• Genomics & Informatics
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• v.21 no.1
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• pp.11.1-11.5
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• 2023

Breast cancer is the most common cancer worldwide, and advanced breast cancer with metastases is incurable mainly with currently available therapies. Therefore, it is essential to understand molecular characteristics during the progression of breast carcinogenesis. Here, we report a dataset of whole genomes from the human mammary epithelial cell system derived from a reduction mammoplasty specimen. This system comprises pre-stasis 184D cells, considered normal, and seven cell lines along cancer progression series that are immortalized or additionally acquired anchorage-independent growth. Our analysis of the whole-genome sequencing (WGS) data indicates that those seven cancer progression series cells have somatic mutations whose number ranges from 8,393 to 39,564 (with an average of 30,591) compared to 184D cells. These WGS data and our mutation analysis will provide helpful information to identify driver mutations and elucidate molecular mechanisms for breast carcinogenesis.

• Journal of Microbiology and Biotechnology
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• v.12 no.3
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• pp.398-405
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• 2002

Bifidobacteria have been previously shown to stimulate the immune functions and cytokine production in macrophages and T-lymphocytes. Accordingly, the RAW 264.7 murine macrophage cell line was used to assess the effects of Bifidobacterium on the proliferation and cytoskeleton reorganization of the cells. Cytokine production after exposure to Bifidobacterium was also monitored in both whole cells and cell-free extracts. When RAW 264.7 cells were cultured for 24 h in the presence of heat-killed Bifidobacterium bifidum BGN4, the proliferation of macrophages was slowed down in a dose-dependent manner and cell differentiation was observed by staining with the actin-specific fluorescent dye, rhodamin-conjugated phalloidin. Although EL-4 cells, a T-cell line, stimulated RAW 264.7 cells to produce TNF-${\alpha}$ and IL-6, the stimulatory activity of B. bifidum BGN4 decreased as the EL-4 cell number increased. When disrupted and fractionated BGN4 was used, the whole cell fraction was more effective than the other fractions for the TNF-${\alpha}$ production. In contrast, the cell-free extract exhibited the highest IL-6 production level among the fractions, which was evident even at a $1{\mu}g/ml$ concentration. The current results demonstrate that Bifidobacterium induced differentiation of the macrophages from the fast proliferative stage and that the cytokine production was differentially induced by the whole cells and cell-free extracts. The in vitro approaches employed herein are expected to be useful in further characterization of the effects of bifidobacteria with regards to gastrointestinal and systemic immunity.

• Journal of Microbiology and Biotechnology
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• v.20 no.4
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• pp.712-717
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• 2010

Cytochrome P450 enzymes (P450s) are involved in the synthesis of a wide variety of valuable products and in the degradation of numerous toxic compounds. The P450 BM3 (CYP102A1) from Bacillus megaterium was the first P450 discovered to be fused to its redox partner, a mammalian-like diflavin reductase. Here, we report the development of a whole-cell biocatalyst using ice-nucleation protein (Inp) from Pseudomonas syringae to display a hemeand diflavin-containing oxidoreductase, P450 BM3 (a single, 119-kDa polypeptide with domains of both an oxygenase and a reductase) on the surface of Escherichia coli. The surface localization and functionality of the fusion protein containing P450 BM3 were verified by flow cytometry and measurement of enzymatic activities. The results of this study comprise the first report of microbial cell-surface display of a heme- and diflavin-containing enzyme. This system should allow us to select and develop oxidoreductases containing heme and/or flavins into practically useful whole-cell biocatalysts for extensive biotechnological applications, including selective synthesis of new chemicals and pharmaceuticals, bioconversion, bioremediation, live vaccine development, and biochip development.

