• Journal of Microbiology and Biotechnology
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• v.19 no.11
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• pp.1447-1455
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• 2009

Two novel avian $\beta$-defensins (AvBDs) isolated from duck liver were characterized and their homologies with other AvBDs were analyzed. They were shown to be duck AvBD9 and AvBD10. The mRNA expression of the two genes was analyzed in 17 different tissues from 1-28-day-old ducks. AvBD9 was differentially expressed in the tissues, with especially high levels of expression in liver, kidney, crop, and trachea, whereas AvBD10 was only expressed in the liver and kidney of ducks at all the ages investigated. We produced and purified GST-tagged recombinant AvBD9 and AvBDI0 by expressing the two genes in Escherichia coli. Both recombinant proteins exhibited antimicrobial activity against several bacterial strains. The results revealed that both recombinant proteins retained their antimicrobial activities against Staphylococcus aureus under a range of different temperatures ($-70^{\circ}C-100^{\circ}C$) and pH values (pH 3-12).

• Proceedings of the Botanical Society of Korea Conference
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• 1996.07a
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• pp.40-47
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• 1996

The promoters of a variety of plant genes are characterized by the presence of TGACG motif-containing sequences. These genes often exhibit quite diverse expression characteristics and in many case the TGACG-motif has been demonstrated to be essential for expression. Here we report the isolation and characterization of a soybean cDNA that encodes a novel basic/leucine zipper (bZIP) protein, STF1, that specifically interacts with Hex (TGACGTGG) and CRE (TGACGTCA) sequences. This protein contains a bZIP motif at C-teminus and an acidic domain at N-terminus. DNA binding specificities, heterodimer formation, and expression characteristics of STF1 were compared with a soybean TGA1 protein, STGA1. The soybean STF1 interacts with TGACG-sequences containing an ACGT core, while STGA1 requires TGACG as a sufficient binding sequence. The flanking sequences to the TGACG motif affected DNA binding of STF1 siginificantly. The STF1 mRNA is found mainly in dark grown soybean seedling with higher expression in apical and elongating hypocotyl, while STGA1 mRNA is highly abundant in roots of light grown plants. Furthermore, we demonstrate that STF1 heterodimerzes with G-box binding factorss (GBFs) which was not observed with TGA1. The fact that STF1 possesses both distinct DNA binding speficities and heterodimerization properties suggest that STF1 belongs to a new family of plant bZIP proteins which recognize the Hex/CRE motif.

• Journal of Genetic Medicine
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• v.15 no.1
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• pp.24-27
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• 2018

Cornelia de Lange syndrome (CdLS) is a rare, clinically and genetically heterogeneous, multi-system developmental disorder caused by mutations in genes that encode components of the cohesin complex. X-linked CdLS caused by an SMC1A mutation is an extremely rare disease characterized by phenotypes milder than those of classic CdLS. In the Republic of Korea, based on a literature review, one family with SMC1A-related CdLS with mild phenotypes has been genetically confirmed to date. In this study, we describe the clinical features of a Korean boy with a hemizygous novel missense mutation and his mother with a heterozygous mutation, i.e., c.2447G>A (p.Arg816His) in SMC1A, identified by multi-gene panel sequencing. The proband had a mild phenotype with typical facial features and his mother exhibited a mild, subclinical phenotype. This study expands the clinical spectrum of patients with X-linked CdLS caused by SMC1A variants. Moreover, these findings reinforce the notion that a dominant negative effect in a carrier female with a heterozygous mutation in SMC1A results in a phenotype milder than that in a male patient with the same mutation.

