• Molecules and Cells
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• 제42권2호
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• pp.104-112
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• 2019

Tracking the fate of individual cells and their progeny through lineage tracing has been widely used to investigate various biological processes including embryonic development, homeostatic tissue turnover, and stem cell function in regeneration and disease. Conventional lineage tracing involves the marking of cells either with dyes or nucleoside analogues or genetic marking with fluorescent and/or colorimetric protein reporters. Both are imaging-based approaches that have played a crucial role in the field of developmental biology as well as adult stem cell biology. However, imaging-based lineage tracing approaches are limited by their scalability and the lack of molecular information underlying fate transitions. Recently, computational biology approaches have been combined with diverse tracing methods to overcome these limitations and so provide high-order scalability and a wealth of molecular information. In this review, we will introduce such novel computational methods, starting from single-cell RNA sequencing-based lineage analysis to DNA barcoding or genetic scar analysis. These novel approaches are complementary to conventional imaging-based approaches and enable us to study the lineage relationships of numerous cell types during vertebrate, and in particular human, development and disease.

• Bulletin of the Korean Chemical Society
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• 제24권6호
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• pp.797-801
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• 2003

One of the largest challenges for quantum chemistry today is to obtain accurate results for large complex molecular systems, and a variety of approaches have been proposed recently toward this goal. We have developed the ONIOM method, an onion skin-like multi-level method, combining different levels of quantum chemical methods as well as molecular mechanics method. We have been applying the method to many different large systems, including thermochemistry, homogeneous catalysis, stereoselectivity in organic synthesis, solution chemistry, fullerenes and nanochemistry, and biomolecular systems. The method has recently been combined with the polarizable continuum model (ONIOM-PCM), and was also extended for molecular dynamics simulation of solution (ONIOM-XS). In the present article the recent progress in various applications of ONIOM and other electronic structure methods to problems of homogeneous catalyses and nanochemistry is reviewed. Topics include 1. bond energies in large molecular systems, 2. organometallic reactions and homogeneous catalysis, 3. structure, reactivity and bond energies of large organic molecules including fullerenes and nanotubes, and 4. biomolecular structure and enzymatic reaction mechanisms.

• Interdisciplinary Bio Central
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• 제2권2호
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• pp.6.1-6.5
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• 2010

Fragment molecular orbital (FMO) method provides a novel tool for ab initio calculations of large biomolecules. This method overcomes the size limitation difficulties in conventional molecular orbital methods and has several advantages compared to classical force field approaches. While there are many features in this method, we here focus on explaining the issues related to protein-ligand binding: FMO method provides useful interaction-analysis tools such as IFIE, CAFI and FILM. FMO calculations can provide not only binding energies, which are well correlated with experimental binding affinity, but also QSAR descriptors. In addition, FMO-derived charges improve the descriptions of electrostatic properties and the correlations between docking scores and experimental binding affinities. These calculations can be performed by the ABINIT-MPX program and the calculation results can be visualized by its proper BioStation Viewer. The acceleration of FMO calculations on various computer facilities is ongoing, and we are also developing methods to deal with cytochrome P450, which belongs to the family of drug metabolic enzymes.

• Nuclear Medicine and Molecular Imaging
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• 제42권2호
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• pp.145-152
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• 2008

Nuclear medicine imaging has an unique advantage of absolute quantitation of radioactivity concentration in body. Tracer kinetic analysis has been known as an useful investigation methods in quantitative study of in-vivo physiological function. The use of nuclear medicine imaging and kinetic analysis together can provide more useful and powerful intuition in understanding biochemical and molecular phenomena in body. There have been many development and improvement in kinetic analysis methodologies, but the conventional basic concept of kinetic analysis is still essential and required for further advanced study using new radiopharmaceuticals and hybrid molecular imaging techniques. In this paper, the basic theory of kinetic analysis and imaging techniques for suppressing noise were summarized.

• Biomolecules & Therapeutics
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• 제21권6호
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• pp.423-434
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• 2013

The adoption of oligonucleotide aptamer is well on the rise, serving an ever increasing demand for versatility in biomedical field. Through the SELEX (Systematic Evolution of Ligands by EXponential enrichment), aptamer that can bind to specific target with high affinity and specificity can be obtained. Aptamers are single-stranded nucleic acid molecules that can fold into complex three-dimensional structures, forming binding pockets and clefts for the specific recognition and tight binding of any given molecular target. Recently, aptamers have attracted much attention because they not only have all of the advantages of antibodies, but also have unique merits such as thermal stability, ease of synthesis, reversibility, and little immunogenicity. The advent of novel technologies is revolutionizing aptamer applications. Aptamers can be easily modified by various chemical reactions to introduce functional groups and/or nucleotide extensions. They can also be conjugated to therapeutic molecules such as drugs, drug containing carriers, toxins, or photosensitizers. Here, we discuss new SELEX strategies and stabilization methods as well as applications in drug delivery and molecular imaging.

