• Journal of Microbiology
• /
• v.44 no.6
• /
• pp.617-621
• /
• 2006

Coprinellus congregatus secreted a laccase isozyme when the culture was transferred to an acidic liquid medium (pH 4.1). The laccase cDNA gene (clac2) was used as a probe for cloning of the genomic laccase gene (lac2) including the promoter (Plac2). The open reading frame (ORF) of lac2 had 526 deduced amino acids and four conserved copper binding domains as other fungal laccases. Recombinant plasmid (pRSlac2p-cDNA) of lac2 cDNA with its own promoter was transformed in Saccharomyces cerevisiae. Expression of the transformed lac2 gene was induced by oxidative stress ($H_2O_2$) in yeast and the survival rate of the transformed yeast strain was greatly increased when compared with that of the control strain transformed with pRS316 yeast vector.

• Journal of Microbiology and Biotechnology
• /
• v.24 no.11
• /
• pp.1490-1494
• /
• 2014

To probe the genomic properties of microbes thriving in desert lakes, we sequenced the full genome of a betaproteobacterial strain (SL110) belonging to the understudied genus Caenimonas of the family Comamonadaceae. This strain was isolated from a freshwater lake in the western Gobi Desert, Northern China. Its genome contains genes encoding carbon monoxide dehydrogenase, nitrate reductase, nitrite reductase, nitric oxide reductase, and sulfur oxidation enzymes, highlighting the potentially important contribution of this group of bacteria to the cycling of inorganic elements in nature. Unexpectedly, a coenzyme $F_{420}$ biosynthesis gene cluster was identified. A further search for $F_{420}$ biosynthesis gene homologs in genomic databases suggests the possible widespread presence of $F_{420}$ biosynthesis gene clusters in proteobacterial genomes.

• Journal of fish pathology
• /
• v.6 no.2
• /
• pp.111-122
• /
• 1993

The mechanism by which $V_H$ region gene segments is selected in B lymphocyte is not known. Moreover, evidence for both random and nonrandom expression of $V_H$ genes in matured B cells has been presented previously. In this report, the technique of in situ hybridization allowed us to analyze expressed $V_H$ gene families in normal B lymphocyte at the single cell level. The analysis of normal B cells in this study eliminated any posssible bias resulting from transformation protocols used previously and minimized limitation associated with sampling size. Therefore, an accurate measure of the functional and expressed $V_H$ gene repertoire in B lymphocyte could be made. One of the most important controls for the optimization of in situ hybridization is to establish probe concentration and washing stringency due to the degree of nucleotide sequence similarlity between different families which in some cases can be as high as 70%. When the radioactive $C{\mu}$ and $V_{H}J558$ RNA probes are tested on LPS-stimulated adult spleen cells, $2{\sim}4{\times}106cpm$/slide shows low background and reasonable frequency of specific positive cells. For the washing condition. 40~50% formamide at $54^{\circ}C$ is found to be optimum for the $C{\mu}$. $V_{H}S107$ and $V_{H}J558$ probes. The analyzed results clearly demonstrate that the level of each different $V_H$ gene family expression is dependent upon the complexity or size of that family. These findings are also extended to the level of $V_H$ gene family expression in separated bone marrow B cells depend upon the various stage of differentiation and conclude no preferential utilization of specific $V_H$ gene family. Thus, the utilization of VH gene segments in B lymphocyte of adult BALB/c mice is random and is not regulated or changed during the differentiation of B cells.

• 한국생물공학회:학술대회논문집
• /
• 2000.11a
• /
• pp.660-664
• /
• 2000

To clone genes related UK-58,852 production, genomic DNA of strain Actinodura roseorufa was used for the construction of genomic library using pOJ446 cosmid vector. The genomic library was screened rising dehydratase PCR product and eryA gene as a DNA hybridization probe. pHD54 was isolated, which contained an approximately 35kb of inserted DNA. BamHI, SmaI and sonicater fragments hybridized to eryA probe. All of pHD54 BgmHI, SmaI and sonicater fragments were subcloned into pGEM7 and some fragments which hybridized to eryA probe were sequenced. The nucleotide sequence was analysed using BLAST program. The sequence identities were observed in KS,AT, KR, ER and PKS loading domains. Also oxidoreductase showed similarity to rifamycin module10, and dTDP-D-glucose 4,6 dehydratase and TDP-D-glucose synthase involved in biosynthesis of sugar showed similarity to Streptomyces argillaceus.

