• Journal of Genetic Medicine
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• v.1 no.1
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• pp.45-50
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• 1997

Neuroblastoma, a pediatric malignant neoplasm of neural crest origin, has a wide range of clinical virulence. The mechanisms contributing to the development of neuroblastomas are largely unclear, but non-random chromosomal changes identified over the past years suggest the involvement of genetic alterations. Amplification of the human N-myc proto-oncogene is frequently seen either in extrachromosomal double minutes or in homogeneously staining regions (HSRs) of aggressively growing neuroblastomas. N-myc maps to chromosome 2 band 24, but HSR have never been observed at this band, suggesting transposition of N-myc during amplification. We have constructed and analyzed the region-specific painting probe for HSR in neuroblastoma IMR-32 to determine the derivative chromosomes. Microdissection was performed on HSR using an inverted microscope with the help of microglass needles and an micromanipulator. We pretreated the microdissected fragments with Topoisomerase I which catalyzes the relaxation of supercolled DNA, and performed two initial rounds of DNA synthesis with T7 DNA polymerase followed by conventional PCR to enable the reliable preparation of Fluorescent in situ hybridization probe from a single microdissected chromosome. With this method, it was possible to construct the region-specific painting probe for HSR. The probe hybridized specifically to the HSRs of IMR-32, and to 2p24, 2p13 of normal chromosome. Our results suggest there was coamplification of N-myc together with DNA of the chromosome 2p24 and 2p13. Moreover, the fluorescent signals for the amplified chromosomal regions in IMR-32 cells were also easily recognized at a Thus this painting probe can be applied to detect the similar amplification of N-myc in neuroblastoma tissue, and the probe pool for HSR may be used to identify the cancer-relevant genes.

• Journal of Life Science
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• v.14 no.5
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• pp.815-820
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• 2004

A bacterum containing antitumor activity was isolated from traditional korean food, Jeotgal. Through the 16s rRNA sequence analysis, the bacterium was identitied as a strain of Bacillus subtilis SW-l. The best culture condition for antitumor activity of the bacterium is 3% of soluble starch and 1 % of yeast extract as corbon and nitrogen sources, respectively. Cytotoxicitic concentrations of the culture supernatant of B. subtilis SW-1 against cancer cell lines, A549 and SK-OV3 were 30 ul/ml and 40 ul/ml, respectively, as $IC_{50}$/ values. In DNA fragmentation assay, the culture supernatant showed the programmed cell death (apoptosis) to cause degrading the chromosomal DNA like ladder. Taken together, the culture supernatant of the B. subtilis SW-1 has some possibility to be used as an antitumor agent.

• Korean Journal of Microbiology
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• v.29 no.2
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• pp.75-79
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• 1991

The yeast L-A virus (4.6 kb dsRNA genome) encodes the major coat protein and a "gag-pol" fusion minor coat protein that separately encapsidate itself and $M_{1}$, a 1.8 kb dsRNA satellite virus encoding a secreted protein toxin (the killer toxin). The teast chromosomal SKI genes prevent viral cytopathology by lowering the virus copy number. Thus, $ski^{-}$ mutants are ts and cs for growth. We transformed a ski2-2 virus-infested mutant with a yeast bank in a high copy cloning vector and selected the rare healthy transformants for analysis. One type of transformant segregated M-O L-A-O cells with high frequency. Elimination of the DNA clone from the ski2-2 strain eliminated this phinotype and introduction of the DNA clone recovered from such transformants into the parent ski2-2 strain, or into ski3 or ski6 mutants gave the same phenotype. This killer-curing phenotype was due to the curing of the helper L-A dsRNA virus. The 6.5 kb insert only had this activity when carried on a high copy vector and in $ski^{-}$ cells (not in $SKI^{+}$ cells). This 6.5 kb insert acts as a mutagen on L-A dsRNA producing a high rate of deletion mutations.mutations.

