• Molecules and Cells
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• 제46권2호
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• pp.106-119
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• 2023

With the increased number of single-cell RNA sequencing (scRNA-seq) datasets in public repositories, integrative analysis of multiple scRNA-seq datasets has become commonplace. Batch effects among different datasets are inevitable because of differences in cell isolation and handling protocols, library preparation technology, and sequencing platforms. To remove these batch effects for effective integration of multiple scRNA-seq datasets, a number of methodologies have been developed based on diverse concepts and approaches. These methods have proven useful for examining whether cellular features, such as cell subpopulations and marker genes, identified from a certain dataset, are consistently present, or whether their condition-dependent variations, such as increases in cell subpopulations in particular disease-related conditions, are consistently observed in different datasets generated under similar or distinct conditions. In this review, we summarize the concepts and approaches of the integration methods and their pros and cons as has been reported in previous literature.

• Mass Spectrometry Letters
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• 제13권4호
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• pp.115-124
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• 2022

Emerging evidence has shown that RNA-binding proteins (RBPs) dynamically regulate all aspects of RNA in cells and involve in major biological processes of RNA, including splicing, modification, transport, transcription and degradation. RBPs, as powerful and versatile regulatory molecule, are essential to maintain cellular homeostasis. Perturbation of RNA-protein interactions and aberration of RBPs function is associated with diverse diseases, such as cancer, autoimmune disease, and neurological disorders. Therefore, it is crucial to systematically investigate the RNA-binding proteome for understanding interactions of RNA with proteins. Thanks to the development of the mass spectrometry, a variety of proteome-wide methods have been explored to define comprehensively RNA-protein interactions in recent years and thereby contributed to speeding up the study of RNA biology. In this review, we systematically described these methods and summarized the advantages and disadvantages of each method.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2013년도 제45회 하계 정기학술대회 초록집
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• pp.277.1-277.1
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• 2013

Molecular diagnostics consists of three processes, which are a sample pretreatment, a nucleic acid amplification, and an amplicon detection. Among three components, sample pretreatment is an important process in that it can increase the limit of detection by purifying nucleic acid in biological sample from contaminants that may interfere with the downstream genetic analysis such as nucleic acid amplification and detection. To achieve point-of-care virus detection system, the sample pretreatment process needs to be simple, rapid, and automatic. However, the commercial RNA extraction kits such as Rneasy (Qiagen) or MagnaPure (Roche) kit are highly labor-intensive and time-consuming due to numerous manual steps, and so it is not adequate for the on-site sample preparation. Herein, we have developed a rotary microfluidic system to extract and purify the RNA without necessity of external mechanical syringe pumps to allow flow control using microfluidic technology. We designed three reservoirs for sample, washing buffer, and elution buffer which were connected with different dimensional microfluidic channels. By controlling RPM, we could dispense a RNA sample solution, a washing buffer, and an elution buffer successively, so that the RNA was captured in the sol-gel solid phase, purified, and eluted in the downstream. Such a novel rotary sample preparation system eliminates some complicated hardwares and human intervention providing the opportunity to construct a fully integrated genetic analysis microsystem.

• 한국식물병리학회지
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• 제11권4호
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• pp.367-373
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• 1995

The cDNAs derived from the coat protein (CP) genes of six plant RNA viruses, tobacco mosaic virus-pepper strains (TMV-P) and -ordinary strain (TMV-OM), potato virus Y (PVY), turnip mosaic virus (TuMV), cucumber mosaic virus (CMV) and potato leafroll virus (PLRV), were subcloned into the transcription vector, pSPT18, containing SP6 and T7 promoters. The digoxigenin (DIG)-labeled RNA polymerase after linearlization of the cloned pSPTs with XbaI or SacI, and were tested for their sensitivities for the detection of the six viruses. In slot-blot hybridization, dilution end points for the detection of TMV-P and TMV-OM were 10-4, while those of PVY, TuMV and CMV were 10-3. PLRV was detected at the dilution of 10-2. When each RNA probe was applied for the detection of the viruses in the preparations from the leaf disks (8 mm in diameter, and 12 to 15 mg in weight) of infected natural host plants, TMV-P, TMV-OM and TuMV could be detected from one disk, while PVY from 1 or 2 disks. CMV was detected in the preparation from two disks, and PLRV from three disks. With DIG-labeled RNA probe, PVY was detected at 5 days after inoculation, but with ELISA the virus was detected at 8 days after inoculation to tobacco (Nicotiana tabacum cv. Xanthi nc) plants on which symptoms appeared at 9 days after inoculation. No difference was observed in cross reaction between the RNA probes for the detection of TMV-P and TMV-OM.

