• Applied Microscopy
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• v.20 no.2
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• pp.57-70
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• 1990

Characterization and electron microscopic visualization of the plasmid and the gene expression of Escherichia coli were carried out. Transcriptional units of active structural genes were observed after lysis of Escherichia coli cells. The ribosomes attached to the E. coli genome on mRNA molecule as polyribosomes. From this gradient of polyribosome length, we estimated location of mRNA synthesis initiation site. In this experiment, a granule is ofen present which may correspond to a RNA polymerase at the promoter site. pOX1, pOX7, pOX7A, $pOX7{\Delta}1$, pSTP36, pSTP21, pBR322, and pJH12 were visualized by way of electron microscope, and their estimated sizes were determined to be $5.70{\pm}0.08{\mu}m,\;2.15{\pm}0.10{\mu}m,\;2.14{\pm}0.12{\mu}m,\;7.39{\pm}0.08{\mu}m,\;4.03{\pm}0.04{\mu}m,\;1.50{\pm}0.03{\mu}m\;and\;1.25{\pm}0.09{\mu}m$ respectively. One micrometer of measured length corresponded to about 3.0 Kb. Mica-press adsorption method that allows selectivs visualization of the plasmid DNA released in situ from the bacterial cell is rapid and useful for visualization of plasmids. The released plasmid DNA was adsorbed preferently on mica in a divalent cation-free solution. Miller chromatin-spreading method was useful to observe the plasmid and transcripts. BAC method and cytochrome C monolayer were useful to observe the plasmid DNA. Our ability to visualize ultrastructural aspects of the expression of E. coli has given us a unique tool with which to study the regulation the level of an individual gene.

• The Plant Pathology Journal
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• v.30 no.4
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• pp.367-374
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• 2014

Genomes contain a large number of unique genes which have not been found in other species. Although the origin of such "orphan" genes remains unclear, they are thought to be involved in species-specific adaptive processes. Here, we analyzed seven orphan genes (MoSPC1 to MoSPC7) prioritized based on in planta expressed sequence tag data in the rice blast fungus, Magnaporthe oryzae. Expression analysis using qRT-PCR confirmed the expression of four genes (MoSPC1, MoSPC2, MoSPC3 and MoSPC7) during plant infection. However, individual deletion mutants of these four genes did not differ from the wild-type strain for all phenotypes examined, including pathogenicity. The length, GC contents, codon adaptation index and expression during mycelial growth of the four genes suggest that these genes formed during the evolutionary history of M. oryzae. Synteny analyses using closely related fungal species corroborated the notion that these genes evolved de novo in the M. oryzae genome. In this report, we discuss our inability to detect phenotypic changes in the four deletion mutants. Based on these results, the four orphan genes may be products of de novo gene birth processes, and their adaptive potential is in the course of being tested for retention or extinction through natural selection.

• Korean Journal of Medicinal Crop Science
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• v.14 no.2
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• pp.96-100
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• 2006

Regions of allelic loss on chromosomes in many tumors of human and some experimental animals are generally considered to harbor tumor-suppressor genes involved in tumorigenesis. Allelotype analyses have greatly improved our under-standing of the molecular mechanism of radiation lymphomagenesis. Previously, we and others found frequent loss of heterozygosity (LOH) on chromosomes 4, 11, 12, 16 and 19 in radiation-induced lymphomas from several $F_1$, hybrid mice. To examine possible contributions of individual tumor-suppressor genes to tumorigenesis in p53 heterozygous deficiency, we investigated the genome-wide distribution and status of LOH in radiation-induced lymphomas from $F_1$ mice with different p53 status. In this study, we found frequent LOH (more than 20%) on chromosomes 4 and 12 and on chromosomes 11, 12, 16 and 19 in radiation-induced lymphomas from $(STS/A{\times}MSM/Ms)F_1$ mice and $(STS/A{\times}MSM/Ms)F_1-p53^{KO/+}$ mice, respectively. Low incidences of LOH (10-20%) were also observed on chromosomes 11 in mice with wild-type p53, and chromosomes 1, 2, 9, 17 and X in p53 heterozygous-deficient mice. The frequency of LOH on chromosomes 9 and 11 increased in the $(STS/A{\times}MSM/Ms)F_1-p53^{KO/+}$ mice. Preferential losses of the STS-derived allele on chromosome 9 and wild-type p53 allele on chromosome 11 were also found in the p53 heterozygous-deficient mice. Thus, the putative tumor-suppressor gene regions responsible for lymphomagenesis might considerably differ due to the p53 status.

