• Plant Breeding and Biotechnology
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• v.6 no.4
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• pp.426-433
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• 2018

Plant tissue culture is a technique that has invariably been used for various purposes such as obtaining transgenic plants for crop improvement or functional analysis of genes. However, this process can be associated with a variety of genetic and epigenetic instabilities in regenerated plants, termed as somaclonal variation. In this study, we investigated mutation spectrum, chromosomal distributions of nucleotide substitution types of single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) by whole genome re-sequencing between Dongjin and Nipponbare along with regenerated plants of Dongjin from different induction periods. Results indicated that molecular spectrum of mutations in regenerated rice against Dongjin genome ranged from $9.14{\times}10^{-5}$ to $1.37{\times}10^{-4}$ during one- to three-month callus inductions, while natural mutation rate between Dongjin and Nipponbare genomes was $6.97{\times}10^{-4}$. Non-random chromosome distribution of SNP and InDel was observed in both regenerants and Dongjin genomes, with the highest densities on chromosome 11. The transition to transversion ratio was 2.25 in common SNPs of regenerants against Dongjin genome with the highest C/T transition frequency, which was similar to that of Dongjin against Nipponbare genome.

• Molecules and Cells
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• v.42 no.1
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• pp.8-16
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• 2019

Mutations in the ${\beta}-catenin$ gene (CTNNB1) have been implicated in the pathogenesis of some cancers. The recent development of cancer genome databases has facilitated comprehensive and focused analyses on the mutation status of cancer-related genes. We have used these databases to analyze the CTNNB1 mutations assembled from different tumor types. High incidences of CTNNB1 mutations were detected in endometrial, liver, and colorectal cancers. This finding agrees with the oncogenic role of aberrantly activated ${\beta}-catenin$ in epithelial cells. Elevated frequencies of missense mutations were found in the exon 3 of CTNNB1, which is responsible for encoding the regulatory amino acids at the N-terminal region of the protein. In the case of metastatic colorectal cancers, in-frame deletions were revealed in the region spanning exon 3. Thus, exon 3 of CTNNB1 can be considered to be a mutation hotspot in these cancers. Since the N-terminal region of the ${\beta}-catenin$ protein forms a flexible structure, many questions arise regarding the structural and functional impacts of hotspot mutations. Clinical identification of hotspot mutations could provide the mechanistic basis for an oncogenic role of mutant ${\beta}-catenin$ proteins in cancer cells. Furthermore, a systematic understanding of tumor-driving hotspot mutations could open new avenues for precision oncology.

• Journal of mucopolysaccharidosis and rare diseases
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• v.5 no.1
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• pp.29-33
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• 2021

Prader-Willi Syndrome (PWS) is a neurodevelopmental genomic imprinting disorder involving a lack of gene expression from the paternal chromosome 15q11-q13 region. This is typically due to paternal 15q11-q13 deletions (in approximately 60% of cases), maternal uniparental disomy 15, or when both 15s are from the mother (about 35% of cases). An imprinting center controls the expression of imprinted genes in the chromosome 15q11-q13 region. PWS is a neurodevelopmental disorder characterized by mental retardation and distinct physical, behavioral, and psychiatric features. Characteristic behavioral disturbances in PWS include excessive interest in food, skin picking, difficulty with a change in routine, temper tantrums, obsessive and compulsive behaviors, and mood fluctuations. Individuals with PWS typically have intellectual disabilities (borderline to mild/moderate mental retardation) and exhibit a higher overall level of behavior disturbances compared to individuals with similar intellectual disabilities. This condition severely limits social adaptations and quality of life. Different factors have been linked to the intensity and form of these behavioral disturbances, but there is no consensus regarding the cause. Consequently, there is still controversy surrounding management strategies and there is a need for new data. PWS is a multisystem disorder. Family members, caregivers, physicians, dieticians, and speech-language pathologists all play an important role in the management and treatment of symptoms in an individual with PWS. Here we analyze behavioral problems in children and adults with PWS by age and review appropriate management and treatment strategies for these symptoms.

