thick (> 400 m thick) conglomerate sequence with rare intervening fine-grained deposits. Paleoflows are toward SW. The north-to-south variations are also distinct in sedimentary facies. The conglomerate bodies in the southern part are mainly composed of clast-supported conglomerate with sandy matrix, which is interpreted to be deposited from highly concentrated bedload layers under turbidity currents. Those in the northern part are dominated by matrix- to clast-supported conglomerate with muddy matrix, which is interpreted as the products of composite mass flows comprising a turbidity current, a gravelly hyperconcentrated flow and a mud-rich debris flow. All these characteristics suggest that the Lago Sofia conglomerate was formed in centripetally converging submarine channels, not in centrifugally diverging channels of submarine fans. The tributaries in the north were dominated by mass flows, probably affected by channel-bank failures or basin-marginal slope instability processes. In contrast, the trunk channel in the south was mostly filled by tractive processes, which resulted in the vertical and lateral accretion of gravel bars, deposition of gravel dunes and filling of scours and channels, similar to deposits of terrestrial gravel-bed rivers. The trunk channel developed along the axis of foredeep trough and its confinement within the trough is probably responsible for the thick, interconnected channel fills. The large-scale architecture of the trunk-channel fills shows an eastward offset stacking pattern, suggesting that the channel migrated eastwards most likely due to the uplift of the Andean Cordillera.

RAPD와 SRAP 마커를 이용한 참다래 유전자원의 유전적 다양성 (Genetic diversity in kiwifruit germplasm evaluated using RAPD and SRAP markers)

  • 조강희;곽용범;박서준;김세희;이한찬;김미영
    • Journal of Plant Biotechnology
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    • 제44권3호
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    • pp.303-311
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    • 2017
  • 본 연구는 참다래(Actinidia spp.) 유전자원의 유전적 다양성을 평가하기 위하여 재배품종 및 국내 외에서 수집한 참다래 61점을 대상으로 RAPD와 SRAP 분석을 수행하였다. RAPD 분석에서 40종의 선발 primer를 이용하여 230개의 다형성 밴드를 얻었으며, 평균 다형성 밴드 수는 5.75개였다. 32종의 primer 조합을 이용한 SRAP 분석에서 204개의 다형성 밴드를 획득하였고, 평균 다형성 밴드 수는 6.38 개였다. RAPD와 SRAP 분석에서 획득된 434개의 다형성 밴드를 이용하여 비가중 평균결합 방식으로 집괴분석한 결과 유전적 유사도 지수 0.680을 기준으로 3개의 그룹으로 분류되었다. 제1그룹에는 A. deliciosa와 A. chinensis에 속하는 품종과 A. deliciosa ${\times}$ A. arguta, A. chinensis ${\times}$ A. arguta, A. chinensis ${\times}$ A. deliciosa의 교잡종에 속하는 46점의 유전자원이 포함되었다. 제2그룹에는 A. arguta에 속하는 유전자원 7점과 A. arguta ${\times}$ A. deliciosa의 교잡종인 '스키니그린'이 포함되었다. 제3그룹에는 A. rufa, A. hemsleyana, A. macrosperma, A. polygama, A. eriantha 종에 속하는 유전자원 7점이 포함되었다. 참다래 유전자원 간 유전적 유사도 값은 0.479~0.991의 범위로 평균 유전적 유사도는 0.717이었다. 가장 높은 유사도 값(0.991)을 나타낸 유전자원은 NHK0038(A. deliciosa)과 NHK0040(A. deliciosa) 간이었고 가장 낮은 유사도 값(0.479)을 나타낸 유전자원은 '헤이워드'(A. deliciosa)와 K5-1-22(A. arguta) 간이었다.