• Korean Journal of Microbiology
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• v.43 no.1
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• pp.1-6
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• 2007

We describe a multiplex PCR method that can detect and differentiate simultaneously four different kinds of DNA viruses, Epstein-Barr virus (EBV), cytomegalovirus (CMV), hepatitis B virus (HBV) and parvovirus B19 (B19). Primers for the multiplex PCR reaction were designed to amplify specific regions of the EBV (pol), CMV (pol), HBV (pol) and B19 (ns) viral genomes and used to simultaneously detect individual viruses. In order to achieve optimal sensitivity and specificity for multiplex PCR, the thermo-cycling parameters, primer sequences, and concentration of each reaction components were optimized systematically. The sensitivity of the detection method ranged between 5 and 10 copies of viral genome with a mixture of multiple primer pairs. Furthermore, this highly sensitive test showed no cross-reactivity among the four viruses. Thus, the results obtained in this study provide evidence that the assay system is a good tool for supporting the diagnosis of viral infection and contamination.

• The Korean Journal of Applied Statistics
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• v.25 no.2
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• pp.269-277
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• 2012

In microarray data analysis, recent efforts have focused on the discovery of gene sets from a pathway or functional categories such as Gene Ontology terms(GO terms) rather than on individual gene function for its direct interpretation of genome-wide expression data. We introduce a meta-analysis method that combines $p$-values for changes of each gene in the group. The method measures the significance of overall treatment-induced change in a gene group. An application of the method to a real data demonstrates that it has benefits over other statistical methods such as Fisher's exact test and permutation methods. The method is implemented in a SAS program and it is available on the author's homepage(http://cafe.daum.net/go.analysis).

• International Journal of Industrial Entomology and Biomaterials
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• v.31 no.2
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• pp.62-69
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• 2015

The Asian cavity-nesting honeybee, Apis cerana (Hymenoptera: Apidae), has been extensively studied for its biogeography and genetic diversity, but the molecules utilized in past studies were mainly ~90 bp long mitochondrial non-coding sequences, located between $tRNA^{Leu}$ and COII. Thus, additional molecular markers may enrich our understanding of the biogeography and genetic diversity of this valuable bee species. In this study, we reviewed the public genome database to find introns of cDNA sequences, with the assumption that these introns may have less evolutionary constraints. The six introns selected were subjected to preliminary tests. Thereafter, two introns, titled White gene and MRJP9 gene, were selected. Sequencing of 552 clones from 184 individual bees showed a total of 222 and 141 sequence types in the White gene and MRJP9 gene introns, respectively. The sequence divergence ranged from 0.6% to 7.9% and from 0.26% to 17.6% in the White gene and the MRJP9 introns, respectively, indicating higher sequence divergence in both introns. Analysis of population genetic diversity for 16 populations originating from Korea, China, Vietnam, and Thailand shows that nucleotide diversity (π) ranges from 0.003117 to 0.025837 and from 0.016541 to 0.052468 in the White gene and MRJP9 introns, respectively. The highest π was found in a Vietnamese population for both intron sequences, whereas the nine Korean populations showed moderate to low sequence divergence. Considering the variability and diversity, these intron sequences can be useful as non-mitochondrial DNA-based molecular markers for future studies of population genetics.

• Toxicological Research
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• v.26 no.3
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• pp.171-175
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• 2010

The human genome contains approximately 13 orphan cytochrome P450 (P450, CYP) genes, of which the apparent function or substrate has not been identified. However, they seem to possess their own biological relevance in some tissues or developmental stages. Here, we characterized the heterologously expressed CYP2W1, an orphan P450 enzyme. The recombinant CYP2W1 protein containing a $6{\times}$(His)-tag at Nterminus has been expressed in Escherichia coli and purified. Expression level of CYP2W1 holoenzyme was around 500 nmol P450 holoenzyme per liter culture medium. The reduced CO difference spectrum of CYP2W1 showed a maximum absorption at 449 nm. CYP2W1 indicated the significant induction to bioactivate Trp-P-1, MeIQ, and IQ in E. coli DJ701 tester strain. However, the bioactivation of B[$\alpha$]P, and NNK by CYP2W1 was relatively low. The model structure of CYP2W1 suggested the characteristic P450 folds with the lengths and orientations of the individual secondary elements. The F-G loop is situated on the distal side of heme to accommodate the flexibility of active site of CYP2W1. These studies can provide useful information for the finding of its biological roles and structure-function relationships of an orphan CYP2W1 enzyme.

