주형기반 단백질 모델 구조의 정밀화

Contemporary template-based modeling techniques allow applications of modeling methods to vast biological problems. The proportion of proteins that template-based modeling can generate reasonably accurate models is rapidly increasing due to the continuous growth of both structure and sequence databases. However, they tend to fail to provide accurate structures for less-conserved local regions in sequence even when the overall structure can be modeled reliably. These regions in template-based models are named as unreliable local regions (ULRs). Accurate modeling of ULRs is of enormous value because they are frequently involved in functional specificity. In this thesis, a new method for template-based model refinement is introduced by which ULRs are intensively refined with protein loop modeling techniques. The method attempts to model three types of ULRs in template-based models, loop, terminus, and secondary structure segments with related approaches. These methods follow a general global optimization procedure, guided by hybrid-type energy function combining physico-chemical force fields with statistical potentials. During global optimization, relatively accurate framework structure is fixed and sophisticated loop modeling technique is applied to ULR as a geometric operator to enhance sampling efficiency. Large-scale tests are carried out for intensive reconstruction of ULRs in native structure as well as in CASP (Critical Assessment of techniques for Protein Structure prediction) template-based model structures. In addition, the method is extended to simultaneous modeling of template-based model structure with ULR. In all tests ULR structures are improved over initial template-based models. The results show that a careful application of loop modeling supported by theories from physical chemistry and bioinformatics can be a promising avenue for model refinement in template-based modeling.최근 들어 주형기반 단백질 구조 예측 기법은 다양한 생명과학 관련 문제들에 적용되고 있다. 지속적인 단백질 구조 및 아미노산 서열 데이터베이스의 증가 덕분에, 주형기반 모델링 방법이 그 구조를 정확히 예측해낼 수 있는 대상 단백질의 비율이 갈수록 증가하고 있다. 이 방법은 단백질의 전체적인 구조는 잘 예측해내지만 아미노산 서열상 잘 보존되지 않는 구조 영역은 좋은 구조를 만들어내지 못하는 한계가 있다. 주형기반 단백질 모델링에서 바로 이런 영역을 본 논문에서는 ULR (국소 문제 영역, Unreliable local region)이라 부르기로 한다. 이 논문에서는 단백질 루프 모델링 방법을 접목하여 ULR들을 집중적으로 정밀화하는 방법을 소개하고자 한다. 이 방법은 주형기반 단백질 구조에서 나타나는 세 가지 서로 다른 ULR들, 루프, 말단부, 이차구조 조각에 대해 유사한 접근 방법을 취한다. 이 방법에서는 물리화학 및 통계적 에너지의 조합으로 이뤄진 하이브리드 에너지 함수에 의해 광역 최적화를 진행한다. 광역최적화 동안 단백질의 전체적 뼈대 구조는 고정된 가운데 ULR에 대해 국소적으로 루프 모델링 기법을 동원하여 구조 샘플링을 한다. 이 연구에서는 ULR의 집중 정밀화를 고유 구조에서의 구조 재구성뿐 아니라 CASP (Critical Assessment of techniques for Proteins Structure Prediction) 주형기반 모델링 구조들에 대해서도 광범위하게 테스트하였다. 더 나아가 ULR 뿐 아니라 주형기반 단백질 전체 구조를 동시에 정밀화하는 방법으로도 확장하였다. 모든 테스트에 대해 ULR 구조들은 초기 주형기반 구조에 비해 향상됨을 발견할 수 있었다. 본 연구 결과는 물리화학과 생물정보학에 기반한 단백질 고리 모델링 기법 적용이 주형기반 단백질 구조 정밀화에 기여하는 새로운 방법임을 제시하고 있다.Docto

X-ray Tube System for insertion into affected parts and X-ray Brachytherapy System comprising the same

본 발명은 환부 삽입용 X-선 튜브 시스템 및 이를 포함하는 X-선 근접 치료 시스템에 관한 것으로, 본 발명의 실시 예를 따르는 삽입용 X-선 튜브 시스템은, X-선을 방출하는 X-선 타겟을 포함하는 X-선 튜브; 상기 X-선 튜브와 연결된 전원 연결부; 및 상기 X-선 튜브를 둘러싸고, 상기 X-선 튜브에서 방출된 X-선을 외부로 방출하는 어플리케이터;를 포함하고, 상기 어플리케이터는 상기 X-선 튜브에서 방출된 X-선이 외부로 방출되는 X-선의 양을 감소시키거나 차단하는 제1부 및 상기 제1부를 지지하는 제2부를 포함한다