• Journal of Microbiology and Biotechnology
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• v.14 no.6
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• pp.1227-1231
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• 2004

Campylobacter, one of the emerging foodborne pathogens, is highly adaptable to the external environments by changing its morphology. In the present study, a question of whether the whole-cell antibody would still be effective for its detection even though the morphology of C. jejuni was changed was examined. When microaerophilic C. jejuni was exposed to aerobic conditions for 48 h, its morphological change was detected by confocal laser scanning microscope: Its morphology was confirmed as a spiral-bacilli form in microaerobic condition, however, as a coccoid form with a little spiral-bacilli form, when exposed to aerobic conditions. Also, the expressions of the whole-cell proteins of C. jejuni, and the suppression or induction of newly synthesized proteins in both aerobic and microaerobic conditions were analyzed by two dimensional gel electrophoresis. Additionally, immunoblotting assay with the whole cell antibody for the proteins expressed under the two conditions was performed. It was confirmed that the commercial whole-cell antibody of C. jejuni raised in rabbit was reactive. When analyzed with MALDI- TOF MS, the expressed proteins were confirmed as flagellins. Therefore, even though the morphology changed in aerobic condition, these flagellins were expressed and worked as the eitope proteins, thus making it possible to utilize for the development of an immunosensor for real-time detection of any kind of C. jejuni cell.

• Journal of Microbiology and Biotechnology
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• v.26 no.7
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• pp.1278-1284
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• 2016

Rhizopus chinensis cells immobilized on loofah (Luffa cylindrica) sponges were used to produce biodiesel via the transesterification of soybean oil. In whole-cell immobilization, loofah sponge is considered to be a superior alternative to conventional biomass carriers because of its biodegradable and renewable properties. During cell cultivation, Rhizopus chinensis mycelia can spontaneously and firmly adhere to the surface of loofah sponge particles. The optimal conditions for processing 9.65 g soybean oil at 40℃ and 180 rpm using a 3:1 methanol-to-oil molar ratio were found to be 8% cell addition and 3-10% water content (depending on the oil's weight). Under optimal conditions, an over 90% methyl ester yield was achieved after the first reaction batch. The operational stability of immobilized Rhizopus chinensis cells was assayed utilizing a 1:1 methanol-to-oil molar ratio, thus resulting in a 16.5-fold increase in half-life when compared with immobilized cells of the widely studied Rhizopus oryzae. These results suggest that transesterification of vegetable oil using Rhizopus chinensis whole cells immobilized onto loofah sponge is an effective approach for biodiesel production.

• Preventive Nutrition and Food Science
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• v.15 no.4
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• pp.255-261
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• 2010

Ischemic stroke, a major cause of death and disability worldwide, is caused by occlusion of cerebral arteries that, coupled with or without reperfusion, results in prolonged ischemia (hypoxia and hypoglycemia) and, ultimately, brain damage. In this study, we examined whether methanol extract of the whole plant of Cassia mimosoides var. nomame Makino that grows naturally in Korea, as well as Japan and China, and some of its fractions obtained by partitioning with organic solvents could protect human hepatocellular carcinoma cells (HepG2) under hypoxic condition by inhibiting apoptosis. We also investigated if these extracts could attenuate brain damage in a rat model of 2 hr of ischemia, generated by middle cerebral artery occlusion, and 22 hr of reperfusion. The whole extract ($100{\mu}g$/mL) maintained the cell number at more than half of that initially plated, even after 24 hr of cell culture under hypoxic condition (3% $O_2$). In the absence of the whole extract, almost all of the cells were dead by this time point. This improvement of cell viability came from a delay of apoptosis, which was confirmed by observing the timing of the formation of a DNA ladder when assessed by gel electrophoresis. Of fractions soluble in hexane, ethyl acetate (EA), butanol and water, EA extracts were selected for the animal experiments, as they improved cell viability at the lowest concentration ($10{\mu}g$/mL). The whole extract (200 mg/kg) and EA extract (10 and 20 mg/kg) significantly reduced infarct size, a measure of brain damage, by 34.7, 33.8 and 45.2.0%, respectively, when assessed by 2,3,5-triphenyl tetrazolium chloride staining. The results suggest that intake of Cassia mimosoides var. nomame Makino might be beneficial for preventing ischemic stroke through inhibition of brain cell apoptosis.