• Bulletin of the Korean Chemical Society
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• 제23권3호
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• pp.417-422
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• 2002

Comparison studies of the Quantitative Structure Activity Relationship (QSAR) methods with new imidazo-quinolinedione derivatives were conducted using Comparative Molecular Field Analysis (CoMFA), Comparative Molecular Similarity Indices Analysis (CoMSIA), and the Hologram Quantitative Structure Activity Relationship (HQSAR). When the CoMFA crossvalidation value, q2, was 0.625, the Pearson correlation coefficient, r2, was 0.973. In CoMSIA, q2 was 0.52 and r2 was 0.979. In the HQSAR, q2 was 0.501 and r2 was 0.924. The best result was obtained using the CoMSIA method according to a comparison of the calculated values with the real in vitro cytotoxic activities against human ovarian cancer cell lines.

• 제어로봇시스템학회논문지
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• 제11권4호
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• pp.353-362
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• 2005

This article describes a state-of-the art review in nano-biomanipulation technologies. Nanomanipulation of biological objects enables an in-depth study of single molecules such as DNA and RNA, and of biophysical events at the molecular level like molecular motors. Controlled nanomanipulation is challenging but essential for precisely engineering biomolecules or cells and for manufacturing functional nano-biosystems. In this paper, we summarize several contact, non-contact and hybrid methods available for nanomanipulation of biological objects. Advantages currently available methods and their limitations are also compared. Finally, we discuss possible applications of nano-biomanipulation technologies to life science and molecular medicine including cell biology, genetic engineering, biophysics, and biochemistry.

• 대한화학회지
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• 제6권1호
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• pp.94-98
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• 1962

The polycondensates of isophthalic acid-cinnamic acid-glycerine system were synthesized. The molecular weights of these products were determined by two methods, viscosity method and osmotic pressure methods. In the synthesis of resin, the reaction temperature was kept at 232$^{\circ}C$ and the mole ratio of the reactants was chosen as follows: Glycerine ;1.0 Isophthalic acid ;1.0 Cinnamic acid ;2.8 Excessive cinnamic acid prevented gelation of reaction mixtures. As the solution became very dilute, reduced osmotic pressure P/C (at the concentration of solution below 0.24g/100 ml of acetone) and reduced viscosity ${\eta}_{sp}/C$ (at the concentration of solution below 0.32 g/100 ml of acetone) increased rapidly. The correspondence between molecular weights determined by the two methods made Huggin's equation applicable to the prepared polymer. The values of K and a are $2.77{\times}10^{-5}$ and 1.063, respectively.

• 대한소화기학회지
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• 제72권5호
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• pp.229-236
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• 2018

Accurate diagnosis of Helicobacter pylori (H. pylori) infection is mandatory for the effective management of many gastroduodenal diseases. Currently, various diagnostic methods are available for detecting these infections, and the choice of method should take into account the clinical condition, accessibility, advantage, disadvantage, as well as cost-effectiveness. The diagnostic methods are divided into invasive (endoscopic-based) and non-invasive methods. Non-invasive methods included urea breath test, stool antigen test, serology, and molecular methods. Invasive methods included endoscopic imaging, rapid urease test, histology, culture, and molecular methods. In this article, we provide a review of the currently available options and recent advances of various diagnostic methods.

• Bulletin of the Korean Chemical Society
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• 제25권7호
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• pp.1061-1064
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• 2004

Molecular visualization software has the common objective of manipulation and interpretation of data from numerical simulations. They visualize many complicated molecular structures with personal computer and workstation, to help analyze a large quantity of data produced by various computational methods. However, users are often discouraged from using these tools for visualization and analysis due to the difficult and complicated user interface. In this regard, we have developed an easy-to-use three-dimensional molecular visualization and analysis program named POSMOL. This has been developed on the Microsoft Windows platform for the easy and convenient user environment, as a compact program which reads outputs from various computational chemistry software without editing or changing data. The program animates vibration modes which are needed for locating minima and transition states in computational chemistry, draws two and three dimensional (2D and 3D) views of molecular orbitals (including their atomic orbital components and these partial sums) together with molecular systems, measures various geometrical parameters, and edits molecules and molecular structures.