• Molecules and Cells
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• v.44 no.8
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• pp.602-612
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• 2021

DNA methylation is an important epigenetic mechanism affecting genome structure, gene regulation, and the silencing of transposable elements. Cell- and tissue-specific methylation patterns are critical for differentiation and development in eukaryotes. Dynamic spatiotemporal methylation data in these cells or tissues is, therefore, of great interest. However, the construction of bisulfite sequencing libraries can be challenging if the starting material is limited or the genome size is small, such as in Arabidopsis. Here, we describe detailed methods for the purification of Arabidopsis embryos at all stages, and the construction of comprehensive bisulfite libraries from small quantities of input. We constructed bisulfite libraries by releasing embryos from intact seeds, using a different approach for each developmental stage, and manually picking single-embryo with microcapillaries. From these libraries, reliable Arabidopsis methylome data were collected allowing, on average, 11-fold coverage of the genome using as few as five globular, heart, and torpedo embryos as raw input material without the need for DNA purification step. On the other hand, purified DNA from as few as eight bending torpedo embryos or a single mature embryo is sufficient for library construction when RNase A is treated before DNA extraction. This method can be broadly applied to cells from different tissues or cells from other model organisms. Methylome construction can be achieved using a minimal amount of input material using our method; thereby, it has the potential to increase our understanding of dynamic spatiotemporal methylation patterns in model organisms.

• Journal of Applied Biological Chemistry
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• v.58 no.1
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• pp.9-11
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• 2015

Tissue extracts were prepared from liquid-cultured Arabidopsis and reacted with UDP-[$^3H$]-GlcNAc. Phospholipid fractions were then extracted by butanol partitioning. Consecutive thin-layer chromatography identified two glycolipids sensitive to PI-specific phospholipase C, known as early intermediates in glycosylphosphatidylinositol anchor biosynthesis; phosphatidylinositol N-acetylglucosamine and phosphatidylinositol glucosamine.

• 한국전자현미경학회:학술대회논문집
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• 2004.11a
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• pp.23-34
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• 2004

• The Microorganisms and Industry
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• v.15 no.1
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• pp.29-34
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• 1989

It is our common understanding that biological materials like microorganisms, tissue and cell cultures, seeds, plants and animals are inevitable resources for the development of science and technology. Culture collections which are reservior of biological materials now occupy a central position in life sciences and biotechnology. The World Data Center of Microorganisms (WDC) is a infrastructure of culture collections in the world realizing quick and smooth exchanges of information and microorganisms to support research and development in those fields. The WDC was relocated from University of Queensland in Australia to out institute RIKEN in 1986. This article introduces a function for WDC in RIKEN (RIKAGAKU-KENKYUUSHO, the Institute of Physical and Chemical Research)

• Transactions of the Korean Society of Mechanical Engineers B
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• v.39 no.11
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• pp.853-859
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• 2015

In this study, the temperature change in an imitational biological tissue, when its surface is irradiated with bio-light, was measured by experiments. Using the experimental data, an equation for temperature as a function of time was developed in order to use it as a boundary condition in numerical studies for the model. The temperature profile was measured along the depth for several wavelengths and distances of the light source from the tissue. It was found that the temperature of the tissue increased with increasing wavelength and irradiation time; however, the difference in the temperatures with red light and near infrared light was not large. The numerical analysis results obtained by using the developed equation as boundary condition show good agreement with the measured temperatures.

• Journal of Applied Biological Chemistry
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• v.59 no.1
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• pp.49-56
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• 2016

The current study investigated the anti-obesity effect of Cissus quadrangularsis extracts (CQR-300) and its molecular action mechanism on obese mice induced high-fat diet (HFD). To induce the obesity, mice were fed a HFD for 6 weeks and then fed HFD only or HFD with CQR-300 at 50 and 200 mg/kg. Then, body weight gain and white adipose tissue weights were measured. We investigated the reduction in body fat and the regulation of fatty acid synthesis was measured by dual energy X-ray absorptiometry and real-time PCR with Western blot, respectively. In vitro study, CQR-300 inhibited pancreatic lipase activity. The CQR-300 treatment was significantly decreased the body weight gain and adipocytes size as well as white adipose tissues weights in HFD-induced obese mice. Furthermore, CQR-300 reduced the body fat and fat mass with regulating of adipose tissue hormones as leptin. Treatment with 50 mg/kg CQR-300 showed effectively lower expression levels of adipogenesis/lipogenesis related genes and proteins such as CCAAT/enhancer binding protein ${\alpha}$ ($C/EBP{\alpha}$), peroxisome proliferator-activated receptor ${\gamma}$ ($PPAR{\gamma}$), Sterol regulatory element binding protein-1c (SREBP-1c), and fatty acid synthase (FAS) in white adipose tissue (WAT) as compared with the HFD fed only mice. These results suggest that the CQR-300 has an anti-obesity effect via inhibition of lipase activity, decrease the body fat mass by regulating the adipogenesis and lipogenesis related genes and proteins in epididymal adipose tissue with evaluate body fat reduce in the HFD-induced obese mice.