• Korean Journal of Plant Taxonomy
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• v.52 no.3
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• pp.127-143
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• 2022

This study was conducted to clarify the phylogenetic position and relationships of Korean Poaceae taxa. A total of 438 taxa including 155 accessions of Korean Poaceae (representing 92% and 72% of Korean Poaceous genera and species, respectively) were employed for phylogeny reconstruction. Sequence data of eight chloroplast DNA markers were used for molecular phylogenetic analyses. The resulted phylogeny was mostly concordant with previous phylogenetic hypotheses, especially in terms of subfamilial and tribal relationships. Several taxa-specific indels were detected in the molecular phylogeny, including a 45 bp deletion in rps3 (PACMAD [Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, Danthonioideae] clade), a 15 bp deletion in ndhF (Oryzeae + Phyllorachideae), a 6 bp deletion in trnLF (Poeae s.l.), and two (17 bp and 378 bp) deletions in atpF-H (Pooideae). The Korean Poaceae members were classified into 23 tribes, representing eight subfamilies. The subfamilial and tribal classifications of the Korean taxa were generally congruent with a recently published system, whereas some subtribes and genera were found to be non-monophyletic. The taxa included in the PACMAD clade (especially Andropogoneae) showed very weak and uncertain phylogenetic relationships, presumably to be due to evolutionary radiation and polyploidization. The reconstructed phylogeny can be utilized to update the taxonomic positions of the newly examined grass accessions.

• Journal of Mushroom
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• v.19 no.4
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• pp.336-340
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• 2021

The cleaved amplified polymorphic sequence (CAPS) marker uses a restriction enzyme recognition site resulting from single nucleotide polymorphisms and insertions and deletions on the DNA sequence. This technique does not require expensive equipment, the process is simple, and clear results can be obtained reliably. In this study, Agaricus bisporus cultivars SaeA, SaeDo, SaeHan, SaeYeon, SaeJeong, Dodam, Seolgang, Dahyang, Hogam, and Hadam developed in Korea were discriminated using four CAPS markers. Our results indicated that it is possible to distinguish the ten cultivars and determine the genetic diversity among them.

• The Korean Journal of Zoology
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• v.13 no.1
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• pp.29-33
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• 1970

The conclusions established in the present study on the chromosomes in vitro of the uterine carcinomas of Korean women are as follows: 1. The pattern of the distribution of chromosome number in uterine carcinoma cells was quite different from that of normal cells, and modal number of the chromosome was 45 and 46. 2. The frequency of diplochromosomes was 0.053 per cell (5.3%) and that of chromosome aberration was 0.16 per cell (16%), which are significantly higher than each of normal cells. In chromosome aberration types, chromatid and isochromatid deletions (chromatid type) and dicentric (chromosome type) were observed. 3. Idiogram analysis showed a tendency that the number of chromosomes belonging to group F increased while that of chromosomes in groups B and E decreased in total. The number of chromosomes in groups C and G in the hypodiploidy cells decreased, but it increased in the hyperdiploidy cells.

• International Journal of Stem Cells
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• v.16 no.2
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• pp.234-243
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• 2023

The recent advances in human pluripotent stem cells (hPSCs) enable to precisely edit the desired bases in hPSCs to be used for the establishment of isogenic disease models and autologous ex vivo cell therapy. The knock-in approach based on the homologous directed repair with Cas9 endonuclease, causing DNA double-strand breaks (DSBs), produces not only insertion and deletion (indel) mutations but also deleterious large deletions. On the contrary, due to the lack of Cas9 endonuclease activity, base editors (BEs) such as adenine base editor (ABE) and cytosine base editor (CBE) allow precise base substitution by conjugated deaminase activity, free from DSB formation. Despite the limitation of BEs in transition substitution, precise base editing by BEs with no massive off-targets is suggested to be a prospective alternative in hPSCs for clinical applications. Considering the unique cellular characteristics of hPSCs, a few points should be considered. Herein, we describe an updated and optimized protocol for base editing in hPSCs. We also describe an improved methodology for CBE-based C to T substitutions, which are generally lower than A to G substitutions in hPSCs.

