• Journal of Life Science
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• v.11 no.3
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• pp.279-283
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• 2001

Amyotrophic lateral sclerosis(ALS) is a progressive neurologic disorder resulting from the degeneration of upper and lower motor neurons, and is inherited in 10% of cases. About 20% of familial ALS, clinically indistinguishable from sporadic ALS, is caused by mutations of Cu/Zn superoxide dismutase on chromosome 21q22.21 inherited as an autosomal dominant trait. We now report a new locus in the non-SOD1 dominantly inherited ALS. We screened a large ALS family with 11 affected individuals and one obligate gene carrier with genome-wide ABI polymorphic markers using the ABI 377 automated system. No evidence of linkage was obtained with the autosomal markers. We next screened this family with X chromosome markers as there was no evidence of male-to-male tran-smission of the disease. Linkage was established with several X chromosome markers with a lod score up to 3.8; almost the maximum possible score in this family. Our finding imply that a gene for the dominant expression of a neuronal degeneration is coded on X chromosome and raise the question of the role of X-linked genes that escape inactivation in this pathogenesis. More importantly, our finding that a gene causing ALS is localized on X-chromosome has direct investigational relevance to sporadic ALS, where epidemiological studies show male gender predominance(1.3:1) and earlier onset in men by 5-10 years.

• Genomics & Informatics
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• v.5 no.3
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• pp.107-112
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• 2007

MicroRNAs (miRNAs) are known to negatively control protein-coding genes by binding to messenger RNA (mRNA) in the cytoplasm. In innate immunity, the role of miRNA gene silencing is largely unknown. In this study, we performed microarray-based experiments using lipopolysaccharide (LPS)-stimulated macrophages derived from wild-type, MyD88 knockout (KO), TRIF KO, and MyD88/TRIF double KO mice. We employed a statistical approach to determine the importance of the commonality and specificity of miRNA binding sites among groups of temporally co-regulated genes. We demonstrate that both commonality and specificity are irrelevant to define a priori groups of co-down regulated genes. In addition, analyzing the various experimental conditions, we suggest that miRNA regulation may not only be a late-phase process (after transcription) but can also occur even early (1h) after stimulation in knockout conditions. This further indicates the existence of dynamic interactions between miRNA and signaling molecules/transcription factor regulation; this is another proof for the need of shifting from a 'hard-wired' paradigm of gene regulation to a dynamical one in which the gene co-regulation is established on a case-by-case basis.

• Genomics & Informatics
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• v.16 no.3
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• pp.44-51
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• 2018

Fluoroquinolone (FQ) antibiotics are an important class of synthetic antibacterial agents. These are the most extensively used drugs for treating bacterial infections in the field of both human and veterinary medicine. Herein, the antibacterial and pharmacological properties of four fluoroquinolones: lomefloxacin, norfloxacin, ciprofloxacin, and ofloxacin have been studied. The objective of this study was to analyze the antibacterial characteristics of the different fluoroquinolones. Also, the pharmacological properties of the compounds including the Lipinski rule of five, absorption, distribution, metabolism, and excretion, LD50, drug likeliness, and toxicity were evaluated. We found that among all four FQ molecules, ofloxacin showed the highest antibacterial activity through in silico assays with a strong interaction (-38.52 kJ/mol) with the antibacterial target protein (topoisomerase-II DNA gyrase enzyme). The pharmacological and pharmacokinetic analysis also showed that the compounds ciprofloxacin, ofloxacin, lomefloxacin and norfloxacin have good pharmacological properties. Notably, ofloxacin was found to possess an IGC50 (concentration needed to inhibit 50% growth) value of $0.286{\mu}g/L$ against the Tetrahymena pyriformis protozoa. It also tested negative for the Ames toxicity test, showing its non-carcinogenic character.