• Journal of Biomedical Engineering Research
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• v.30 no.4
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• pp.333-340
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• 2009

MR compatible coaxial-slot antenna for microwave hyperthermia was developed while its structure and size of each part were determined by computer simulation using finite element method(FEM). Its local heating performance was evaluated using tissue-mimic phantom and swine muscles. 2% agarose gel mixed with 6mM/$\ell$ $MnCl_2$ as a biological tissue-mimic phantom was heated by the proposed antenna driven by a 2.45GHz microwave generator. The temperature changes of the phantom were monitored using multi-channel digital thermometer at the distance of 0mm, 5mm, 10mm and 20mm from the tip center of the antenna. Also muscle tissue of swine was heated for 2 and 5minutes with 50W and 30W of microwave generator powers, respectively, to evaluate the local heating performance of the antenna. MRI compatibility was also verified by acquiring MR images and MR temperature map. MR signals were acquired from the agarose gel phantom using $T2^*$ GRE sequence with 1.5T clinical MRI scanner(Signa Echospeed, GE, Milwaukee, WI, U.S.A.) at Pusan Paik Hospital and were transferred to PC in order to reconstruct MR images and temperature map using proton resonance frequency(PRF) method and laboratory-developed phase unwrapping algorithm. Authors found that it has no severe distortion due to the antenna inserted into the phantom. Finally, we can conclude that the suggested coaxial-slot antenna has an excellent local heating performance for both of tissue-mimic phantom and swine muscle, and it is compatible to 1.5T MRI scanner.

• Journal of Korean Biological Nursing Science
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• v.3 no.2
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• pp.91-103
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• 2001

The bone is composed of the bone matrix of collagen and hydroxyapatite, the mixture of calcium and phosphours. The bone tissue is considered to the special connective tissue that possesses extracellular matrix made by collagen fiber deposited with mineral complex. In order to maintain bone mass measured by the sum of bone matrix and hydroxyapatite, bone resorption by osteoclast during lifetime and bone remodeling to form bone by osteoblast in its resorption region repeat continuously. The osteoblast has a mesodermic fetal origin like fibroblast for the formation of form tissues. Two cells express identical genes and synthesize the identical collagen type I as the major component of the formation of bone matrix and skin. Therefore, it is considered that the decrease of skinfold thickness and the decrease of bone mass related to the age, the change of two tissues composed of collagen type I is caused by the same genetic mechanism. The decrease of bone mass is caused by the change of the amount and structure of bone matrix by several factors and the amount of minerals deposited on bone matrix. Especially, in case of female, the deficiency of estrogen by menopause makes these changes rapidly increased. The decrease of bone mass and skinfold thickness is due to the decrease of the amount of collagen and its structural change the common component of bone tissue and skin tissue. Therefore, the relationship of the amount of cross-linked peptide N-telopeptide, collagen metabolite which excretes as urine. Based upon the proved results about the significant relationship of bone mass, the amount of bone collagen, the amount of skin collagen and skinfold thickness, the bone mass may be expected through a facile determination of skinfold thickness.

• Mass Spectrometry Letters
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• v.5 no.1
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• pp.16-23
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• 2014

Liquid chromatography based mass spectrometry (LC-MS) is a key technology for analyzing highly complex and dynamic proteome samples. With highly accurate and sensitive LC-MS analysis of complex proteome samples, efficient data processing is another critical issue to obtain more information from LC-MS data. A typical proteomic data processing starts with protein database search engine which assigns peptide sequences to MS/MS spectra and finds proteins. Although several search engines, such as SEQUEST and MASCOT, have been widely used, there is no unique standard way to interpret MS/MS spectra of peptides. Each search engine has pros and cons depending on types of mass spectrometers and physicochemical properties of peptides. In this study, we describe a novel data process pipeline which identifies more peptides and proteins by correcting precursor ion mass numbers and unifying multi search engines results. The pipeline utilizes two open-source software, iPE-MMR for mass number correction, and iProphet to combine several search results. The integrated pipeline identified 25% more proteins in mouse epididymal adipose tissue compared with the conventional method. Also the pipeline was validated using control and colitis induced colon tissue. The results of the present study shows that the integrated pipeline can efficiently identify increased number of proteins compared to the conventional method which can be a breakthrough in identification of a potential biomarker candidate.

• Applied Biological Chemistry
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• v.38 no.5
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• pp.414-421
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• 1995

In order to establish informations important to the measurement of lipoxygenase (LOX) activity, providing conditions most favorable for its action and determining factors that inhibit activity, the influence of extraction buffer, substrate, pH, storage, temperature, NaCl, $CaCl_2$, other cations and antioxidants on LOX activity, and localization of LOX in cucumber tissues were carried out. The most favored substrate for LOX was linolenic acid followed by linoleic and arachidonic acids. LOX activity in both peel and mesocarp tissue extracts was maximum at pH 5.5 and relatively stable at $40^{\circ}C\;and\;50^{\circ}C$ temperature. The condition of 0.2 M NaCl with pH 5.0 was observed to provide optimum LOX stability. The enzyme activity was reduced by addition of cations, $Mn^{2+},\;Cu^{2+}\;or\; Al^{3+}$, except $Ca^{2+}$ which stimulated activity of LOX. Butylated hydroxy anisole (BHA) and propyl gallate decreased LOX activity with increasing concentration. Cucumber peel had higher activity than other tissues, locule or mesocarp, of cucumber.