• Korean Journal of Microbiology
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• v.31 no.4
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• pp.286-291
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• 1993

The $Km^{r}$ gene and plasmid of natural isolate and genetically modified microorganisms (GMM) rearranged by conjugation in water environments were comparatively analyzed by agarose gel electrophoresis and Southern analysis. The transfer rates of the $Km^{r}$ gene from GMM strains were generally 100 times higher than thosc of natural iso]ate(DKI) under laboratory cnvironments, but their transfer rate was not much different in Moosimcheon River water. The conjugants obtained in LB(Luria-Bertani broth) and FW(filtered river water) water under laboratory conditions showed same number of the plasmids. but the sizes of the plasmids were changed. The $Km^{r}$ gene in the conjugants was found in the same position as the pDKJO] $Km^{r}$ plasmid. In case of the GMM strains as donor. the large plasmids of 180 kb appeared in conjugants obtained in LB and FW water. Especially, the $Km^{r}$ gene in the donor of DKC600 was found to be inserted into chromosome of the conjugant obtained in FW water. However. in the conjugants obtained from DKl and DKB 701 in Moosimcheon River water, the plasmids were rearranged by 4 and 8. respectively, and all of them showed hybridization by the $Km^{r}$ probe. But the small plasmids of the recipient disappeared in the conjugant from DKC600 as donor, and the rearranged plasm ids and chromosome in the conjugants were observed to be hybridized with the $Km^{r}$ probe. Therefore, rearrangement of $Km^{r}$ gene and plasmids by conjugation was found to be afTected diversely by cellular characteristics as well as by environmental factors.

• Korean Journal of Head & Neck Oncology
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• v.35 no.1
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• pp.33-36
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• 2019

Mucosa-associated lymphoid tissue (MALT) lymphoma has specific clinical and pathologic features. The most common site MALT lymphomas is the stomach; however, it can also occur in other organs, such as the salivary glands. MALT lymphoma is rare, but its prognosis is good. A 32-year-old man visited Konyang university hospital with parotid mass. Superficial partial parotidectomy was performed to exclude lymphoid neoplasms. IgH gene rearrangement analysis of the surgical specimen led to the diagnosis of MALT lymphoma. The patient underwent esophagogastroduodenoscopy, positron emission tomography-computed tomography, and whole-body bone scan. Regional or distant metastasis was not observed on staging workup. The patient underwent postoperative radiation therapy, there has been no recurrence of MALT lymphoma to date. Here, we report this rare case of parotid MALT lymphoma that was treated with surgery and postoperative radiation therapy.

• Environmental Mutagens and Carcinogens
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• v.19 no.1
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• pp.7-13
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• 1999

The mouse lymphoma thymidine kinase (tk+/-) gene assay (MOLY) using L5178Y tk+/- mouse lymphoma cell line is one of the mammalian forward mutation assays. It is well known that MOLY has many advantages and more sensitive than the other mammalian forward mutation assays such as x-linked hyposanthine phosphoribosyltransferase (hprt) gene assay. The target gene of MOLY is a heterozygous tk+/- gene located in 11 chromosome of L5178Y tk+/- cell, so it is able to detect the wide range of genetic changes like point mutation, deletion, rearrangement, and mitotic recombination within tk gene or deletion of entire chromosome 11. MOLY has relatively short expression time (2-3 days) compared to 1 week of hprt gene assay. MOLY can also induce relatively high mutant frequency so a large number of events can be recorded. The bimodal distribution of colony size which may indicate gene mutation and chromosome breakage potential of chemicals according to mutation scale such as large normal-growing mutants and small slow-growing mutants can be observed in this assay. The statistical analysis of data can be performed using the MUTANT program developed by York Electronic Research in association with Hazelton as recommended by the UKEMS (United Kingdom Environmental Mutagen Society) guidelines. This report reviewed MOLY using the microtiter cloning technique (microwell assay).

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.9
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• pp.4247-4250
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• 2016

Background: Pax8 and peroxisome proliferator-activated receptor gamma 1 gene (Pax8-$PPAR{\gamma}1$) are important factors in tumors. Several studies have suggested that follicular thyroid cancer may arise from Pax8- $PPAR{\gamma}1$ rearrangement. In order to have a better understanding of the association between Pax8-$PPAR{\gamma}1$ rearrangement and follicular thyroid cancer, we conducted the presenmt meta-analysis. Materials and Methods: The information was extracted from PubMed, EMBASE and Web of Science. Statistic analysis was performed with Stata12.0 software. Odds ratios (ORs) were calculated using a fixed-effects model. We also performed heterogeneity and publication bias analyses. Results: Nine studies including 198 follicular thyroid cancer patients and 268 controls were considered eligible. The frequency of Pax8-$PPAR{\gamma}1$ rearrangement was significantly higher in the follicular thyroid cancer group than in the control group, with a pooled OR of 6.63 (95%CI=3.50-12.7). In addition, through subgroup analysis, the OR between Pax8-$PPAR{\gamma}1$ rearrangement and follicular thyroid cancer was 6.04 (95%CI = 3.18-11.5) when using benign tumor tissues as controls. The OR for the method subgroup was 9.99 (95% CI =4.86-20.5) in the RT-PCR. Conclusions: The final results demonstrated that Pax8-$PPAR{\gamma}1$ rearrangement has significant association with follicular thyroid cancer.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.7
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• pp.3057-3063
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• 2014