• Journal of Microbiology and Biotechnology
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• v.19 no.3
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• pp.217-228
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• 2009

Mobile genetic segments, or transposons, are also referred to as jumping genes as they can shift from one position in the genome to another, thus inducing a chromosomal mutation. According to the target site-specificity of the transposon during a transposition event, the result is either the insertion of a gene of interest at a specific chromosomal site, or the creation of knockout mutants. The former situation includes the integration of conjugative transposons via site-specific recombination, several transposons preferring a target site of a conserved AT-rich sequence, and Tn7 being site-specifically inserted at attTn7, the downstream of the essential glmS gene. The latter situation is exploited for random mutagenesis in many prokaryotes, including IS (insertion sequence) elements, mariner, Mu, Tn3 derivatives (Tn4430 and Tn917), Tn5, modified Tn7, Tn10, Tn552, and Ty1, enabling a variety of genetic manipulations. Randomly inserted transposons have been previously employed for a variety of applications such as genetic footprinting, gene transcriptional and translational fusion, signature-tagged mutagenesis (STM), DNA or cDNA sequencing, transposon site hybridization (TraSH), and scanning linker mutagenesis (SLM). Therefore, transposon-mediated genetic engineering is a valuable discipline for the study of bacterial physiology and pathogenesis in living hosts.

• Microbiology and Biotechnology Letters
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• v.13 no.3
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• pp.251-255
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• 1985

Nitrogen-fixing bacteria were isolated from the rice rhizosphere of various paddy fields in our country. The screening of 235 isolates for nitrogen-fixing ability resulted in the isolation of Enterobacter agglomerans NFB264 and three Klebsiella pneumoniae NFB 3, NFB 320. Plasmids of various molecular weight from 1.7 to more than 84 Mal. were detected by agarose gel electrophoresis in three out of four isolates. But, these plasmids had not any nitrogen-fixing genes. Hybridization experiments using Klebsiella pneumoniae M5al nitrogen-fixing genes, nif Q-K and nif DH, as probes revealed the presence of homologous sequences in the chromosomal DNA of all isolates. However the restriction patterns of nif genes of the isolates by various restriction endonucleases were different to those of Klebsiella pneumoniae M5al.

• Journal of Microbiology and Biotechnology
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• v.18 no.12
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• pp.1884-1889
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• 2008

The ${\beta}$-lactamase inhibitory protein, BLIP-II, found in the culture supernatant of Streptomyces exfoliatus SMF19, shows no discernible sequence identity with other ${\beta}$-lactamase inhibitory proteins identified in Streptomyces spp. A null mutant of the gene encoding BLIP-II (bliB::$hyg^r$) showed a bald appearance on solid media. Although BLIP-II was initially isolated from the supernatant of submerged cultures, sites of BLIP-II accumulation were seen in the cell envelope. Mutation of bliB was also associated with changes in the formation of septa and condensation of the chromosomal DNA associated with sporulation. The bliB mutant exhibited infrequent septa, showing dispersed chromosomal DNA throughout the mycelium, whereas the condensed chromosomes of the wild-type were separated by regularly spaced septa giving the appearance of a string of beads. Therefore, on the basis of these results, it is suggested that BLIP-II is a regulator of morphological differentiation in S. exfoliatus SMF19.

• Journal of Microbiology and Biotechnology
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• v.6 no.6
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• pp.386-390
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• 1996

The ${\beta}$-galactosidase gene from Lactococcus lactis subsp. lactis ATCC 7962 was cloned and its enzymatic properties were characterized, with a view to assessing its potential use as a selection marker in the food-grade cloning vector. Chromosomal DNA from L. lactis subsp. lactis 7962 was cleaved with PstI and ligated into pBR322 for transformation into Escherichia coli TGl. Transformants showing ${\beta}$-galactosidase activity possessed the pBR322 plasmid containing a 10 kilobase (kb) PstI fragment and this plasmid was named pCKL11. The cloned ${\beta}$-galactosidase gene came from the chromosomal DNA of L. lactis subsp. lactis 7962 was confirmed by Southern hybridization. A restriction map of pCKL11 was constructed from the cleavage of both pCKL11 and the purified 10kb insert fraqment. The. optimum pH of the ${\beta}$-galactosidase determined with the E. coli harboring the pCKL11 was 7.0. The optimum temperature was $50^{\circ}C$, while the pI of the enzyme was 7.4. These values were the same as those of the enzyme from the parent strain.

