• Journal of Microbiology and Biotechnology
• /
• v.1 no.1
• /
• pp.45-49
• /
• 1991

The complete nucleotide sequence of alkalophilic Bacillus sp. K-17 $\beta$-xylosidase gene and its flanking regions were established. A 1263-bp of an open reading frame for $\beta$-xylosidase was observed. The molecular weight (50, 521 dalton), deduced from the nucleotide sequence of $\beta$-xylosidase gene, agreed with the result obtained by SDS-polyacrylamide gel electrophoresis of the purified enzyme (51, 000 dalton). The Shine-Dalgarno sequence, 5'-GAGGAGG-3', was found 8 bp upstream of the initiation codon ATG. The -10 sequence (TAAAAT) in the promoter region for $\beta$-xylosidase gene was similar to the consensus sequence for Bacillus subtilis RNA polymerase, whereas the -35 sequence (TCGATCA) different from all the known -35 regions in the promoter for Bacillus subtilis RNA polymerase.

• International Journal of Industrial Entomology and Biomaterials
• /
• v.46 no.2
• /
• pp.41-54
• /
• 2023

The blue-tailed damselfly, Ischnura elegans Van der Linden, 1820 (Odonata: Coenagrionidae), is a climate-sensitive indicator species in South Korea. In this study, we sequenced the complete mitochondrial genome (mitogenome) of I. elegans collected from South Korea for subsequent population genetic analysis, particularly to trace population movements in response to climate change. The 15,963 base pair (bp)-long complete mitogenome of I. elegans has typical sets of genes including a major non-coding region (the A+T-rich region), and an arrangement identical to that observed in ancestral insect species. The ATP6, ND3 and ND1 genes have the TTG start codon, which, although rare, is the canonical start codon for animal mitochondrial tRNA. The A/T content was 71.4% in protein-coding genes, 72.1% in tRNAs, 72.9% in the whole genome, 74.7% in srRNA, 75.3% in lrRNA, and 83.8% in the A+T-rich region. The A+T-rich region is unusually long (1,196 bp) and contains two subunits (192 bp and 176-165 bp), each of which is tandemly triplicated and surrounded by non-repeat sequences. Comparison of the sequence divergence among available mitogenomes of I. elegans, including the one from the current study, revealed ND2 as the most variable gene, followed by COII and COI, suggesting that ND2 should be targeted first in subsequent population-level studies. Phylogenetic reconstruction based on all available mitogenome sequences of Coenagrionidae showed a strong sister relationship between I. elegans and I. senegalensis.

• The Journal of the Convergence on Culture Technology
• /
• v.3 no.4
• /
• pp.1-19
• /
• 2017

Death culture continues to lead human history with complementarity in the sense that it is half of life culture. The three sacred gates and the two tombs are connected to the olegil space. In this space, the principle of complementarity in which coexistence exist between life and death is hidden in Jeju culture. It is a question and wait. Contrarily, the opposite is complementary. (Contraria Sunt Complementa Latin) This refers to the relationship of each other in relation to one another and in a mutually dependent relationship. The Jong Nang is used as basic logic in DNA codon of human body as well as communication principle. In addition, there is a pattern of similarity of the linkage between the square oval ear of the grave, the Korean Taegeukguk and 卦, the genome (DNA) 卦. The Jong Nang 'Batdam' and 'Sandam' are conneted like 'black dragon ten thousand', and stone walls are connected to each other as the stone network, which is called as the 'Goendam' (and conventionally is told as the 'Goendang') and is related to the Family networks. The relationship between the Tomb of the ancestors and their offspring is believed to be "Soul Synchronizing the Ancestor to Offspring" and becomes "Change in Future", and Genetic factors in the physical blood are transmitted directly to the children. The DNA RNA was represented by the determinant.

• Journal of Plant Biotechnology
• /
• v.34 no.4
• /
• pp.307-312
• /
• 2007

Chlamydomonas reinhardtii was transformed with the coding sequence of the Tombus virus gene p19 to determine whether the gene functions as an RNAi suppressor in C. reinhardtii. Transformants were confirmed to have 1 to several copies of p19 gene in their chromosomes. When an RNAi strain of C. reinhardtii generated by transforming the inverted repeat (IR) sequence homologous to the 3'UTR region of the MAA7 gene was re-transformed with the gene p19, MAA7 transcript levels of transformants fluctuated and proliferation of trans-formants on the medium containing 5-FI was suppressed. Overall results suggest that p19-mediated silencing suppression works at a low level in C. reinhardtii because of difference in codon usage resulting in weak P19 expression unless p19-mediated silencing suppression in C. reinhardtii works in a different manner from higher plants.

