• Journal of Microbiology
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• v.40 no.4
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• pp.319-326
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• 2002

Cellular DNA in prokaryotes is organized in nucleic acid-protein self-assemblies referred to as the nucleoid. The physical forces responsible for its stability inside the poor solvent properties of the cytoplasm and their functional implications are not understood. Studies on the organisation and functioning of the cytosol of cells largely rely on experimental protocols performed in highly dilute solutions using biochemically purified molecules, which is not a reliable substitute for the situation existing in vivo. Our current research interest is focused on the characterization of biological and physical forces determining the compaction and phase separation of DNA in Escherichia coli cytoplasm. We have emphasized the effect of excluded volume in solutions with high macromolecular concentrations (macromolecular crowding) upon self-association patterns of reactions. The prokaryotic cytosol was simulated by addition of inert polymer polyethylene glycol (PEG) (average molecular weight 20000), as an agent which afterwards facilitates the self-association of macromolecules. Fluorescence microscopy was used for direct visualization of nucleoids in intact cells, after staining with DAPI (4',6-diamidino-2-phenylindole dihydrochloride). Addition of the crowding agent PEG 20,000, in increasing concentrations generated progressively enhanced nucleoid compaction, the effect being stronger in the presence of 0.2 M NaCl and 5 mM MgCl$\_$2/. Under these conditions, the nucleoids were compacted to volumes of around 2 ㎛$\^$3/ or comparable sizes with that of living cells.

• Journal of the Korea Computer Graphics Society
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• v.10 no.2
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• pp.1-9
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• 2004

본 논문에서는 바이러스와 같은 생화학 물질의 분자구조를 3 차원 모델로 시각화하여 관찰하고, 그 분자모델을 직관적인 방법으로 조작하기 위한 가상 현실 분자 모델링 시스템을 제안한다. 이 시스템을 사용하면, 입체영상 디스플레이 장치와 데이터 글러브 및 동작 추적 장치를 사용하여 3 차원 분자 모델을 실감나게 조작할 수 있어서 효율적으로 분자들을 관찰하고 결합, 분리하는 등의 분자 모델링 작업이 가능하다. 사용자들은 마우스나 키보드 등의 장비 대신에 자연스러운 몸 동작이나 손 동작을 이용하여 분자 모델링 작업을 위한 동작을 하게 된다. 분자들의 결합을 화학적으로 정확하게, 그리고 실시간으로 시뮬레이션 하기 위해서 에너지 계산 알고리즘을 구현하였으며 이러한 작업이 가능하도록 분자 구조를 표현하는 새로운 자료구조를 제안하였다. 본 연구에서 제안하는 동작 기반의 VR 분자 모델링 시스템의 타당성을 검증하기 위하여 HIV 바이러스 분자를 가지고 분자 모델링 작업을 수행하였고, 사용자 테스트를 실시하여 기존의 방식과 작업 성능 및 사용자 만족도를 비교하였다.

• Korean Journal of Environmental Biology
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• v.38 no.3
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• pp.350-354
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• 2020

Many parrots are considered endangered species due to threats from human activities. Gender determination is of great importance for biological studies and the conservation of endangered parrots. However, like other birds, gender determination in parrots is hindered due to the lack of external dimorphism between males and females. A molecular approach using the chromo-helicase-DNA binding protein 1 (CHD1) gene is commonly used for sexing birds. This study aimed to determine the gender of parrots from Korean zoos based on amplification and visualization of the partial CHD1 gene. The samples of 13 parrot species were collected from three different zoos in Korea and the extracted DNA templates were amplified using CHD1 gene primers. The gender of 27 samples of 13 species was determined by visualizing the PCR products on an agarose gel. While male parrots were indicated by a single band, female parrots were indicated by double bands. The findings provide additional information, which might be helpful for the management and care of parrots in Korean zoos.

• Journal of Institute of Control, Robotics and Systems
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• v.11 no.10
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• pp.830-836
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• 2005

Application of microarray technologies which monitor simultaneously the expression pattern of thousands of individual genes in different biological systems results in a tremendous increase of the amount of available gene expression data and have provided new insights into gene expression during drug development, within disease processes, and across species. There is a great need of data mining methods allowing straightforward interpretation, visualization and analysis of the relevant information contained in gene expression profiles. Specially, classifying biological samples into known classes or phenotypes is an important practical application for microarray gene expression profiles. Gene expression profiles obtained from tissue samples of patients thus allowcancer classification. In this research, molecular classification of microarray gene expression data is applied for multi-class cancer using computational biology such gene selection, principal component analysis and fuzzy clustering. The proposed method was applied to microarray data from leukemia patients; specifically, it was used to interpret the gene expression pattern and analyze the leukemia subtype whose expression profiles correlated with four cases of acute leukemia gene expression. A basic understanding of the microarray data analysis is also introduced.