• Journal of Microbiology and Biotechnology
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• v.33 no.11
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• pp.1457-1466
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• 2023

Enteric fever is caused by typhoidal Salmonella serovars (Typhi, Paratyphi A, Paratyphi B, and Paratyphi C). Owing to the importance of Salmonella serovars in clinics and public hygiene, reliable diagnostics for typhoidal serovars are crucial. This study aimed to develop a novel diagnostic tool for typhoidal Salmonella serovars and evaluate the use of human blood for clinically diagnosing enteric fever. Five genes were selected to produce specific PCR results against typhoidal Salmonella serovars based on the genes of Salmonella Typhi. Heptaplex PCR, including genetic markers of generic Salmonella, Salmonella enterica subsp. enterica, and typhoidal Salmonella serovars, was developed. Typhoidal Salmonella heptaplex PCR using genomic DNAs from 200 Salmonella strains (112 serovars) provided specifically amplified PCR products for each typhoidal Salmonella serovar. These results suggest that heptaplex PCR can sufficiently discriminate between typhoidal and non-typhoidal Salmonella serovars. Heptaplex PCR was applied to Salmonella-spiked blood cultures directly and provided diagnostic results after 12- or 13.5-h blood culture. Additionally, it demonstrated diagnostic performance with colonies recovered from a 6-h blood culture. This study provides a reliable DNA-based tool for diagnosing typhoidal Salmonella serovars that may be useful in clinical microbiology and epidemiology.

• Molecules and Cells
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• v.41 no.6
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• pp.506-514
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• 2018

The transcriptional regulation of genes determines the fate of animal cell differentiation and subsequent organ development. With the recent progress in genome-wide technologies, the genomic landscapes of enhancers have been broadly explored in mammalian genomes, which led to the discovery of novel specific subsets of enhancers, termed super-enhancers. Super-enhancers are large clusters of enhancers covering the long region of regulatory DNA and are densely occupied by transcription factors, active histone marks, and co-activators. Accumulating evidence points to the critical role that super-enhancers play in cell type-specific development and differentiation, as well as in the development of various diseases. Here, I provide a comprehensive description of the optimal approach for identifying functional units of super-enhancers and their unique chromatin features in normal development and in diseases, including cancers. I also review the recent updated knowledge on novel approaches of targeting super-enhancers for the treatment of specific diseases, such as small-molecule inhibitors and potential gene therapy. This review will provide perspectives on using super-enhancers as biomarkers to develop novel disease diagnostic tools and establish new directions in clinical therapeutic strategies.

• Mycobiology
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• v.49 no.1
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• pp.54-60
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• 2021

During the screening of Korean microflora, a fungal strain (KNU-PT-1804) belonging to the genus Pestalotiopsis was isolated from persimmon tree (Diospyros kaki) bark collected from North Gyeongsang Province, Korea. The strain, KNU-PT-1804, produced smaller conidia compared with related species P. kenyana, P. neglecta, and P. telopeae. The novelty of the strain was confirmed based on phylogenetic analysis using molecular datasets of internal transcribed spacer (ITS) regions, β-tubulin (TUB2), and translation elongation factor 1-alpha (TEF1α) genes. Molecular phylogeny strongly supports that the strain is distinct from previously known Pestalotiopsis species, and we proposed the novel species, Pestalotiopsis kaki sp. nov., and provide a detailed description and illustration.

• Journal of Microbiology and Biotechnology
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• v.19 no.12
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• pp.1497-1505
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• 2009

The thermophile Bacillus fordii MH602 was screened for stereospecifically hydrolyzing DL-5-substituted hydantoins to L-$\alpha$-amino acids. Since the reaction occurs at higher temperature, the advantages for enhancement of substrate solubility and for racemization of DL-5-substituted hydantoins during the conversion were achieved. The hydantoin metabolism gene cluster from thermophile is firstly reported in this paper. The genes involved in hydantoin utilization (hyu) were isolated on an 8.2-kb DNA fragment by restriction site-dependent PCR, and six ORFs were identified by DNA sequence analysis. The hyu gene cluster contained four genes with novel cluster organization characteristics: the hydantoinase gene hyuH, putative transport protein gene hyuP, hyperprotein gene hyuHP, and L-carbamoylase gene hyuC. The hyuH and hyuC genes were heterogeneously expressed in E. coli. The results indicated that hyuH and hyuC are involved in the conversion of DL-5-substituted hydantoins to an N-carbamyl intermediate that is subsequently converted to L-$\alpha$-amino acids. Hydantoinase and carbamoylase from B. fordii MH602 compared respectively with reported hydantoinase and carbamoylase showed the highest identities of 71% and 39%. The novel cluster organization characteristics and the difference of the key enzymes between thermopile B. fordii MH602 and other mesophiles were presumed to be related to the evolutionary origins of concerned metabolism.