• Journal of Genetic Medicine
• /
• v.10 no.2
• /
• pp.109-112
• /
• 2013

Treacher Collins syndrome (TCS) is the most common and well known mandibulofacial dysostosis with characteristic clinical features including downward slanting of palpebral fissures, coloboma of the lower eyelid, hypoplastic zygomatic arches, micrognathia, macrostomia, microtia, and other deformities of the ears. TCS is caused by mutations in at least 3 genes involved in pre-rRNA transcription: TCOF1, POLR1D and POLR1C. We experienced a 1-day-old female infant with characteristic clinical features of TCS. A novel, heterozygotic mutation within the TCOF1 gene (c.3874_3875insG, p.Ala1292Glyfs*30) was identified to cause a premature stop codon.

• Journal of Animal Science and Technology
• /
• v.46 no.6
• /
• pp.937-946
• /
• 2004

Duroc is widely used to improve the meat quality and productivity. To elucidate the phylogenetic relation and the sequence specificity for the maternal property, the complete sequence of mitochondrial genome was determined and the population diversity of Duroc was investigated in this study. The length of mtDNA tested is 16,584-bp. There are several insertion/deletion mutations in the control region and coding regions for tRNA and rRNA, respectively, but not in peptide-coding regions. Four peptide-coding genes(COⅡ, COⅢ, ND3 and ND4) showed incomplete termination codon sequences such as T--, and two(ND2 and ND4L) did alternative initiation codons(AIC), respectively. Especially, the initiation codon sequences of ND2 gene were polymorphic in this population. Polymorphisms were detected in 11-bp duplication motif within control region as well as ND2 and CYTB. Variation patterns observed from the tests on three mtDNA regions were linked completely and then two haplotypes obtained from combining the data dividing this population. Duroc mtDNA is observed at the European pig cluster in the phylogenetic tree, however, the results from the population analyses supported previous opinions. This study suggests that the breed Duroc was mainly originated from the European pig lineage, and Asian lineage was also used to form the pig breed Duroc as maternal progenitors.

• The Korean Journal of Physiology and Pharmacology
• /
• v.2 no.1
• /
• pp.101-108
• /
• 1998

We investigated the effect of ${\alpha}-subunit$ of the stimulatory GTP-binding protein ($G{\alpha}_s$) gene mutation on the expression of the thyrotropin-releasing hormone (TRH) receptor (TRH-R) gene in GH3 cells and in growth hormone (GH)-secreting adenomas of acromegalic patients. In the presence of cyclohexicmide, forskolin and isobutylmethylxanthine, cholera toxin, and GH-releasing hormone (GHRH) decreased rat TRH-R (rTRH-R) gene expression by about 39%, 43.7%, and 46.7%, respectively. Transient expression of a vector expressing mutant-type $G{\alpha}_s$ decreased the rTRH-R gene expression by about 50% at 24 h of transfection, whereas a wild-type $G{\alpha}_s$ expression vector did not. The transcript of human TRH-R (hTRH-R) gene was detected in 6 of 8 (75%) tumors. Three of them (50%) showed the paradoxical GH response to TRH and the other three patients did not show the response. The relative expression of hTRH-R mRNA in the tumors from patients with the paradoxical response of GH to TRH did not differ from that in the tumors from patients without the paradoxical response. Direct PCR sequencing of $G{\alpha}_s$ gene disclosed a mutant allele and a normal allele only at codon 201 in 4 of 8 tumors. The paradoxical response to TRH was observed in 2 of 4 patients without the mutation, and 2 of 4 patients with the mutation. The hTRH-R gene expression of pituitaty adenomsa did not differ between the tumors without the mutation and those with mutation. The present study suggests that the expression of TRH-R gene is not likely to be a main determinant for the paradoxical response of GH to TRH, and that $G{\alpha}_s$ mutation may suppress the gene expression of TRH-R in GH-secreting adenoma. However, a certain predisposing factor(s) may play an important role in determining the expression of TRH-R.