• Journal of Microbiology and Biotechnology
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• v.34 no.5
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• pp.1126-1134
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• 2024

The production of disulfide bond-containing recombinant proteins in Escherichia coli has traditionally been done by either refolding from inclusion bodies or by targeting the protein to the periplasm. However, both approaches have limitations. Two broad strategies were developed to allow the production of proteins with disulfide bonds in the cytoplasm of E. coli: i) engineered strains with deletions in the disulfide reduction pathways, e.g. SHuffle, and ii) the co-expression of oxidative folding catalysts, e.g. CyDisCo. However, to our knowledge, the relative effectiveness of these strategies has not been properly evaluated. Here, we systematically compare the purified yields of 14 different proteins of interest (POI) that contain disulfide bonds in their native state when expressed in both systems. We also compared the effects of different background strains, commonly used promoters, and two media types: defined and rich autoinduction. In rich autoinduction media, POI which can be produced in a soluble (non-native) state without a system for disulfide bond formation were produced in higher purified yields from SHuffle, whereas all other proteins were produced in higher purified yields using CyDisCo. In chemically defined media, purified yields were at least 10x higher in all cases using CyDisCo. In addition, the quality of the three POI tested was superior when produced using CyDisCo.

• Korean Journal of Plant Resources
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• v.26 no.3
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• pp.397-402
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• 2013

Morus Folium (Sang-yeop in Korean) is one of the most important Oriental medicinal plants. In Korea, both M. alba and M. cathayana are regarded as the botanical sources for Morus Folium. In order to discriminate M. alba and M. cathayana from their adulterant, M. tricuspidata, mitochondrial NADH dehydrogenase subunit 7 (nad7) intron 2 region was targeted for molecular analysis with universal primers. DNA polymorphisms, including SNP sites, insertions, and deletions, were detected among these three species sequencing data. Based on these DNA polymorphisms, specific primers were designed for the three species respectively. Multiplex PCR was conducted for molecular authentication of M. alba, M. cathayana, and M. tricuspidata with specific primers. The present results indicate that it is possible to identify Morus Folium from its adulterant using mitochondrial nad7 intron 2 region. The established multiplex-PCR system was proved to be effective for identification of Morus Folium. The results indicate that mitochondrial introns can be used for inter-specific polymorphic study, and the described method can be applied for molecular identification of medicinal materials.

• Journal of Korean Academy of Nursing
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• v.36 no.4
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• pp.637-644
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• 2006

Purpose. The purpose of this study was to construct a measurement instrument for climacteric symptoms among Korean and Japanese women. Methods. From Dec. $1^{st}$ of 2003 to March $30^{th}$ of 2004, in-depth interviews were made with 26 women (15 in Jinju, Korea and 11 in Nagasaki, Japan) aged from 45 to 59 years who had not taken hormone replacement therapy to relieve the climacteric symptoms. A draft questionnaire with 45 items was constructed on the basis of the interview data and literature review. Three obstetricians, three PhDs in nursing science, and a chief nurse who was exclusively in charge of the climacteric management, examined the draft questionnaire to evaluate content validity. After deletions 39 items remained for a preliminary questionnaire. A survey was conducted by using a convenient sampling method in Jinju of Korea and Nagasaki of Japan during the period from April $1^{st}$, 2004 to July $10^{th}$, 2005. Results. Factor analysis identified 4 factors, which were 'mental and psychological symptoms', 'physical symptoms', 'loss of autonomic nervous system symptoms', 'sexual symptoms'. These four factors explained 46.9% of total variance. Conclusions. The results demonstrated that climacteric symptom scale was multidimensional, and the reliability and validity of the scale was supported.