Cellular and Molecular Pathology of Fungi on Plants Studied by Modern Electron Microscopy

  • Sanwald, Sigrun-Hippe
    • 한국식물병리학회:학술대회논문집
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    • 한국식물병리학회 1995년도 Proceedings of special lectures on Molecular Biological Approaches to Plant Disease National Agricultural Science and Technology Institute Suwon, Korea
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    • pp.27-53
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    • 1995
  • In plant pathology there is an increasing necessity for improved cytological techniques as basis for the localization of cellular substances within the dynamic fine structure of the host-(plant)-pathogen-interaction. Low temperature (LT) preparation techniques (shock freezing, freeze substitution, LT embedding) are now successfully applied in plant pathology. They are regarded as important tools to stabilize the dynamic plant-pathogen-interaction as it exists under physiological conditions. - The main advantage of LT techniques versus conventional chemical fixation is seen in the maintenance of the hydration shell of molecules and macromolecular structures. This results in an improved fine structural preservation and in a superior retention of the antigenicity of proteins. - A well defined ultrastructure of small, fungal organisms and large biological samples such as plant material and as well as the plant-pathogen (fungus) infection sites are presented. The mesophyll tissue of Arabidopsis thaliana is characterized by homogeneously structured cytoplasm closely attached to the cell wall. From analyses of the compatible interaction between Erysiphe graminis f. sp. hordei on barley (Hordeum vulgare), various steps in the infection sequence can be identified. Infection sites of powdery mildew on primary leaves of barley are analysed with regard to the fine structural preservation of the haustoria. The presentation s focussed on the ultrastructure of the extrahaustorial matrix and the extrahaustorial membrane. - The integration of improved cellular preservation with a molecular analysis of the infected host cell is achieved by the application of secondary probing techniques, i.e. immunocytochemistry. Recent data on the characterization of freeze substituted powdery mildew and urst infected plant tissue by immunogold methodology are described with special emphasis on the localization of THRGP-like (threonine-hydrxyproline-rich glycoprotein) epitopes. Infection sites of powdery mildew on barley, stem rust as well as leaf rust (Puccinia recondita) on primary leaves of wheat were probed with a polyclonal antiserum to maize THRGP. Cross-reactivity with the anti-THRGP antiserum was observed over the extrahaustorial matrix of the both compatible and incompatible plant-pathogen interactions. The highly localized accumulation of THRGP-like epitopes at the extrahaustorial host-pathogen interface suggests the involvement of structural, interfacial proteins during the infection of monocotyledonous plants by obligate, biotrophic fungi.

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배추에서 신규 염 저항성 관련 유전자 분리 및 검정 (Isolation and Identification of a New Gene Related to Salt Tolerance in Chinese Cabbage)

  • 유재경;박영두
    • 원예과학기술지
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    • 제31권6호
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    • pp.748-755
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    • 2013
  • 본 연구는 배추에서 염 저항성 관련 유전자를 발굴하기 위해 수행되었다. 우선 염처리(250mM NaCl)된 순계배추 'Chiifu'를 이용한 KBGP-24K oligo chip 데이터[BrEMD(B. rapa EST and microarray database)]를 분석하였다. 그 결과, 염처리 시 크게 반응하는 202개의 unigene들을 1차 선발하였고, 이들 중 기능이 정확히 알려지지 않았으나 완전장을 갖추고 있는 1개의 유전자를 최종선발하여 BrSSR(B. rapa salt sensitive resistance)로 명명하였다. BrSSR은 94개의 아미노산으로 번역되는 총 285bp의 오픈리딩프레임을 가지고 있으며, DUF581 도메인을 지니고 있다. 염 저항성을 분석하기 위하여 BrSSR이 과발현된 pSL94 vector를 제작하여 담배에 형질전환시켰다. BrSSR이 과발현된 $T_1$ 세대 담배 형질전환체들은 PCR과 DNA blot 분석에 의해 선발하였다. Quantitative real-time RT PCR 분석 결과, 형질 전환된 담배에서 BrSSR의 발현이 대조군 보다 약 3.8배까지 높게 발현되었다. 이는 RNA blot 분석 결과와도 일치했다. 또한 표현형 분석에서 5일간 250mM NaCl 염 처리 후 BrSSR이 과발현된 형질전환체들이 대조군보다 우수한 염 저항성을 보여 주었다. 위 결과들에 근거하여 염 스트레스 환경 하에서 BrSSR 유전자의 과발현은 식물의 염 저항성을 향상과 매우 밀접한 관계가 있는 것으로 판단된다.