Background: Anaplastic lymphoma kinase (ALK) gene rearrangement in non-small cell lung cancer (NSCLC) has been intensively studied. The gold standard for ALK detection is FISH, but this is not routinely conducted in clinical practice, so that the IHC method has a role. The aim of this study was to identify the incidence of ALK rearrangement and risk or prognostic factors for ALK positivity using both of IHC and FISH methods. Materials and Methods: From January 2008 to December 2012, 267 completely resected NSCLC patients in Chiang Mai University Hospital were enrolled in this study. Clinical and pathological variables and outcomes of treatment were retrospectively reviewed. IHC and FISH were used to evaluate ALK rearrangement. Sensitivity and specificity of IHC were analyzed. Multivariable analysis was used to identify clinico-pathological correlations with positive results of IHC and clinical outcomes. Results: Twenty-two (8.2%) of 267 specimens were IHC-positive for ALK with intense cytoplasmic staining, whereas only 10 (3.8%) were FISH-positive. Sensitivity, specificity and the positive likelihood ratio with IHC were 80.0%, 94.9%, and 15.8 respectively. Age less than 55 years (RR 4.4, 95%CI 1.78-10.73, p value=0.001) and presence of visceral pleural invasion (VPI) (RR 2.9, 95%CI 1.21-6.78, p value =0.017) were identified as risk factors for ALK rearrangement with FISH. There were no statistically significant differences in other clinical and pathological variables. ALK rearrangement was not a prognostic factor for tumor recurrence or overall survival. Conclusions: The incidences of ALK positivity in completely resected NSCLCs in northern Thailand were 8.2% by IHC and 3.8% by FISH. IHC with mouse monoclonal, Ventana D5F3 antibody can be used as a screening tool before FISH method because of high specificity and high positive likelihood ratio. Age less than 55 years and VPI are risk factors for ALK positivity.

• Microbiology and Biotechnology Letters
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• v.20 no.4
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• pp.483-490
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• 1992

In order to understand the transfer behavior of a particular gene in water environments, kanamycin resistance ($Km^r$) gene was tracked by Southern hybridization with DNA probe in its conjugal transfer. A $Km^r$ natural bacterial isolate and genetically modified microorganisms (GMMs) constructed from the isolate were used as donor for conjugal transfer of the $Km^r$ gene. The transfer frequencies of the $Km^r$ gene from GMM strains were generally 10 to 100 times higher than those from the natural isolate. The conjugants obtained from GMM strains in LB broth had more plasmids newly appeared, and particularly the conjugants in A Wand FW waters revealed more rearrangement in their plasmids as a function of conjugation time. When plasmids of the conjugants obtained in LB broth were Southern hybridized with DNA probe of the $Km^r$ gene, the $Km^r$ plasmids in the conjugants were detected at the same position of the plasmids in donor cells, in spite of the fact that the plasmids were highly rearranged in conjugant cells. But the $Km^r$ plasmids in the donor of DKI and DKC601, and DKC600 were not identified in the conjugants obtained after 50 h conjugation in AW and after 30 h in AW, respectively. The size of the $Km^r$ plasmids showing hybridization signal were a little changed in the conjugants obtained in A Wand FW waters. Therefore, the method of Southern hybridization with DNA probe was proved to be very specific and useful for tracking of particular genes in water environments.

• Korean Journal of Plant Tissue Culture
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• v.25 no.2
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• pp.109-113
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• 1998

In this study we tried to transform an antimicrobial peptide gene (Shiva) under the promoter of tomato phenylalanine ammonia-lyase (tPAL5) into tobacco and potato plants. Antimicrobial peptide gene was isolated originally from giant silk moth (Hyalophora cecropia) and modified ie nucleotide sequence to increase antimicrobial activity. Transgenic tobacco plants were regenerated and their seeds were tested on the media containing kanamycin (500 mg/L). The results of PCR amplification and genomic Southern blot hybridization confirmed the integration of construct (tPAL5 promoter-Shiva-NOS-GUS-NOS) into chromosome. We observed that one of the transgenic tobacco plants showed chromosome rearrangement when integrated. In case of potato transformation, the efficiency of regeneration was maximized at the medium containing Zeatin 2mg/L, NAA 0.01mg/L, GA$_3$ 0.1mg/L. We also observed the high expression of GUS (${\beta}$-glucuronidase) enzyme which was located next to the terminator sequence of nopaline synthase gene (NOS) in the vascular tissue of stem, leaves of transgenic potatoes. This result suggested that a short sequence of Shiva gene (120 bp) and NOS terminator sequence might be served as a leader sequence of transcript when translated.

