• BMB Reports
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• v.56 no.12
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• pp.633-644
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• 2023

Epigenetic mechanisms, primarily mediated through histone and DNA modifications, play a pivotal role in orchestrating the functional identity of a cell and its response to environmental cues. Similarly, the spatial arrangement of chromatin within the three-dimensional (3D) nucleus has been recognized as a significant factor influencing genomic function. Investigating the relationship between epigenetic regulation and 3D chromatin structure has revealed correlation and causality between these processes, from the global alignment of average chromatin structure with chromatin marks to the nuanced correlations at smaller scales. This review aims to dissect the biological significance and the interplay between the epigenome and 3D chromatin structure, while also exploring the underlying molecular mechanisms. By synthesizing insights from both experimental and modeling perspectives, we seek to provide a comprehensive understanding of cellular functions.

• Molecules and Cells
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• v.42 no.7
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• pp.512-522
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• 2019

Chromosomes located in the nucleus form discrete units of genetic material composed of DNA and protein complexes. The genetic information is encoded in linear DNA sequences, but its interpretation requires an understanding of three-dimensional (3D) structure of the chromosome, in which distant DNA sequences can be juxtaposed by highly condensed chromatin packing in the space of nucleus to precisely control gene expression. Recent technological innovations in exploring higher-order chromatin structure have uncovered organizational principles of the 3D genome and its various biological implications. Very recently, it has been reported that large-scale genomic variations may disrupt higher-order chromatin organization and as a consequence, greatly contribute to disease-specific gene regulation for a range of human diseases. Here, we review recent developments in studying the effect of structural variation in gene regulation, and the detection and the interpretation of structural variations in the context of 3D chromatin structure.

• Journal of Biomedical Engineering Research
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• v.36 no.6
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• pp.271-275
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• 2015

The aim of this study was to develop a multi-nozzle based bioprinting system for fabrication of three-dimensional (3D) biological structure. In this study, a thermoplastic biomaterial that has relatively high mechanical stability, polycaprolactone (PCL) was used to make the 3D structure. A multi-nozzle bioprinting system was designed to dispense thermoplastic biomaterial and hydrogel simultaneously. The system that consists of 3-axes of x-y-z motion control stage and a compartment for injection syringe control mounted on the stage has been developed. Also, it has 1-axis actuator for position change of nozzle. The controllability of the printed line width with PCL was tested as a representative performance index.

• Genomics & Informatics
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• v.7 no.4
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• pp.212-216
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• 2009

WebChemDB is an integrated chemical database retrieval system that provides access to over 8 million publicly available chemical structures, including related information on their biological activities and direct links to other public chemical resources, such as PubChem, ChEBI, and DrugBank. The data are publicly available over the web, using two-dimensional (2D) and three-dimensional (3D) structure retrieval systems with various filters and molecular descriptors. The web services API also provides researchers with functionalities to programmatically manipulate, search, and analyze the data.

• Journal of Biomedical Engineering Research
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• v.15 no.2
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• pp.201-208
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• 1994

Many three-dimensional object modeling and display methods for computer graphics and computer vision have been developed. Recently, with the help of medical imaging devices such as computerized tomography, magnetic resonance image, etc., some of those object modeling and display methods have been widely used for capturing the shape, structure and other properties of real objects in many medical applications. In this paper, we propose the reconstruction and display method of the three-dimensional object from a series of the cross sectonal image. It is implemented by using the automatic threshold selection method and the contour following algorithm. The combination of curvature and distance, we select feature points. Those feature points are the candidates for the tiling method. As a results, it is proven that this proposed method is very effective and useful in the comprehension of the object's structure. Without the technician's responce, it can be automated.

• Applied Biological Chemistry
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• v.38 no.6
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• pp.516-521
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• 1995

In order to find a potent anti-methicillin resistant Staphylococcus aureus (MRSA) antibiotic, actinomycetes isolated from the samples collected in Korean marine silt were screened. From the culture broth of the isolated Streptamyces strain AM045, a substance showing excellent biological activity against MRSA was found, isolated and named AM3. The compound showed strong activities against MRSA, S. epidermidis, E. faecium and E. faecalis, which were better than those of vancomycin and teicoplanin. Unfortunately, AM3 was identified as Actinomycin V. However, this paper reports the three dimensional study of AM3 based on high resolution nmr and Computer Aided Molecular Modeling(CAMM), and the fact that the structure of the pentapeptide lactone ring with oxo-proline in chloroform solution does not have 'C conformation' any more.

• Proceedings of the KOSOMBE Conference
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• v.1989 no.05
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• pp.39-43
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• 1989

In this paper, hierachical representation method with a 1-to-4 and 1-to-8 data structure is used to reconstruct the three-dimensional scene from two-dimensional cross sections provided by computed tomography with small memory computer system. To reduce the internal memory use, 2-D section is represented by quadtree, and 3-D scene is represented by octree. Octree is constructed by recursively merging consecutive quadtrees. This method uses 7/200 less memory than pointer type structure with all the case, and less memory up to 60.3% than linear octree with experimental data.

• Proceedings of the KOSOMBE Conference
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• v.1997 no.11
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• pp.137-141
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• 1997

In this study, in order to improve visualization and enhance the ability of the surgeon to perform delicate endoscopic surgery, three dimensional endoscopic system is designed. These 3D systems have our features of stereoendoscopic image processing: real time image capture and retrieve; presentation of left and right image on a single monitor; separable processing of the left and right eye images; coding of the 3D endoscopic video. For 3D endoscopic video coding, three approaches are presented based on interlaced picture structure, side-field format structure, and simulcast technique. Experimental results and performances comparisons are presented and analyzed or these approaches. Digital video coding techniques are presented or 3D endoscopic video sequences by means of an MPEG-2 video coding.

• Molecules and Cells
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• v.22 no.1
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• pp.13-20
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• 2006

Hepatitis C virus (HCV) non-structural protein 5A protein (NS5A), which consists of three functional domains, is involved in regulating viral replication, interferon resistance, and apoptosis. Recently, the three-dimensional structure of the domain 1 was determined. However, currently the molecular basis for the domains 2 and 3 of HCV NS5A is yet to be defined. Toward this end, we expressed, purified the domain 2 of the NS5A (NS5A-D2), and then performed biochemical and structural studies. The purified domain 2 was active and was able to bind NS5B and PKR, biological partners of NS5A. The results from gel filtration, CD analysis, 1D $^1H$ NMR and 2D $^1H-^{15}N$ heteronuclear single quantum correlation (HSQC) spectroscopy indicate that the domain 2 of NS5A appears to be flexible and disordered.

• Molecules and Cells
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• v.41 no.10
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• pp.889-899
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• 2018

Intrinsically disordered proteins (IDPs) are highly unorthodox proteins that do not form three-dimensional structures under physiological conditions. The discovery of IDPs has destroyed the classical structure-function paradigm in protein science, 3-D structure = function, because IDPs even without well-folded 3-D structures are still capable of performing important biological functions and furthermore are associated with fatal diseases such as cancers, neurodegenerative diseases and viral pandemics. Pre-structured motifs (PreSMos) refer to transient local secondary structural elements present in the target-unbound state of IDPs. During the last two decades PreSMos have been steadily acknowledged as the critical determinants for target binding in dozens of IDPs. To date, the PreSMo concept provides the most convincing structural rationale explaining the IDP-target binding behavior at an atomic resolution. Here we present a brief developmental history of PreSMos and describe their common characteristics. We also provide a list of newly discovered PreSMos along with their functional relevance.