국내에 자생하는 큰엉겅퀴와 고려엉겅퀴의 분자유전학적 및 화학적 분석 (Phylogenetic and Chemical Analyses of Cirsium pendulum and Cirsium setidens Inhabiting Korea)

  • 유선균;배영민
    • 생명과학회지
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    • 제22권8호
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    • pp.1120-1125
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    • 2012
  • 국내에 자생 중인 큰엉겅퀴(Cirsium pendulum)를 강원도의 홍천, 원주, 평창, 양양 및 경기도 가평과 충청북도의 충주에서 채취하고, 고려엉겅퀴(Cirsium setidens)를 강원도의 태백 및 경상북도의 봉화에서 채취하였다. 채취된 식물들의 genomic DNA를 분리하여서 18S rDNA, ITS1, 5.8S rDNA, ITS2 및 28S rDNA의 일부를 증폭하고, 그 염기서열을 분석하였다. 이렇게 얻어진 염기서열을 GenBank에 등록하고, 서로 비교해 보았다. 그 결과 큰엉겅퀴는 6개체 모두에서 18S rDNA 및 5.8S rDNA의 염기서열은 서로 완전히 일치하고 있으나, ITS1과 ITS2의 염기서열에서는 약간의 차이를 보였다. 고려엉겅퀴의 경우에는 18S rDNA, ITS1 및 ITS2에서 2개체가 서로 비교적 큰 차이를 보였다. 일본의 홋카이도에서 채취된 큰엉겅퀴와 중국의 안휘성에서 채취된 엉겅퀴(Cirsium japonicum)를 포함하여서 ITS1과 ITS2 염기서열을 비교한 결과, 엉겅퀴, 큰엉겅퀴, 고려엉겅퀴는 확연하게 서로 다른 그룹을 형성하는 것으로 나타났다. 또한 채취된 큰엉겅퀴 및 고려엉겅퀴들의 silymarin 함량을 분석해 본 결과, 모두에서 그 함량이 2 mg/ml가 넘는 것으로 나타났다. 따라서 엉겅퀴뿐만 아니라 큰엉겅퀴나 고려엉겅퀴도 여러 가지 약리작용을 가진 것으로 보고된 silymarin을 상당히 높은 농도로 함유하고 있는 것으로 나타났다.

제주 연안 퇴적층에서 분리된 미생물의 동정 및 단백질분해효소 특성 (Identification of Microorganisms Isolated from Jeju Coastal Sedimentary Layer and Characterization of Their Proteases.)

  • 김만철;장태원;김주상;한용재;;한송헌;오덕철;허문수
    • 생명과학회지
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    • 제19권6호
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    • pp.787-792
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    • 2009
  • 제주도 양식장 배출수 퇴적층에서 단백질 분해 효소를 생산하는 세균을 분리하였으며, 각각 SK-2, 및 SK-125라고 명명하였다. 분리균주 SK-2의 16S rDNA의 염기서열 분석 결과 Baeillus lieheniformis와 Baeillus subtillis의 염기서열과 99%의 상동성을 보였으며, BIOLOG를 이용한 생화학적 분석에서도 Bacillus family와 유사한 특성을 보여 최종적으로 분리균주 SK-2를 Baeillus sp. SK-2으로 명명하였다. 또한 분리균주 SK-125의 16S rDNA의 염기서열 분석 결과 Pseudoal teromonas haloplanktis의 염기서열과 99% 의 상동성을 보였으며, BIOLOG를 이용한 생화학적 분석에서도 Pseudoalteromonas family와 유사한 특성을 보여 최종적으로 분리균주 SK-125를 Pseudoalteromonas sp. SK-125라고 명명하였다. Baeillus sp. SK-2와 Pseudoalteromonas sp. SK-125균주의 온도별 실험에서는 $40^{\circ}C$에서 가장 높은 생육도를 보였으며, 효소활성은 Bacillus sp. SK-2와 Pseudoalteromonas sp. SK-125 두 균주 모두 $30^{\circ}C$에서 가장 높은 활성을 보였다.