• 한국생물공학회:학술대회논문집
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• 2003.10a
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• pp.468-472
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• 2003

Recently, genetic engineering techniques have been used to display various heterologous peptides and proteins (enzyme, antibody, antigen, receptor and fluorescence protein, etc.) on the yeast cell surface. Living cells displaying various enzymes on their surface could be used repeatedly as 'whole cell biocatalysts' like immobilized enzymes. We constructed a yeast based whole cell biocatalyst displaying T. reesei cellobiohydrolase I (CBH I ) on the cell surface and endowed the yeast-cells with the ability to degrade cellulose. By using a cell surface engineering system based on ${\alpha}-agglutinin,$ CBH I was displayed on the cell surface as a fusion protein containing the N-terminal leader peptide encoding a Gly-Ser linker and the $Xpress^{TM}$ epitope. Localization of the fusion protein on the cell surface was confirmed by confocal microscopy. In this study, we report on the genetic immobilization of T. reesei CBH I on the S. cerevisiae and hydrolytic activity of cell surface displayed CBH I.

• IMMUNE NETWORK
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• v.12 no.6
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• pp.223-229
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• 2012

Clinical and preclinical in vivo immune cell imaging approaches have been used to study immune cell proliferation, apoptosis and interaction at the microscopic (intra-vital imaging) and macroscopic (whole-body imaging) level by use of ex vivo or in vivo labeling method. A series of imaging techniques ranging from non-radiation based techniques such as optical imaging, MRI, and ultrasound to radiation based CT/nuclear imaging can be used for in vivo immune cell tracking. These imaging modalities highlight the intrinsic behavior of different immune cell populations in physiological context. Fluorescent, radioactive or paramagnetic probes can be used in direct labeling protocols to monitor the specific cell population. Reporter genes can also be used for genetic, indirect labeling protocols to track the fate of a given cell subpopulation in vivo. In this review, we summarized several methods dealing with dendritic cell, macrophage, and T lymphocyte specifically labeled for different macroscopic whole-body imaging techniques both for the study of their physiological function and in the context of immunotherapy to exploit imaging-derived information and immune-based treatments.

• IMMUNE NETWORK
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• v.5 no.2
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• pp.55-67
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• 2005

Cancer vaccine is an active immunotherapy to stimulate the immune system to mount a response against the tumor specific antigen. Working as a stimulant to the body's own immune system, cancer vaccines help the body recognize and destroy targeted cancers and may help to shrink advanced tumors. Research is currently underway to develop therapeutic cancer vaccines. It is also possible to develop prophylactic vaccines in the future. The whole cell approach to eradicate cancer has used whole cancer cells to make vaccine. In an early stage of this approach, whole cell lysate or a mixture of immunoadjuvant and inactivated cancer cells has been used. Improved vaccines are being developed that utilize cytokines or costimulatory molecules to mount an attack against cancer cells. In case of melanoma, these vaccines are expected to have a therapeutic effect of vaccine. Furthermore, it is attempting to treat stomach cancer, colorectal cancer, pancreatic cancer, and prostate cancer. Other vaccines are being developing that are peptide vaccine, recombinant vaccine and dendritic cell vaccine. Out of them, reintroduction of antigen-specific dendritic cells into patient and DNA vaccine are mostly being conducted. Currently, research and development efforts are underway to develop therapeutic cancer vaccine such as DNA vaccine for the treatment of multiple forms of cancers.

• Journal of Microbiology and Biotechnology
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• v.30 no.5
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• pp.681-688
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• 2020

Bacterial cell-based biosensors, or whole-cell bioreporters (WCBs), are an alternative tool for the quantification of hazardous materials. Most WCBs share similar working mechanisms. In brief, the recognition of a target by sensing domains induces a biological event, such as changes in protein conformation or gene expression, providing a basis for quantification. WCBs targeting heavy metal(loid)s employ metalloregulators as sensing domains and control the expression of genes in the presence of target metal(loid) ions, but the diversity of targets, specificity, and sensitivity of these WCBs are limited. In this study, we genetically engineered the metal-binding loop (MBL) of ZntR, which controls the znt-operon in Escherichia coli. In the MBL of ZntR, three Cys sites interact with metal ions. Based on the crystal structure of ZntR, MBL sequences were modified by site-directed mutagenesis. As a result, the metal-sensing properties of WCBs differed depending on amino acid sequences and the new selectivity to Cr or Pb was observed. Although there is room for improvement, our results support the use of currently available WCBs as a platform to generate new WCBs to target other environmental pollutants including metal(loid)s.