• Korean Journal of Ichthyology
• /
• v.34 no.3
• /
• pp.208-217
• /
• 2022

We wanted to develop a real-time PCR assay capable of detecting Liobagrus obesus in environmental DNA (eDNA) extracted from freshwater samples using a pair of species-specific primers and probe for the endangered fish, L. obesus. The species-specific primers and probe were designed in consideration of single nucleotide polymorphisms between 65 species of freshwater fish living in the Republic of Korea within the cytochrome b (cytb) gene of mitochondrial DNA. The species-specific primers and probe, in the real-time PCR assay, showed high specificity as only the L. obesus genomic DNA (gDNA) was found to be positive in the specificity verification using 65 species gDNA of freshwater fish in the Republic of Korea. In addition, in the detection limit analysis using the serial dilution concentrations of L. obesus gDNA, it was found that it was possible to detect up to 0.2 pg, showing high sensitivity. Afterwards, using the species-specific primers and probe, real-time PCR assay was performed on freshwater samples obtained from 8 stations in the mid-upper basin of Geum River. As a result, the cytb gene of L. obesus was detected in total 5 stations including all 3 stations where this species was collected at the time of field survey. Therefore, the species-specific primers and probe developed in present study, and the real-time PCR assay using them, can accurately detect the cytb gene of L. obesus from eDNA samples, which can be utilized to monitor the existing habitats of this species and to discover potential new habitats.

• Horticultural Science & Technology
• /
• v.30 no.2
• /
• pp.192-200
• /
• 2012

For the development of genetically modified plants, it is important to verify various factors which potentially affect the risk assessment as well as to establish an experimental program to produce scientific and reliable data. However, it is a time and cost consuming process to develop GM plants as well as to prepare scientific and convincible data for government's approval. Therefore, using the transgenic hot pepper tolerant to a new CMV pathotype, we attempted to suggest few methodological procedures, such as probe saturation for southern blot analysis and RT-PCR and ELISA for expression analysis, for identification and stability evaluation of inserted gene in genetically modified plant which are required for submission for approval. Ten partially overlapped probes covering full length of inserted gene were produced. We could identify that the inserted gene was stacked as a single copy as well as no partial element existed. Also, we could identify the stability of the inserted gene stacked in hot pepper using probe saturation. In the expression analysis with RT-PCR and ELISA, we also could provide the stable expression of transcript and proteins in leaves and placenta and pericarp of fruits of the CMV-resistant hot pepper.

• Asian Pacific Journal of Cancer Prevention
• /
• v.16 no.17
• /
• pp.7997-8002
• /
• 2015

Gene amplification is an important mechanism in the development and progression of cancer. Currently, gene amplification status is generally determined by in situ hybridization (ISH). Multiplex ligation-dependent probe amplification (MLPA) is a PCR-based method that allows copy number detection of up to 50 nucleic acid sequences in one reaction. The aim of the present study was to compare results for HER2, CCND1, MYC and ESR1 gene amplification detected by MLPA with fluorescent in situ hybridization (FISH) and chromogenic in situ hybridization (CISH) as clinically approved methods. Tissue samples of 170 invasive breast cancers were collected. All were ER positive. Tissue samples had previously been tested for HER2 using immunohistochemistry. Amplification of the selected genes were assessed using MLPA, FISH and CISH and results were compared. HER2 MLPA and ISH results were also compared with HER2 immunohistochemistry (IHC) which detects protein overexpression. Amplification of HER2, CCND1, MYC and ESR1 by MLPA were found in 9%, 19%, 20% and 2% of samples, respectively. Amplification of HER2, CCND1, MYC and ESR1 by FISH was noted in 7%, 16%, 16% and 1% of samples, respectively. A high level of concordance was found between MLPA/FISH (HER2: 88%, CCND1: 88%, MYC: 86%, ESR1: 92%) and MLPA/CISH (HER2: 84%). Of all IHC 3+ cases, 91% were amplified by MLPA. In IHC 2+ group, 31% were MLPA amplified. In IHC 1+ group, 2% were MLPA amplified. None of the IHC 0 cases were amplified by MLPA. Our results indicate that there is a good correlation between MLPA, IHC and ISH results. Therefore, MLPA can serve as an alternative to ISH for detection of gene amplification.