The First Identified Citrus tristeza virus Isolate of Turkey Contains a Mixture of Mild and Severe Strains

  • Cevik, Bayram;Yardimci, Nejla;Korkmaz, Sava
    • The Plant Pathology Journal
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    • 제29권1호
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    • pp.31-41
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    • 2013
  • The presence of Citrus tristeza virus (CTV) has previously been reported in citrus growing regions of Turkey. All serologically and biologically characterized isolates including I$\breve{g}$d${\i}$r, which was the first identified CTV isolates from Turkey, were considered mild isolates. In this study, molecular characteristics of the I d r isolate were determined by different methods. Analysis of the I$\breve{g}$d${\i}$r isolate by western blot and BD-RT-PCR assays showed the presence of MCA13 epitope, predominantly found in severe isolates, in the I$\breve{g}$d${\i}$r isolate revealing that it contains a severe component. For further characterization, the coat protein (CP) and the RNA-depen-dent RNA polymerase (RdRp) genes representing the 3' and 5' half of CTV genome, respectively, were amplified from dsRNA by RT-PCR. Both genes were cloned separately and two clones for each gene were sequenced. Comparisons of nucleotide and deduced amino acid sequences showed that while two CP gene sequences were identical, two RdRp clones showed only 90% and 91% sequence identity in their nucleotide and amino acid sequences, respectively, suggesting a mixed infection with different strains. Phylogenetic analyses of the CP and RdRp genes of I$\breve{g}$d${\i}$r isolate with previously characterized CTV isolates from different citrus growing regions showed that the CP gene was clustered with NZRB-TH30, a resistance breaking isolate from New Zealand, clearly showing the presence of severe component. Furthermore, two different clones of the RdRp gene were clustered separately with different CTV isolates with a diverse biological activity. While the RdRp-1 was clustered with T30 and T385, two well-characterized mild isolates from Florida and Spain, respectively, the RdRp-2 was most closely related to NZRB-G90 and NZRB-TH30, two well-characterized resistance breaking and stem pitting (SP) isolates from New Zealand confirming the mixed infection. These results clearly demonstrated that the I$\breve{g}$d${\i}$r isolate, which was previously described as biologically a mild isolate, actually contains a mixture of mild and severe strains.

옥천대(沃川帶)의 지질(地質) 및 광물자원(鑛物資源)에 관(關)한 연구(硏究) -평창(平昌)~주천지역(酒泉地域)에 있어서의 광화작용(鑛化作用)- (Geology and Mineral Resources of the Ogcheon Zone: Mineralization in the Pyeongchang-Jucheon Area, Kangwon-Do, Korea)