• Journal of Aquaculture
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• v.16 no.1
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• pp.8-14
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• 2003

To generate expressed sequence tags for genomics research involving genetic linkage analysis, to examine gene expression profiles in muscles of channel catfish in a non-normalized muscle cDNA library, to compare gene expression in young and mature channel catfish muscles using the EST reagents and gene filters to demonstrate the feasibility of functional genomics research in small laboratories. 102 randomly picked cDNA clones were analyzed from the catfish muscle cDNA library. Of the sequences generated, 90.2% of ESTs was identified as known genes by identity comparisons. These 92 clones of known gene products represent transcriptional products of 24 genes. The 10 clones of unknown gene products represent 8 genes. The major transcripts (70.1% of the analyzed ESTs) in the catfish muscle are from many major genes involved in muscle contraction, relaxation, energy metabolism and calcium binding such as alpha actin, creatine kinase, parvalbumin, myosin, troponins, and tropomyosins. Gene expression of the unique ESTs was comparatively studied in the young and adult catfish muscles. Significant differences were observed for aldolase, myostatin, myosin light chain, parvalbumin, and an unknown gene. While myosin light chain and an unknown gene (CM 192) are down-regulated in the mature fish muscle, the aldolase, myostatin, and parvalbumin are significantly up-regulated in the mature fish muscle. Although the physiological significance of the changes in expression levels needs to be further addressed, this research demonstrates the feasibility and power of functional genomics in channel catfish. Channel catfish muscle gene expression profiles provide a valuable molecular muscle physiology blueprint for functional comparative genomics.

• Animal cells and systems
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• v.1 no.1
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• pp.135-142
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• 1997

Random sequencing of expressed sequence tags in roots of Chinese cabbage led to isolation of a partial cDNA clone, BR77, which encoded a putative protein kinase. Using the BR77 cDNA as a probe, we isolated a full-length cDNA encoding the Brassica campestris protein kinase 1 (Bcpk1). The Bcpt1 cDNA contained one open reading frame encoding a polypeptide of 439 amino acids. The putative polypeptide consisted of a short N-terminal region and a protein kinase catalytic domain. The catalytic domain of Bcpkl showed a high homology to cAMP- and calcium- phospholipid-dependent subfamilies of serine/threonine protein kineses. Eleven major catalytic domains in protein kineses were well conserved in Bcpk1. However, Bcpk1 contained a unique nonhomologous intervening sequence between subdomains VII and VIII, which was not found in protein kineses of animals and lower eukaryotes. Genomic DNA gel blot analysis showed that Bcpt1 genes might be present as three copies in the Chinese cabbage genome. These imply that Bcpk1 belongs to a plant-specific serine/threonine protein kinase subfamily.

• Korean Journal of Plant Resources
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• v.11 no.2
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• pp.188-194
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• 1998

This experiment was conducted to introduce phosphinothricin acetyl -transferase(PAT) gene, resistant to basta and non-selective herbidide, into tobacco(Nicotiana tabacum cv.BY4). For shoot formation,tobacco leaf disks were placed on the MS medium supplemented with 2.0mg/L BA and 0.1mg/L NAA. In this medium condition, tobacco leaf disces were cocultivated with A. tumefaciens MP90 containing NPT IIand PAT resistant to kanamycin and Basta, respectively. Shoots were obtained in the medium containing antibiotics, and those were transferred to rooting medium supplemented with 0.1mg/L NAA and antibiotics. The plants obtaining roots were transplanted into soil. Phenotype of transgenic tobacco plant was mostly as normal plant. However, about 5% was abnormal plant, which did not set seeds. PCR analysis and southern blot were performed to determine transformation. As the results, it was confirmed that PAT gene was stably integrated into tobacco genome.When herbicide, basta, was sprayed to the plants confirmed by PCR, the transgenic plants showed normal growth, whereas normal plants died. Therefore, the result of this experiment show that tobacco transformation for the resistance to basta, non-selective herbicide, was successful because PAT gene was stably integrated into tobacco.

• Plant Resources
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• v.6 no.2
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• pp.108-113
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• 2003

This study was carried out to obtain basic information for possibility of oral vaccine in carrot using Agrobacteruim -mediated transformation system. The epitope region of porcine epidemic diarrhea virus (PEDV) spike gene which is classified as a member of the Coronaviridae and causes an acute enteritis in pigs was successfully expressed in carrot (Daucus carota) using the Agrobacterium-mediated transformation system. Hypocotyl segments of in vitro germinated plantlets were infected with Agrobacteriun tumefaciens LBA 4404 harboring PEDV spike gene. Embryogenic callus (EC) was induced on MS selection medium with 1 mg/L 2,4-D, 50 mg/L kanamycin and 300 mg/L cefotaxime after 45 days of culture. Subcultured ECs on MS selection medium without 2,4-D were converted to somatic embryos (SE) of various stage; globular, heart and torpedo stage. Putative transgenic embryos were selected on MS medium with 50 mg/L kanamycin and 300 mg/L cefotaxime. Regenerated plantlets from transformed SE were induced on MS medium containing 50 mg/L kanamycin after 30 days of culture. Genomic PCR confirmed the integration of PEDV spike gene into nuclear genome of carrot and northern blot analysis demonstrated the expression of PEDV spike gene in transgenic carrot.