• The Korean Journal of Mycology
• /
• v.26 no.1 s.84
• /
• pp.103-107
• /
• 1998

The trp2 gene encoding trifunctional enzyme in Coprinus cinereus was investigated the expression in the heterothallic mushroom species. To identify the homology of trp2 gene to Schizophyllum commune and Pleurotus ostreatus, southern hybridization was performed with plasmid pHIONA8 containing C. cinereus trp2 gene as a probe, which resulted in a strong signal indicating an homologous sequence to the chromosomal DNA of S. commune. About 50 transformants per dish was appeared in the complementation test by pHIONA8 using S. commune tryptophan auxotroph as host. In the mating test between transformants and other mating type alleles, the fruiting body of S. commune was formed at $30^{\circ}C$ in $2{\sim}3$ weeks.

• Journal of Nutrition and Health
• /
• v.35 no.10
• /
• pp.1053-1059
• /
• 2002

In post-genome period, the technique for identifying gene expression has been changed to high throughput screening. In the field of molecular nutrition, the need for this technique to clarify molecular function of the specific nutrient is essential. In this study, we have tested the zinc-regulated gene expression in zinc-deficient U937 cells, using cDNA microarray which is the cutting-edge technique to screen large numbers of gene expression simultaneously. The study result can be used for the preliminary gene screening data for clarifying, using monocyte U937 cell line, molecular Zn aspect in atherosclerosis. U937 cells were cultured in Zn-adequate (control, 12 $\mu$M Zn) or Zn-deficient (experimental, 0 $\mu$M Zn) ESMI media during 2 days, respectively. Cells were harvested and RNA was extracted. Total RNA was reverse-transcriptinized and synthesized cDNA probe labeled with Cy-3. fluorescent labeled cDNA probe was applied to microarray slide for hybridization slide, and after then, the slide was scanned using fluorescence scanner. ‘Highly expressed genes’ in Zn-deficient U937 cells, comparing to Zn-adequate group, are mainly about the genes for motility protein, immune system protein, oncogene and tumor suppressor and ‘Less highly expressed genes’ are about the genes for transcription, apoptosis associated protein, cell cycle, and several basic transcription factors. The results of this preliminary study imply the effectiveness of cDNA microarray for expression profiling of a singly nutrient deficiency, specially Zn. Furthur study, using tailored-cDNA array and capillary endothelial cell lines, would be beneficial to clarify molecular Zn function, more in detail.

• KSBB Journal
• /
• v.18 no.3
• /
• pp.190-196
• /
• 2003

An analytical system detecting DNA particularly utilizing a concept of membrane strip chromatography initially applied to home-version tests for, such as, pregnancy and ovulation has been developed. We have chosen S. typhimurium as model analyte among food-contaminating microorganisms that occurred in high frequencies, and invA gene, as a detection target, specific to Salmonella species. This gene was able to be amplified by PCR under optimal conditions employing newly designed primers in our laboratory. The PCR product was specifically measured via hybridization between the analyte and a DNA probe, which was a totally different feature from the conventional gel electrophoresis detecting the products based only on the molecular size. It is notable thar the DNA probe sequence was specially designed such that no separation of excess primers present after PCR was required. This was immobilized on a nitrocellulose (NC) membrane via streptavidin-biotin linkage minimizing a steric effect when the hybridization with the amplified DNA took place. The analyrical system detected the microorganism in a concentration of minimum $10^3$ cfu/mL (i.e., 10 cells per system), estimated from the standard curve, 20 to 40 minutes after adding the sample. This sneitivity was approximately 10 times higher than that of gel electrophoresis as an analytical tool conventionally used. Furthermore, the assay was able to be run at room temperature, which would ofter an extra advantage to users.