• Journal of Sericultural and Entomological Science
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• v.38 no.1
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• pp.13-18
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• 1996

To secure the genetic resources of silkworm, Bomyx mori, the cDNA library was constructed with mRNA isolated from fifth instar larvae. Titer of the cDNA library was about 1.3 X 106 plaques in total. We presumed that the titer covered all transcripts existed in Bombyx mori. Meanwhile, it is knowen that partial cDNA sequences, Expressed Sequence Tags(ESTs), have a good value for the discovery of novel genes and the elucidation of their structures. For this purpose, partial cDNA sequencing was carried out from randomly selected cDNA clones in the library. Partial cDNA sequences of 37 clones were determined and an average of 212 nucleotides of sequence can be read from the clone. The ESTs were searched in GenBAnk database and fifteen ESTs showed significant similarities to enlisted sequences. They included the genes of storage protein, heat shock protein, actin, catalase and so forth. We presumed that the 22 unmatched ESTs were novel genes.

• Korean Journal of Head & Neck Oncology
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• v.24 no.2
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• pp.155-161
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• 2008

Head and neck squamous cell carcinoma(HNSCC) still has poor outcome, and laryngeal cancer is the most frequent subtype of HNSCC. Therefore, there is a need to develop novel treatments to improve the outcome of patients with HNSCC. It is critical to gain further understanding on the molecular and chromosomal alteration of HNSCC to identify novel therapeutic targets but genetic etiology of squamous cell carcinoma of the larynx is so complex that target genes have not yet been clearly identified. Array based CGH(array-CGH) allows investigation of general changes in target oncogenes and tumor suppressor genes, which should, in turn, lead to a better understanding of the cancer process. In this study, We used genomic wide array-CGH in tissue specimens to map genomic alterations found in laryngeal squamous cell carcinomas. As results, gains of MAP2, EPHA3, EVI1, LOC389174, NAALADL2, USP47, CTDP1, MASP1, AHRR, and KCNQ5, with losses of SRRM1L, ANKRD19, FLJ39303, ZNF141, DSCAM, GPR27, PROK2, ARPP-21, and B3GAT1 were observed frequently in laryngeal squamous cell carcinoma tissue specimens. These data about the patterns of genomic alterations could be a basic step for understanding more detailed genetic events in the carcinogenesis and also provide information for diagnosis and treatment in laryngeal squamous cell carcinoma. The high resolution of array-CGH combined with human genome database would give a chance to find out possible target genes which were gained or lost clones.

• ALGAE
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• v.36 no.3
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• pp.207-217
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• 2021

An increase in seawater temperature owing to global warming is expected to substantially limit the growth of marine algae, including Pyropia yezoensis, a commercially valuable red alga. To improve our knowledge of the genes involved in the acquisition of heat tolerance in P. yezoensis, transcriptomes sequences were obtained from both the wild-type SG104 P. yezoensis and heat-tolerant mutant Gy500. We selected 1,251 differentially expressed genes that were up- or downregulated in response to the heat stress condition and in the heat-tolerant mutant Gy500, based on fragment per million reads expression values. Among them, PyHRG1 was downregulated under heat stress in SG104 and expressed at a low level in Gy500. PyHRG1 encodes a secretory protein of 26.5 kDa. PyHRG1 shows no significant sequence homology with any known genes deposited in public databases to date. However, PyHRG1 homologs were found in other red algae, including other Pyropia species. When PyHRG1 was introduced into the single-cell green alga Chlamydomonas reinhardtii, transformed cells overexpressing PyHRG1 showed severely retarded growth. These results demonstrate that PyHRG1 encodes a novel red algae-specific protein and plays a role in heat tolerance in algae. The transcriptome sequences obtained in this study, which include PyHRG1, will facilitate future studies to understand the molecular mechanisms involved in heat tolerance in red algae.