• Proceedings of the Botanical Society of Korea Conference
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• 1985.08b
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• pp.59-71
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• 1985

In rice, limited efforts have been made to identify genes by the use of insertional mutagens, especially heterologous transposons such as the maize Ac/Ds. We constructed Ac and gene trap Ds vectors and introduced them into the rice genome by Agrobacterium-mediated transformation. In this report, rice plants that contained single and simple insertions of T-DNA were analyzed in order to evaluate the gene-tagging efficiency. The 3'end of Ds was examined for putative splicing donor sites. As observed in maize, three splice donor sites were identified at the 3'end of the Ds in rice. Nearly 80% of Ds elements wered excised from the original T-DNA sites, when Ac cDNA was expressed under a CaMV 35S promoter. Repetitive ratoon culturing was performed to induce new transpositions of Ds in new plants derived from cuttings. About 30% of the plants carried at least one Ds that underwent secondary transposition in the later cultures. 8% of transposed Ds elements expressed GUS in various tissues of rice panicles. With cloned DNA adjacent to Ds, the genomic complexities of the insertion sites were examined by Southern hybridization. Half of the Ds insertion sites showed simple hybriodization patterns which could be easily utilized to locate the Ds. Our data demonstrate that the Ac/Ds mediated gene trap system could prove an excellent tool for the analysis of functions of genes in rice. We discuss genetic strategies that could be employed in a largee scale mutagenesis using a heterologous Ac/Ds family in rice.

• The Korean Journal of Mycology
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• v.39 no.3
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• pp.235-238
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• 2011

Agrobacterium harboring vector pCHBs with hygromycin phosphotransferase(hph) and hepatitis B virus surface antigen(HBsAg)gene was transformed into the mycelial culture of Flammulina velutipes. In particular, mild NaOH solution was treated to the mycelia before Agrobacterium infection step. This was purposed to generate putative surface wounds in the mycelial cell walls. The results showed that hygromycin-resistant($hyg^r$) mycelia could be obtained only from NaOH-treated mycelia but not from intact mycelia. The integration of $hyg^r$ gene in fungal genome was confirmed by PCR. In addition, a single transgene integration and heterologous protein expression in F. velutipes could be verified by Southern blot hybridization and western blot analysis, respectively. This study demonstrated an efficient tool for the Agrobacterium-mediated transformation of F. velutipes mycelia.

• Journal of Sasang Constitutional Medicine
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• v.32 no.2
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• pp.10-21
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• 2020

Objectives Genome-wide association studies(GWAS) is a useful method to identify genetic associations for various phenotypes. The purpose of this study was to develop predictive models for Sasang constitution types using genetic factors. Methods The genotypes of the 1,999 subjects was performed using Axiom Precision Medicine Research Array (PMRA) by Life Technologies. All participants were prescribed Sasang Constitution-specific herbal remedies for the treatment, and showed improvement of original symptoms as confirmed by Korean medicine doctor. The genotypes were imputed by using the IMPUTE program. Association analysis was conducted using a logistic regression model to discover Single Nucleotide Polymorphism (SNP), adjusting for age, sex, and BMI. Results & Conclusions We developed models to predict Korean medicine constitution types using identified genectic factors and sex, age, BMI using Random Forest (RF), Support Vector Machine (SVM), and Neural Network (NN). Each maximum Area Under the Curve (AUC) of Teaeum, Soeum, Soyang is 0.894, 0.868, 0.767, respectively. Each AUC of the models increased by 6~17% more than that of models except for genetic factors. By developing the predictive models, we confirmed usefulness of genetic factors related with types. It demonstrates a mechanism for more accurate prediction through genetic factors related with type.