Construction and Analysis of the Cosmid Library for the Genome Studies

문은표 한국유전학회 1995 Genes & Genomics Vol.17 No.4

Detailed studies on the gene expression control, the exact genomic locations of genes and the modes of the gene rearrangement require isolation of the larger regions of DNA surrounding the genes. For this purpose a cosmid library was constructed using the total genomic DNA from rice and spinach, respectively. Each clone in the libraries contains a 35-45 kb DNA fragment as an insert. In this communication, I discuss the use of the cosmid library to analyze the interorganellar DNA migration and rearrangement. I also discuss the use of the comid library to select the sublibraries, each representing the whole mitochondrial, chloroplast and nuclear genomes for the detailed studies on these three distinct genomes.

Detection of DNA Rearrangement in Rice Using a Cosmid Library

문은표,남백희,Mun, Eun-Pyo,Nahm, Baek-Hie The Korean Society for Integrative Biology 1997 Korean journal of biological sciences Vol.1 No.4

Previously we reported the migration and rearrangement of a chloroplast gene cluster into mitochondria. The exact genomic locations of the clusters, modes of the gene rearrangement and mechanisms of the interorganellar migration of the clusters have yet to be understood. The detailed analysis needs to include a larger region of DNA surrounding each cluster. To study DNA rearrangement and migration in more detail a cosmid library was constructed using the total rice genomic DNA including nuclear, chloroplast and mitochondrial DNA. From this cosmid library, a sub-library was obtained by selecting the clones hybridized to various regions of chloroplast DNA. According to the hybridization pattern 136 clones from the sub-library were classified into 29 groups. Detailed analysis of these clones revealed that in addition to authentic chloroplast DNA, the clones contain its homologs resulted from rearrangement and mutation. We analyzed two clones in detail, which contain different rp12 homologs resulted from rearrangement and/or migration, respectively.

Internet을 이용한 단백질/핵산 서열의 분석 및 염기 서열과 문헌 데이터 검색

이종협,문은표 한국분자생물학회 1996 분자생물학뉴스 Vol.8 No.2

Antimicrobial Effects of a Hexapetide KCM21 against Pseudomonas syringae pv. tomato DC3000 and Clavibacter michiganensis subsp. michiganensis

최재혁,문은표,백광현 한국식물병리학회 2014 Plant Pathology Journal Vol.30 No.3

Antimicrobial peptides (AMPs) are small but effectivecationic peptides with variable length. In previous study, four hexapeptides were identified that showed antimicrobial activities against various phytopathogenicbacteria. KCM21, the most effective antimicrobial peptide, was selected for further analysis to understand its modes of action by monitoring inhibitory effects of various cations, time-dependent antimicrobial kinetics, and observing cell disruption by electron microscopy. The effects of KCM21 on Gram-negative strain, Pseudomonassyringae pv. tomato DC3000 and Gram-positive strain, Clavibacter michiganensis subsp. michiganensis were compared. Treatment with divalent cations such as Ca2+ and Mg2+ inhibited the bactericidal activities of KCM21 significantly against P. syringae pv. tomato DC3000. The bactericidal kinetic study showed that KCM21 killed both bacteria rapidly and the process was faster against C. michiganensis subsp. michiganensis. The electron microscopic analysis revealed that KCM21 induced the formation of micelles and blebs on the surface of P. syringae pv. tomato DC3000 cells, while it caused cell rupture against C. michiganensis subsp. michiganensis cells. The outer membrane alterationand higher sensitivity to Ca2+ suggest that KCM21 interact with the outer membrane of P. syringae pv. tomatoDC3000 cells during the process of killing, but not with C. michiganensis subsp. michiganensis cells that lack outer membrane. Considering that both strains had similar sensitivity to KCM21 in LB medium, outer membrane could not be the main target of KCM21, instead common compartments such as cytoplasmic membrane or internal macromolecules might be a possibletarget(s) of KCM21.

Functional Characterization of NtCDPK1 in Tobacco

이상숙,윤경미,노은정,문은표,배현숙 한국분자세포생물학회 2006 Molecules and cells Vol.21 No.1

We previously showed that NtCDPK1, a tobacco calcium- dependent protein kinase, interacts with and phosphorylates the Rpn3 regulatory subunit of the 26S proteasome, and that both NtCDPK1 and Rpn3 are mainly expressed in rapidly proliferating tissues, including shoot and root meristem. In this study, we examined NtCDPK1 expression in roots using GUS expression in transgenic Arabidopsis plants, and investigated its function in root development by generating transgenic tobacco plants carrying a sense NtCDPK1 transgene. GUS activity was first detected in roots two days after sowing. In later stages, strong GUS expression was detected in the root meristem and elongation zone, as well as the initiation sites and branch points of lateral roots. Transgenic tobacco plants in which NtCDPK1 expression was suppressed were smaller, and their root development was abnormal, with reduced lateral root formation and less elongation. These results suggest that NtCDPK1 plays a role in a signaling pathway regulating root development in tobacco.