• Fisheries and Aquatic Sciences
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• v.14 no.1
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• pp.22-30
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• 2011

Vitellogenin (Vg) is the precursor of vitellin (Vn), which is the major yolk protein in nearly all oviparous species, including fish, amphibians, reptiles, and most invertebrates. It is one of the most important factors during reproduction, and numerous studies have shown that Vg genes are markers of the reproductive cycle and effecter genes induced by endocrine-disrupting chemicals (EDCs). Previously, we isolated two distinct cDNAs encoding vitellogenin homologs Pj-Vg1 and Pj-Vg2 from Pandalus shrimp Pandalopsis japonica. In this study, full-length genomic sequences of Pj-Vg1 and Pj-Vg2 were determined using a PCR-based genome walking strategy. Isolated Pj-Vg1 and Pj-Vg2 genes were 11,910 and 11,850 bp long, respectively. Both Pj-Vg genes had 15 exons and 14 introns, and the splicing sites were also the same, suggesting that they arose via gene duplication. The similar structural characteristics of decapod Vg genes suggest that they are all orthologs that evolved from the same ancestral gene. Analysis of Pj-Vg1 and Pj-Vg2 expression revealed that the relative copy numbers of Pj-Vg1 and Pj-Vg2 were similar in the hepatopancreas, whereas Pj-Vg2 transcripts were also detected in the ovary. Expression of both Pj-Vg genes was induced in hepatopancreas of mature individuals, whereas only Pj-Vg2 transcripts were upregulated in the ovaries from mature animals, suggesting that both Pj-Vgs are important for oocyte development. A strong positive correlation was found between Pj-Vg1 and Pj-Vg2 transcripts in the same individual, indicating they are under the same control mechanisms. Additionally, a positive correlation was found between ovarian and hepatopancreatic Pj-Vg2 transcripts, suggesting that its dual expression is regulated by similar physiological conditions. Knowledge of the similarities and differences between the two vitellogenin-like genes, Pj-Vg1 and Pj-Vg2, would help us to understand their roles in reproduction and other physiological effects.

• Journal of Marine Bioscience and Biotechnology
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• v.2 no.1
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• pp.68-72
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• 2007

Flounder is one of the major aquacultured fish and of an economically important item in Korean fisheries. Recently, there are trends of research worldwide that aim to analyze and characterize a whole genome or a whole proteome of interesting species. The data are utilized for the understanding and development of preventive and curative technologies for the serious diseases. However, there are very limited information of proteome for marine organisms, we optimized first the conditions for two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) with serum form a marine fish, flounder (Paralichthys olivaceus). A pre-treatment of serum and an optimization of protein concentration analyzed were surveyed for enhancing the separation for proteins. A statistical analysis was performed on the overall 1,820 protein spots to overcome the variability among individual fishes.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.11
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• pp.1521-1528
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• 2012

Previously identified QTL regions on BTA1 and BTA5 were investigated to validate the QTL regions and to identify candidate genes for growth and carcass traits in commercial cattle populations from the USA and Korea. Initially, a total of 8 polymorphic microsatellite (MS) markers in the BTA1 and 5 QTL regions were used for Chi-square tests to compare the frequencies of individual alleles between high and low phenotypic groups for the US (Michigan Cattleman's Association/Michigan State University; MCA/MSU) cattle. For a subsequent study, 24 candidate genes containing missense mutations and located within the QTL regions based on bovine genome sequence data were analyzed for genotyping in the two commercial cattle populations. Re-sequencing analyses confirmed 18 public missense SNPs and identified 9 new SNPs. Seventeen of these SNPs were used for genotyping of the MCA/MSU cattle (n = 98) and Korean native cattle (n = 323). On BTA1, UPK1B, HRG, and MAGEF1 polymorphisms residing between BM1312 and BMS4048 were significantly associated with growth and carcass traits in one or both of the MCA/MSU and Korean populations. On BTA5, ABCD2, IL22 and SNRPF polymorphisms residing between BL4 and BR2936 were associated with marbling and backfat traits in one or both of the MCA/MSU and Korean cattle populations. These results suggested that BTA 1 and 5 QTL regions may be segregating in both Korean Hanwoo and USA commercial cattle populations and DNA markers tested in this study may contribute to the identification of positional candidate genes for marker-assisted selection programs.