Elemental compositions of smectite responding to changes in deposition conditions and sediment provenance during glacial and interglacial periods; Ulleung basin, East Sea

Variation of clay mineral contents have been widely used to understand the changes in paleo-depositional condition and sediment provenance. Especially, smectite with wide range of elemental composition originated from multiple different sources could be used to distinguish the sediment provenances. In this study, sedimentary facies, clay mineral assemblages and C14 age dating in the core sediments (13 m long) from the Ulleung basin were adapted to characterize the depositional units and smectite elemental composition was utilized to distinguish the changes in sediment provenances. Moderate Al, Mg, Fe content smectite was dominantly observed in glacial period core depth sediment, while Al-rich smectite group and Fe-rich smectite group were identified in interglacial period core depth sediment. Observation of quite distinct smectite group between interglacial and glacial period indicated the different sources of sediment affected to Ulleung basin during interglacial and glacial period. These results provide a clue to understand the paleo-depositional condition changes including sea-level and current change in the East Sea and Dokdo island2

Nano-scale study of iron oxide/oxyhydroxide in hydrothermal vent microbial mat

Hydrothermal vent systems consisting of hydrothermal vent, hydrothermal sediment and microbial mat are widely spread around the ocean, particularly spreading axis, continental margin and back-arc basin. Scientists have perceived that the hydrothermal systems, which reflect the primeval earth environment, are one of the best places to reveal the origin of life and extensive biogeochemical process of microbe-mineral interaction. Red-colored microbial mat recovered by Canadian scientific submersible ROPOS on South Pacific North Fiji basin KIOST hydrothermal vent expedition 1602 contains iron oxides and iron oxyhydroxides. Various morphologies of minerals in the red-colored microbial mat observed by Scanning Electron Microscopy (SEM) are mainly showed sheath shaped, resembled with Leptothrix microbial structure and stalks shaped, similar with Marioprofundus microbial structures. They are also detected with DNA analysis. The cross sectional observation of microbial structures encrusted with iron oxide and iron oxyhydroxide at a nano scale by Focused Ion Beam (FIB) technique, Transmission Electron Microscopy (TEM) and Scanning Transmission Electron Microscopy-spectrum image (STEM-SI) analysis was developed to verify the structural/biogeochemical properties in the microbe-mineral interaction. Systematic nano-scale measurements on the biomineralization in the microbial mat leads the understandings of biogeochemical environme1

Mineralogical Characteristics for the Sediments around Dokdo, East Sea, South Korea

There is little understanding of clay mineralogical depositional environment for the subseafloor sediments around Dokdo, East Sea, South Korea, because clay minerals are scarce for the previous expedition (2016.09.07 ~ 2016.09.08). The recent site (132° 00.371’, 37° 24.252’) in the basin-like topography that will collect the clay minerals, was explored to understand clay mineralogy, elemental composition of smectite, grain size distribution of smectite, sedimentary phaseand relative proportion of clay minerals. The change of depositional environment has influenced the mineralogical characteristics of the marine sediment around Dokdo during the interglacial and glacial period. Grain size distribution showed a variation in the proportion of clay, silt and sand size which consistent with the change of sedimentary facies. During the interglacial period bioturbated mud is dominant, while laminated mud is dominant during the glacial period. Variation in the relative proportion of clay minerals such as smectite, illite, chlorite and kaolinite also reflects the change of depositional environments during the glacial-interglacial period. During the interglacial period, smectite is moreabundant than the glacial period. In this study, the interpretation of paleo-depositional environments around Dokdo will be discussed.2

The characterization of ferromanganese crust and its redox change, Western Pacific Magellan seamounts