• Molecules and Cells
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• v.45 no.7
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• pp.444-453
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• 2022

Multivalent macromolecular interactions underlie dynamic regulation of diverse biological processes in ever-changing cellular states. These interactions often involve binding of multiple proteins to a linear lattice including intrinsically disordered proteins and the chromosomal DNA with many repeating recognition motifs. Quantitative understanding of such multivalent interactions on a linear lattice is crucial for exploring their unique regulatory potentials in the cellular processes. In this review, the distinctive molecular features of the linear lattice system are first discussed with a particular focus on the overlapping nature of potential protein binding sites within a lattice. Then, we introduce two general quantitative frameworks, combinatorial and conditional probability models, dealing with the overlap problem and relating the binding parameters to the experimentally measurable properties of the linear lattice-protein interactions. To this end, we present two specific examples where the quantitative models have been applied and further extended to provide biological insights into specific cellular processes. In the first case, the conditional probability model was extended to highlight the significant impact of nonspecific binding of transcription factors to the chromosomal DNA on gene-specific transcriptional activities. The second case presents the recently developed combinatorial models to unravel the complex organization of target protein binding sites within an intrinsically disordered region (IDR) of a nucleoporin. In particular, these models have suggested a unique function of IDRs as a molecular switch coupling distinct cellular processes. The quantitative models reviewed here are envisioned to further advance for dissection and functional studies of more complex systems including phase-separated biomolecular condensates.

• BMB Reports
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• v.34 no.3
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• pp.262-267
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• 2001

A cDNA coding alkaline phosphatase (AP) homologue was isolated from a cDNA library of Schizosaccharomyces pombe by colony hybridization. The nucleotide sequence of the cloned cDNA appeared to lack the N-terminal coding region. The genomic DNA encoding alkaline phosphatase homologue was isolated from S. pombe chromosomal DNA using PCR. The amplified DNA fragment was ligated into plasmid pRS315 to generate the recombinant plasmid pSW20. The DNA insert was subcloned as two smaller fragments for nucleotide sequencing. The sequence contains 2,789 by and encodes a protein of 532 amino acids with a molecular mass of 58,666 daltons. The S. pombe cells containing plasmid pSW20 showed much higher AP activity compared with the yeast cells with vector only This indicates that the cloned AP gene apparently encodes AP The predicted amino acid sequence of the S. pombe AP shares homology with those of other known APs.

• Laboratory Medicine Online
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• v.1 no.2
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• pp.110-114
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• 2011

There have been a few reports of hemophagocytic lymphohistiocytosis (HLH) with chromosomal abnormalities. Clonal chromosomal abnormalities in HLH patients are usually found in association with hematologic malignancies and rarely with epstein-barr virus (EBV) infection. Here, we report a fatal case of HLH with clonal karyotype abnormalities. A 75-yr-old man was admitted with persistent anorexia and high fever. Laboratory data revealed pancytopenia, hypofibrinogenemia, hyperferritinemia, prolonged prothrombin time and activated partial thromboplastin time, and marked elevated level of serum transaminases. In real time-PCR using whole blood, EBV DNA was not detected but cytomegalovirus (CMV) DNA was detected. The bone marrow aspiration smear showed hyperplasia of mature histiocytes with prominent hemophagocytosis. In chromosomal analysis of bone marrow aspirates, complex chromosomal abnormalities were found. In spite of steroid pulse therapy and antibiotic treatment, he died of disseminated intravascular coagulopathy.