• Natural Product Sciences
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• v.27 no.2
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• pp.99-114
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• 2021

Type 2 diabetes mellitus (T2DM) and its complications are important noncommunicable diseases with high mortality rates. Protein tyrosine phosphatase 1B (PTP1B) and aldose reductase inhibitors are recently approached and advanced for T2DM and its complications therapy. Matricaria chamomilla L. is acknowledged as a worldwide medicinal herb that has many beneficial health effects as well as antidiabetic effects. Our research was designed to determine the most potential antidiabetic phytochemicals from M. chamomilla employing in silico study. 142 phytochemicals were obtained from the databases. The first screening employed iGEMdock and Swiss ADME, involving 93 phytochemicals. Finally, 30 best phytochemicals were docked. Molecular docking and visualization analysis were performed using Avogadro, AutoDock 4.2., and Biovia Discovery Studio 2016. Molecular docking results demonstrate that ligand-protein interaction's binding affinities were -5.16 to -7.54 kcal/mol and -5.30 to -12.10 kcal/mol for PTP1B and aldose reductase protein targets respectively. In silico results demonstrate that M. chamomilla has potential antidiabetic phytochemical compounds for T2DM and its complications. We recommended anthecotulide, quercetin, chlorogenic acid, luteolin, and catechin as antidiabetic agents due to their binding affinities against both PTP1B and aldose reductase protein. Those phytochemicals' significant efficacy and potential as antidiabetic must be investigated in further advanced research.

• Molecules and Cells
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• v.45 no.11
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• pp.846-854
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• 2022

Neurons make long-distance connections via their axons, and the accuracy and stability of these connections are crucial for brain function. Research using various animal models showed that the molecular and cellular mechanisms underlying the assembly and maintenance of neuronal circuitry are highly conserved in vertebrates. Therefore, to gain a deeper understanding of brain development and maintenance, an efficient vertebrate model is required, where the axons of a defined neuronal cell type can be genetically manipulated and selectively visualized in vivo. Placental mammals pose an experimental challenge, as time-consuming breeding of genetically modified animals is required due to their in utero development. Xenopus laevis, the most commonly used amphibian model, offers comparative advantages, since their embryos ex utero during which embryological manipulations can be performed. However, the tetraploidy of the X. laevis genome makes them not ideal for genetic studies. Here, we use Xenopus tropicalis, a diploid amphibian species, to visualize axonal pathfinding and degeneration of a single central nervous system neuronal cell type, the retinal ganglion cell (RGC). First, we show that RGC axons follow the developmental trajectory previously described in X. laevis with a slightly different timeline. Second, we demonstrate that co-electroporation of DNA and/or oligonucleotides enables the visualization of gene function-altered RGC axons in an intact brain. Finally, using this method, we show that the axon-autonomous, Sarm1-dependent axon destruction program operates in X. tropicalis. Taken together, the present study demonstrates that the visual system of X. tropicalis is a highly efficient model to identify new molecular mechanisms underlying axon guidance and survival.

• BMB Reports
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• v.42 no.11
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• pp.705-712
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• 2009

Our understanding of the relationships between genes, brains, and behaviors has changed a lot since the first behavioral mutants were isolated in the fly bottles of the Benzer lab at Caltech (1), but Drosophila is still an excellent model system for studying the neurobiology of behavior. Recent advances provide an unprecedented level of control over fly neural circuits. Efforts are underway to add to existing GAL4-driver lines that permit exogenous expression of genetic tools in small populations of neurons. Combining these driver lines with a variety of inducible UAS lines permits the visualization of neuronal morphology, connectivity, and activity. These driver lines also make it possible to specifically ablate, inhibit, or activate subsets of neurons and assess their roles in the generation of behavioral responses. Here, I will briefly review the extensive arsenal now available to drosophilists for investigating the neuronal control of behavior.

• Journal of the Korean Magnetic Resonance Society
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• v.15 no.2
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• pp.157-174
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• 2011

Although the use of apodization functions in connection with postprocessing of a 2D NMR spectrum proves improved spectral quality, there is usually a trade-off between resolution enhancement and noise suppression due to a classical "uncertainty principle." In this study, therefore, a mathematical deconvolution technique called "Maximum Likelihood Deconvolution (MLD)" was adopted to achieve the spectral resolution and sensitivity enhancement simultaneously. The MLD technique greatly facilitates visualization and restoration of the genuine spectral information from complex 2D NMR spectra that would be problematic with the conventional apodization/FT processing. In particular, application of the MLD to the 2D-NOE spectrum would be very useful to derive the important proton connectivities, which are essential to achieve elucidating the 3D molecular structure.

• Nuclear Medicine and Molecular Imaging
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• v.43 no.2
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• pp.154-155
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• 2009

A 45-year-old man presented with fatigue and weight loss underwent a Tc-99m MDP bone scan because of increased serum alkaline phosphatase. Delayed images at 4 hours demonstrated diffuse increased activity throughout both lobes of the thyroid in the absence of activity of the stomach and salivary glands. Thyroid laboratory indices and a Tc-99m pertechnetate thyroid scan suggested Graves' hyperthyroidism.

• BMB Reports
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• v.44 no.5
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• pp.347-351
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• 2011

The testis is major male gonad responsible for spermatogenesis and steroidogenesis. Much knowledge is still remained to be learned about the control of these events. In this study, we performed a comprehensive bioinformatics analysis on 1,196 mouse testis proteins screened from public protein database. Integrated function and pathway analysis were performed through Database for Annotation, Visualization and Integrated Discovery (DAVID) and ingenuity Pathway Analysis (IPA), and significant features were clustered. Protein membrane organization and gene density on chromosomes were analyzed and discussed. The enriched bioinformatics analysis could provide clues and basis to the development of diagnostic markers and therapeutic targets for infertility and male contraception.