Biotic/abiotic redox reaction is a ubiquitous process in mineral formation and growth, and changes in elemental redox states, particularly Fe/Mn may reflect the redox conditions in the sediment/ocean when the mineral forms. Samples were dredged from the seamounts in the western Pacific, OSM11 in order to investigate the formation, growth and its implications to geological history. The crust consist of five well-defined layers (here after called “layer 1” (rim) through “layer 5” (core)). Quartz, feldspar, and hematite are detected only in the layer 1 in addition to the poorly crystallined Fe-rich vernadite, which is likely to be associated with slower growth rate compared to the layers 2-5. CFA were identified in layers 4 and 5 under XRD measurement. Visible size of white colored well crystallined CFA were only observed in layer 4 whereas nano-sized CFA in layer 5 were identified by TEM. Clay minerals such as smectite were observed by TEM with SAED pattern and EDX in layers 1 and 3. The oxidation states of Fe and Mn in Fe-rich vernadite in entire layers were determined by EELS analysis. All the layers of Mn oxide minerals was consisted with dominantly Mn4+, which is consistent with appearance of vernadite in Fe-Mn crust. Fe-rich vernadite in layers 1 and 4 were consisted with 26-52 % of Fe3+/Fetot, dominant reduced form of Fe compared to layers 2, 3, and 5. The observed alternative patterns of Fe oxidation state dged from the seamounts in the western Pacific, OSM11 in order to investigate the formation, growth and its implications to geological history. The crust consist of five well-defined layers (here after called “layer 1” (rim) through “layer 5” (core)). Quartz, feldspar, and hematite are detected only in the layer 1 in addition to the poorly crystallined Fe-rich vernadite, which is likely to be associated with slower growth rate compared to the layers 2-5. CFA were identified in layers 4 and 5 under XRD measurement. Visible size of white colored well crystallined CFA were only observed in layer 4 whereas nano-sized CFA in layer 5 were identified by TEM. Clay minerals such as smectite were observed by TEM with SAED pattern and EDX in layers 1 and 3. The oxidation states of Fe and Mn in Fe-rich vernadite in entire layers were determined by EELS analysis. All the layers of Mn oxide minerals was consisted with dominantly Mn4+, which is consistent with appearance of vernadite in Fe-Mn crust. Fe-rich vernadite in layers 1 and 4 were consisted with 26-52 % of Fe3+/Fetot, dominant reduced form of Fe compared to layers 2, 3, and 5. The observed alternative patterns of Fe oxidation state1

Iron oxide/oxyhydroxide formation in hydrothermal vent area microbial mat nano-scale electron microscopy analysis

Hydrothermal vent systems consisting of hydrothermal vent, hydrothermal sediment and microbial mat are widely spread around the ocean, particularly spreading axis, continental margin and back-arc basin. Scientists have perceived that thehydrothermal systems, which reflect the primeval earth environment, are one of the best places to reveal the origin of life and extensive biogeochemical process of microbe-mineral interaction. Microbial mat sample around the hydrothermal vent area, recovered by Canadian scientific submersible ROPOS on South Pacific North Fiji basin KIOST hydrothermal vent expedition 1602. Various morphologies of minerals in the microbial mat observed by scanning electron microscopy (SEM) showed sheath shaped, resembled with Leptothrix microbial structure, stalks shaped, similar with Mariprofundus microbial structure. Biological association with iron oxide and iron oxyhydroxide formation revealed the variation in crystallinity, iron oxidation states of goethite & iron oxyhydroxide and carbon C-K edge ELNES structure utilizing focused ion beam (FIB) technique, transmission electron microscopy (TEM), scanning transmission electron microscopy-spectrum image (STEM-SI). In this study presents iron oxide & iron oxyhydroxide formation and transformation schematic mechanism with biological effect in natural environment.2

Electron microscopic observation on microbe-like structures in the ferromanganese crust from the western Pacific Magellan Seamount

Understanding the biogeochemical process in the Fe-Mn crust layers is important toreconstruct the paleo-environment when the Fe-Mn crust layers form. Scanning ElectronMicroscopy (SEM), Transmission Electron Microscopy (TEM), Electron Energy LossSpectroscopy (EELS), and Polymerase Chain Reaction (PCR) were utilized to determinethe redox states of Fe/Mn and microbial diversity at each layer. Fe-Mn crust sample wasdredged from the western Pacific Magellan Seamount (OSM11) that consists of five welldefinedlayers from the rim (L1) to the core (L5). Some microbial-like structures andbiogenic-derived structures of sheath-like with filaments, tube-shaped (L1 &#8211 L3), capsuleshaped(L2), fossilized coccolith mounds with phosphatized globules (L4), and beanshaped(L4) were detected in entire layers of Fe-Mn crust.ergy LossSpectroscopy (EELS), and Polymerase Chain Reaction (PCR) were utilized to determinethe redox states of Fe/Mn and microbial diversity at each layer. Fe-Mn crust sample wasdredged from the western Pacific Magellan Seamount (OSM11) that consists of five welldefinedlayers from the rim (L1) to the core (L5). Some microbial-like structures andbiogenic-derived structures of sheath-like with filaments, tube-shaped (L1 &#8211 L3), capsuleshaped(L2), fossilized coccolith mounds with phosphatized globules (L4), and beanshaped(L4) were detected in entire layers of Fe-Mn crust.1