• Interdisciplinary Bio Central
• /
• v.4 no.3
• /
• pp.10.1-10.12
• /
• 2012

Introduction: We investigated frameshift suppressor tRNAs previously reported to use five-base anticodon-codon interactions in order to provide a collection of frameshift suppressor tRNAs to the synthetic biology community and to develop modular frameshift suppressor logic devices for use in synthetic biology applications. Results and Discussion: We adapted eleven previously described frameshift suppressor tRNAs to the BioBrick cloning format, and built three genetic logic circuits to detect frameshift suppression. The three circuits employed three different mechanisms: direct frameshift suppression of reporter gene mutations, frameshift suppression leading to positive feedback via quorum sensing, and enzymatic amplification of frameshift suppression signals. In the course of testing frameshift suppressor logic, we uncovered unexpected behavior in the frameshift suppressor tRNAs. The results led us to posit a four-base binding hypothesis for the frameshift suppressor tRNA interactions with mRNA as an alternative to the published five-base binding model. Conclusion and Prospects: The published five-base anticodon/codon rule explained only 17 of the 58 frameshift suppression experiments we conducted. Our deduced four-base binding rule successfully explained 56 out of our 58 frameshift suppression results. In the process of applying biological knowledge about frameshift suppressor tRNAs to the engineering application of frameshift suppressor logic, we discovered new biological knowledge. This knowledge leads to a redesign of the original engineering application and encourages new ones. Our study reinforces the concept that synthetic biology is often a winding path from science to engineering and back again; scientific investigations spark engineering applications, the implementation of which suggests new scientific investigations.

• Genomics & Informatics
• /
• v.20 no.1
• /
• pp.11.1-11.20
• /
• 2022

Vibrio harveyi belongs to the Vibrio genus that causes vibriosis in marine and aquatic fish species through double-stranded DNA virus replication. In humans, around 12 Vibrio species can cause gastroenteritis (gastrointestinal illness). A large amount of virus particles can be found in the cytoplasm of infected cells, which may cause death. Despite these devastating complications, there is still no cure or vaccine for the virus. As a result, we used an immunoinformatics approach to develop a multi-epitope vaccine against most pathogenic hemolysin gene of V. harveyi. The immunodominant T- and B-cell epitopes were identified using the hemolysin protein. We developed a vaccine employing three possible epitopes: cytotoxic T-lymphocytes, helper T-lymphocytes, and linear B-lymphocyte epitopes, after thorough testing. The vaccine was developed to be antigenic, immunogenic, and non-allergenic, as well as having a better solubility. Molecular dynamics simulation revealed significant structural stiffness and binding stability. In addition, the immunological simulation generated by computer revealed that the vaccination might elicit immune reactions in the actual life after injection. Finally, using Escherichia coli K12 as a model, codon optimization yielded ideal GC content and a higher codon adaptation index value, which was then included in the cloning vector pET2+ (a). Altogether, our experiment implies that the proposed peptide vaccine might be a good option for vibriosis prophylaxis.

• IMMUNE NETWORK
• /
• v.1 no.2
• /
• pp.151-161
• /
• 2001

Background: Inactivation in p53 tumor suppressor gene through a point mutation and deletion is one of the most frequent genetic changes found in human cancer, with 50% of an incidence. This high rate of mutation mostly suggests that the gene plays a central role in the development of cancer and the mutations detected so far were found in exons 5 to 8. Mutation of p53 locus produced accumulation of abnormal p53 protein, and negative regulation of cell proliferation and transcriptional activation as a suppressor of transformation were lost. In addition, inhibition of its normal cellular function of wild-type by mutant is an important step in tumorigenesis. Method: 4 colon cancer cell lines (SNU C1, C2A, C4, C5) were examined for mutation in exons 5 to 8 of the p53 tumor suppressor gene by PCR-SSCP analysis and expression pattern by western blotting and immunoprecipitation. p53-mediated transactivation ability were examined by CAT assay and base substitution of p53 in SNU C2A cell were detected by DNA sequencing. Results: 1) SNU C2A cell and SNU C5 cell were detected mobility shifts each in exon 5 and exon 7 of p53 gene by the PCR-SSCP method, implicating being of p53 mutation. 2) 3 colon cancer cell lines (SNU C1, SNU C2A, SNU C5) expressed wild type and mutant type p53 protein. 3) In northern blot experiment, SNU C2A and SNU C5 cell expressed high level of p53 mRNA. 4) Results of p53-mediated transactivation in colon cancer cell lines by CAT assay represented only SNU C2A cell has transcriptional activity. 5) DNA sequencing in SNU C2A cell showed missense mutation in codon 179 of one allele, histidine to arginine and wild type p53 in the other allele. Conclusion: Colon cancer cell lines showed correlation with mutation in p53 gene and accumulation of abnormal p53 protein. Colon cancer cell SNU C2A retained p53-mediated transactivation as heterozygous p53 with one mutant allele in 179 codon and the other wild-type allele.