• Journal of Microbiology
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• 제45권6호
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• pp.534-540
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• 2007

The Streptomyces coelicolor A3(2) genome contains six operons (rrnA to F) for ribosomal RNA synthesis. Transcription from rrnD occurs from four promoters (p1 to p4). We found that transcripts from the p1 and p3 promoters were most abundant in vivo in the early exponential phase. However, at later phases of exponential and stationary growth, transcripts from the p1 promoter decreased drastically, with the p3 and p4 transcripts constituting the major forms. Partially purified RNA polymerase supported transcription from the p3 and p4 promoters, whereas pure reconstituted RNA polymerase with core enzyme (E) and the major vegetative sigma factor ${\sigma}^{HrdB}$ ($E{\cdot}{\sigma}^{HrdB}$) did not. In order to assess any potential requirement for additional factor(s) that allow transcription from the p3 and p4 promoters, we fractionated a partially purified RNA polymerase preparation by denaturing gel filtration chromatography. We found that transcription from the p3 and p4 promoters required factor(s) of about 30-35 kDa in addition to RNAP holoenzyme ($E{\cdot}{\sigma}^{HrdB}$). Therefore, transcription from the p3 and p4 promoters, which contain a consensus -10 region but no -35 for ${\sigma}^{HrdB}$ recognition, are likely to be regulated by transcription factor(s) that modulate RNA polymerase holoenzyme activity in S. coelicolor.

• 약학회지
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• 제42권2호
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• pp.175-180
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• 1998

Bifidobacterium bifidum OFR9 that exhibits acquired resistance to rifampicin and fluoroquinolones was selected by MNNG and multi-step mutation method. To investigate the resistance mechanism to rifampicin in the strain, RNA polymerase from B. bifidum parent strain and rifampicin-resistance OFR9 was partially purified and its sensitivity to rifampicin was assayed. The profile of RNA polymerase preparation of B. bifidum parent and B. bifidum OFR9 is similar to that of E. coli RNA polymerase that includes the basic subunits of ${\beta}$`, ${\beta},\;{\sigma},\;{\alpha}$ but which are a little different in size when they are compared with E. coli RNA polymerase subunits. RNA polymerase isolated from the parent strain was inhibited by 1${\mu}$g/ml rifampicin but that from B. bifidum OFR9 was not affected by 100${\mu}$g/ml concentration of rifampicin. RNA polymerase activity of B. bifidum OFR9 was maintained over 90% through that rifampicin concentration. This result is consistent with MIC values of in vitro test. It can be concluded that the mechanism of rifampicin resistance in B. bifidum OFR9 is due to an alteration of RNA polymerase.

• Clinical and Experimental Reproductive Medicine
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• 제29권4호
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• pp.295-302
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• 2002

Uterine cells carry out proliferation and differentiation for preparation the embryonic implantation during pregnancy. Therefore regulation of the cell proliferation is an essential step for uterine preparation, but there is not much information about the proliferation related genes in pregnant uterus. To identify these implantation specific genes, a PCR-select cDNA subtraction method was employed and got a few genes. One of the identified genes is a novel gene encoding oral tumor suppressor doc-1. To detect the doc-1 expression on the pregnant uterus, dot blotting, RT-PCR, and in situ hybridization were employed. Dot blotting revealed that doc-1 mRNA expression increase after implantation. During normal pregnancy, doc-1 mRNA expression was detected as early as day 1 of pregnancy with RT-PCR. Its expression was increased about 15 times after embryonic implantation. doc-1 transcript was localized in luminal epithelial cells but it was very faint during preimplantation. After starting the implantation, it localized in the stromal cells; heightened expression of doc-1 correlates with intense stromal cell proliferation surrounding the implanting blastocyst on day 6 morning. However in the decidualized cells, the intensity of localized doc-1 mRNA was weak. From those results, it is revealed that doc-1 express at pregnant uterus of the mouse. In addition it is suggested that doc-1 is the gene regulating the proliferation of the luminal epithelial cells and stromal cells during early implantation and decidualization.

• Journal of Korean Dental Science
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• 제6권1호
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• pp.22-26
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• 2013

Purpose: Transglutaminase 2 (TGase 2) is expressed by tumor necrosis factor-${\alpha}$ in various carcinoma. The role of TGase 2 expression in salivary gland tumors is not clear yet. Established slaivary gland tumor (SGT)cell line has been used to study the pathogenesis of salivary gland adenocarcinoma on a cellular level in vitro. The pupose of this study were to examine mRNA expression of TGase 2 in SGT cell line compared to other tumor cell lines, and to apply these results to the pathogenesis of salivary gland tumor. Materials and Methods: After SGT, SCC-15, HN 4, and HeLa tumor cell lines were cultured under preconfl uency, and 3 days after postconfl uency, the cells were harvested for total RNA extraction and cDNA preparation. Result: Reverse transcription polymerase chain reaction for semiquantitative mRNA analysis was done. TGase 2 mRNA expression was not induced by confl uency in all the cell lines. TGase 2 mRNA expression was variable but markedly enhanced in SGT cell line. Conclusion: mRNA expression of TGase 2 should play an important role in the pathogenesis of SGT cell line originated from ductal cell.

• 한국자기공명학회:학술대회논문집
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• 한국자기공명학회 1999년도 하계총회 및 제15회 자기공명 학술발표회
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• pp.25-25
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• 1999

• Biotechnology and Bioprocess Engineering:BBE
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• 제11권5호
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• pp.420-424
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• 2006

A simple method for depleting E. coliS30 extracts of endogenous tRNA has been developed. An $ethanolamine-Sepharose^{(R)}$ column equilibrated with water selectively captured the tRNA molecules in E. coli S30 extracts. As a result, S30 extracts filtered through this column became completely dependent upon the addition of exogenous tRNA to mediate cell-free protein synthesis reactions. We anticipate that the procedures developed and described will be particularly useful for in vitro suppression reaction studies designed to introduce unnatural amino acids into protein molecules.