A New Antimicrobial Substance Produced by Staphylococcus pasteuri Isolated from Vegetables

홍지수,Lin-Hu Quan,허성기,정규석,한상욱,문은표,노은정 한국식품과학회 2014 Food Science and Biotechnology Vol.23 No.3

Staphylococcus aureus is important food-bornepathogen in agricultural products consumed in a fresh state. The antimicrobial activities of staphylococci isolated fromvegetables in Korea against S. aureus were investigated. Coagulase-negative staphylococci (CNS) isolates (12) withantimicrobial activities against S. aureus were identified asS. xylosus, pasteuri, and epidermidis. CNS isolates exhibitedantimicrobial activities against Gram-positive bacteria. Inactivation of S. pasteuri antimicrobial activity by proteasessuggested that the substances evaluated were antimicrobialpeptides or bacteriocins. None of the S. pasteuri isolatespossessed homologous DNA fragments known to bebacteriocin genes, except for nukacin. The nukM gene thatencodes a post-translational modification enzyme in thenukacin gene cluster was not detected in S. pasteuriisolates. S. pasteuri probably produces one or more newantimicrobial substances.

Nonthermal Plasma Induces Apoptosis in ATC Cells: Involvement of JNK and p38 MAPK-Dependent ROS

이세영,김철호,강성운,김강일,강삼,신유섭,장재원,양상식,이근호,이종수,문은표 연세대학교의과대학 2014 Yonsei medical journal Vol.55 No.6

Purpose: To determine the effects of nonthermal plasma (NTP) induced by helium(He) alone or He plus oxygen (O2) on the generation of reactive oxygen species(ROS) and cell death in anaplastic thyroid cancer cells. Materials and Methods:NTP was generated in He alone or He plus O2 blowing through a nozzle by applying a high alternating current voltage to the discharge electrodes. Optical emission spectroscopy was used to identify various excited plasma species. The apoptotic effect of NTP on the anaplastic thyroid cancer cell lines, such as HTH83, U-HTH 7, and SW1763, was verified with annexin V/propidium staining and TUNEL assay. ROS formation after NTP treatment was identified with fluorescence-activated cell sorting with DCFDA staining. The mitogen-activated proteinkinase pathways and caspase cascade were investigated to evaluate the molecularmechanism involved and cellular targets of plasma. Results: NTP induced significant apoptosis in all three cancer cell lines. The plasma using He and O2 generated more O2-related species, and increased apoptosis and intracellular ROS formation compared with the plasma using He alone. NTP treatment of SW1763 increased the expression of phosphor-JNK, phosphor-p38, and caspase-3, but not phosphor-ERK. Apoptosis of SW1763 as well as expressions of elevated phosphor-JNK, phosphor-p38, and caspase-3 induced by NTP were effectively inhibitedby intracellular ROS scavengers. Conclusion: NTP using He plus O2 induced significant apoptosis in anaplastic cancer cell lines through intracellular ROS formation. This may represent a new promising treatment modality for this highly lethaldisease.

Comparative Effects of Non-Thermal Atmospheric Pressure Plasma on Migration and Invasion in Oral Squamous Cell Cancer, by Gas Type

강성운,김철호,서성진,김연수,신유섭,고윤우,이창민,양상식,이종수,문은표,강하미,려정범,이유지나 연세대학교의과대학 2017 Yonsei medical journal Vol.58 No.2

Purpose: The fourth state of matter, plasma is known as an ionized gas with electrons, radicals and ions. The use of non-thermal plasma (NTP) in cancer research became possible because of the progresses in plasma medicine. Previous studies on the potentialNTP-mediated cancer therapy have mainly concentrated on cancer cell apoptosis. In the present study, we compared the inhibitoryeffect of NTP on cell migration and invasion in the oral squamous cancer cell lines. Materials and Methods: We used oral squamous cancer cell lines (SCC1483, MSKQLL1) and different gases (N2, He, and Ar). To investigate the mechanism of plasma treatment, using different gases (N2, He, and Ar) which induces anti-migration and anti-invasionproperties, we performed wound healing assay, invasion assay and gelatin zymography. Results: The results showed that NTP inhibits cancer cell migration and invasion of oral squamous cancer cell. In addition, focal adhesion kinase expression and matrix metalloproteinase-2/9 activity were also inhibited. Conclusion: The suppression of cancer cell invasion by NTP varied depending on the type of gas. Comparison of the three gases revealed that N2 NTP inhibited cell migration and invasion most potently via decreased expression of focal adhesion kinase and matrix metalloproteinase activity.