  • 윤석규;소칠섭;김규한
    • 자원환경지질
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    • 제19권1호
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    • pp.1-18
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    • 1986
  • A group of 16 $Zn+Pb{\pm}Ag$ deposits distributed in the Pyeongchang-Jucheon area, Kangwon-do, South Korea, were semi-regionally investigated. These deposits are contact metasomatic and/or hydrothermal replacement types hosted in the carbonate-dominated Cambrian Machari Formation and Ordovician Ibtanri Formation, and also in the carbonate interbeds of the Precambrian argillic metasediments. Comparing some key aspects of the individual deposits, it is found that the ore deposits hosted in the Machari and Ibtanri Formations are mostly of steeply-dipping chimneys with or without skarn minerals and are rich in Ag and Pb>Zn in metal grade whereas those occuring in the carbonate interbeds of the Precambrian argillic metasediments are gently-dipping conformable lenticular orebodies mostly with skarn minerals and are generally poor in Ag and Zn>Pb. The skarn mineralization in the area appears to have occurred during the lower Cretaceous (118.7Ma) to mid-Cretaceous (107.8Ma) time assumed from the K-Ar dates of the Dowon and Pyeongchang granites which are closely associated with the skarn ore deposits. The Rb/Ba/Sr ratios of these granites indicate that they are of strongly differentiated anomalous granites, and the Nb vs. Y and Rb vs. Y+Nb plots fall on the field of volcanic arc setting. The contact aureoles are zoned, giving the sequence in order of increasing distance from igneous contact: garnet-wollastonite, granet-wollastonite-clinopyroxene and garnet-clinopyroxene in such as the Pyeongchang and Yeonwol 114 areas. Electron microprobe analyses reveal that garnets and clinopyroxenes are generally low in Fe and Mn. Garnets are grossular to intermediate grandite except for those from the Ogryong exoskarn which are richer in andradite, pyrope and spessartine fractions. This indicates that the oxidation state of skarn-forming environment at Ogryong was higher than at the other deposits. Clinopyroxenes are mostly salitic except for those from the Ogryong exoskarn which involve considerable amounts of hedenbergite and johansenite fractions. The ${\delta}^{18}O$ value of Jurassic biotite granite at Ogryong is higher (+10.21‰) than that of Cretaceous one at Chodun (+8.41‰). The ${\delta}^{13}C$ values of carbonate rocks range from -0.89‰ to 0.68‰ and the ${\delta}^{18}O$ values range from +11.91‰ to + 19.34‰ indicating that these carbonate rocks are of marine origin. However, the ${\delta}^{13}C$ values of skarn calcite and vein calcite are -4.80‰ and -12.92‰, and the ${\delta}^{18}O$ values are +5.56‰ and +10.32‰, respectively, indicating that these calcites are of hydrothermal origin. The ${\delta}^{34}S$ values of sulfide minerals range from +4.4‰ to +8.7‰ suggesting that the sulfurs are of magmatic origin.

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단양지역의 지질구조 (Structural Analysis of the Danyang Area, Danyang Coalfield, Korea)

  • 김정환;고희재
    • 자원환경지질
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    • 제25권1호
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    • pp.61-72
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    • 1992
  • 단양지역은 단양탄전 서남부에 위치하며, 습곡작용과 드러스트 단층운동을 받은 중생대와 고생대 지층들로 구성되어 있다. 연구지역은 대규모의 조구조선, 동으로는 옥동단층과 서쪽에는 각동 드러스트 단층으로 경계지워져 있다. 연구지역내에 발달하고 있는 지질구조 요소들을 해석한 결과 연구지역내의 지층들이 4번에 걸쳐서 변형작용을 받았다. 옥동단층을 따라서 발달하고 있는 압쇄대는 첫번째 변형작용($D_1$) 중에 형성되었으며, 이와 관련된 구조로는 장산규암층내에 불연속적으로 발달하고 있는 압쇄대와 조서누층군내의 지층에 평행하게 발달한 인장(引長, pull-apart)구조들이 관찰된다. 두번째 변형작용중에 형성된 지질구조($D_2$)로는 북서방향의 습곡구조와 선구조들이며, 이러한 구조들은 대동 누층군 내에서는 관찰되지 않는다. 한반도 전역에 영향을 준 대보조산운동의 결과로 형성된 지질 구조들로는 ($D_3$) 각동 드러스트를 비롯한 북동방향의 드러스트 단층들과 습곡구조 등이다. 이 기간 동안에 기존의 지질구조들은 더 tight해졌으며, 변형되고 북동방향으로 회전되었다. 최후기의 변형작용($D_4$) 중에 동-서 방향의 죽령단층과 미약한 습곡구조가 형성되었다. 죽령단층내의 지층들은 주향이동 단층운동중에 회전되고 transpression의 영향을 받았다.

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