• International Journal of Stem Cells
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• v.17 no.1
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• pp.1-14
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• 2024

The clustered regularly interspaced short palindromic repeats (CRISPR) system, a rapidly advancing genome editing technology, allows DNA alterations into the genome of organisms. Gene editing using the CRISPR system enables more precise and diverse editing, such as single nucleotide conversion, precise knock-in of target sequences or genes, chromosomal rearrangement, or gene disruption by simple cutting. Moreover, CRISPR systems comprising transcriptional activators/repressors can be used for epigenetic regulation without DNA damage. Stem cell DNA engineering based on gene editing tools has enormous potential to provide clues regarding the pathogenesis of diseases and to study the mechanisms and treatments of incurable diseases. Here, we review the latest trends in stem cell research using various CRISPR/Cas technologies and discuss their future prospects in treating various diseases.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2023.04a
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• pp.15-15
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• 2023

The chloroplast (cp) is an autonomous plant organelle with an individual genome that codes for essential cellular functions. The architecture and gene content of the cp genome is highly conserved in angiosperms. The plastome of Corydalis belongs to the Papaveraceae family, and the genome is comprised of unusual rearrangements and gene content. Thus far, no extensive comparative studies have been carried out to understand the evolution of Corydalis chloroplast genomes. Therefore, the Corydalis platycarpa cp genome was sequenced, and wide-scale comparative studies were conducted using publicly available twenty Corydalis plastomes. Comparative analyses showed that an extensive genome rearrangement and IR expansion occurred, and these events evolved independently in the Corydalis species. In addition, the protein-coding genes accD and the ndh gene loss events occurred in the common ancestor of the Corydalis and sub-clade of the Corydalis lineage, respectively. The gene ndh lost in the Corydalis-sub clade species is distributed predominantly in the Qinghai-Tibetan plateau (QTP) region. The molecular clock analysis suggests that the divergence time of all the ndh gene lost Corydalis sub-clade species occurred in the 44.31 - 15.71 mya. These results coincide very well with the uplift of the Qinghai-Tibet Plateau in the Oligocene and Miocene periods, and maybe during this period, it probably triggered the radiation of the Corydalis species. To the best of the authors' knowledge, this is the first large-scale comparative study of Corydalis plastomes and their evolution. The present study may provide insights into the plastome architecture and the molecular evolution of Corydalis species.

• The Journal of the Korean Society for Microbiology
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• v.34 no.6
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• pp.519-532
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• 1999

Helicobacter pylori is a causative agent of type B gastritis and plays a central role in the pathogenesis of gastroduodenal ulcer and gastric cancer. To elucidate the host-parasite relationship of the H. pylori infection on the basis of molecular biology, we tried to evaluate the genomic diversity of H. pylori. An ordered overlapping bacterial artificial chromosome (BAC) library of a Korean isolate, H. pylori 51 was constructed to set up a genomic map. A circular physical map was constructed by aligning ApaI, NotI and SfiI-digested chromosomal DNA. When the physical map of H. pylori 51 was compared to that of unrelated strain, H. pylori 26695, completely different restriction patterns were shown. Fifteen known genes were mapped on the chromosome of H. pylori 51 and the genetic map was compared with those of strain 26695 and J99, of which the entire genomic sequences were reported. There were some variability in the gene location as well as gene order among three strains. For further analysis on the genomic diversity of H. pylori, when comparing the genomic structure of 150 H. pylori Korean isolates with one another, genomic macrodiversity of H. pylori was characterized by several features: whether or not susceptible to restriction digestion of the chromsome, variation in chromosomal restriction fingerprint and/or high frequency of gene rearrangement. We also examined the extent of allelic variation in nucleotide or deduced amino acid sequences at the individual gene level. fucT, cagA and vacA were confirmed to carry regions of high variation in nucleotide sequence among strains. The plasticity zone and strain-specific genes of H. pylori 51 were analyzed and compared with the former two genomic sequences. It should be noted that the H. pylori 51-specific sequences were dispersed on the chromosome, not congregated in the plasticity zone unlike J99- or 26695-specific genes, suggesting the high frequency of gene rearrangement in H. pylori genome. The genome of H. pylori 51 shows differences in the overall genomic organization, gene order, and even in the nucleotide sequences among the H. pylori strains, which are far greater than the differences reported on the genomic diversity of H. pylori.