• Korean Journal of Agricultural Science
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• v.46 no.4
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• pp.885-895
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• 2019

Plant biotechnologists have long dreamed of technologies to manipulate genes in plants at will. This dream has come true partly through the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology, which now has been used to edit genes in several important crops. However, there are many restrictions in editing a gene precisely using the CRISPR/Cas9 technology because CRISPR/Cas9 may cause deletions or additions in some regions of the target gene. Several other technologies have been developed for gene targeting and precision editing. Among these, base editors might be the most practically and efficiently used compared to others. Base editors are tools which are able to cause a transition from cytosine into thymine, or from adenine into guanine very precisely on specific sequences. Cytosine base editors basically consist of nCas9, cytosine deaminase, and uracil DNA glycosylase inhibitor (UGI). Adenine base editors consist of nCas9 and adenine deaminase. These were first developed for human cells and have since also been applied successfully to crops. Base editors have been successfully applied for productivity improvement, fortification and herbicide resistance of crops. Thus, base editor technologies start to open a new era for precision gene editing or breeding in crops and might result in revolutionary changes in crop breeding and biotechnology.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.1
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• pp.79-90
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• 2020

Objective: In the present study, an liquid chromatography/mass spectrometry (LC/MS) metabolomics approach was performed to investigate potential biomarkers of milk production in high- and low-milk-yield dairy cows and to establish correlations among rumen fluid metabolites. Methods: Sixteen lactating dairy cows with similar parity and days in milk were divided into high-yield (HY) and low-yield (LY) groups based on milk yield. On day 21, rumen fluid metabolites were quantified applying LC/MS. Results: The principal component analysis and orthogonal correction partial least squares discriminant analysis showed significantly separated clusters of the ruminal metabolite profiles of HY and LY groups. Compared with HY group, a total of 24 ruminal metabolites were significantly greater in LY group, such as 3-hydroxyanthranilic acid, carboxylic acids, carboxylic acid derivatives (L-isoleucine, L-valine, L-tyrosine, etc.), diazines (uracil, thymine, cytosine), and palmitic acid, while the concentrations of 30 metabolites were dramatically decreased in LY group compared to HY group, included gentisic acid, caprylic acid, and myristic acid. The metabolite enrichment analysis indicated that protein digestion and absorption, ABC transporters and unsaturated fatty acid biosynthesis were significantly different between the two groups. Correlation analysis between the ruminal microbiome and metabolites revealed that certain typical metabolites were exceedingly associated with definite ruminal bacteria; Firmicutes, Actinobacteria, and Synergistetes phyla were highly correlated with most metabolites. Conclusion: These findings revealed that the ruminal metabolite profiles were significantly different between HY and LY groups, and these results may provide novel insights to evaluate biomarkers for a better feed digestion and may reveal the potential mechanism underlying the difference in milk yield in dairy cows.

• Journal of Life Science
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• v.9 no.1
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• pp.84-89
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• 1999

To determine phylogenetic relatedness of four silk-producing silkmoths (B. mori, B. mandarina, A. yamamai and A. pernyi), internal coding region of arylphorin which is a storage protein in hemolymph protein of insects were amplified by polymerase chain reaction and then sequenced and compared each other. The nucleotide composition was biased toward adenine and thymine(59% A+T) and a strong bias for use of C in the third position of codons was found for Phe and Tyr. Together TTC(Phe) and TAC(Tyr) account for about 16.8% (10 for TTC and 8 for TAC) of all codon usage. The nucleotide similarity of arylphorin gene from B. mori showed 99%, 98% and 97% homology with those of B. mandarina, A. yamamai and A. pernyi, respectively. Also, the nucleotide sequence of arylphorin gene from B. mandarina showed 98% and 97% homology with those of A. yamamai and A.pernyi, respectively. Between A. yamamai and A. pernyi, the sequence homology was 97%. The deduced amino acid sequences in B. mori, B. mandarina and A. yamamai showed almost 99% homology. Although the aryphorin gene provided insufficient variability among the four insect species, A UPGMA tree is generated that supported the monophyly of silk-producing insects, with M. sexta placed basal to it. It is suggest that silk-producing insects have a close relationship and a homogeneous genetic background from comparison with those of other insects.

• Journal of Plant Biotechnology
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• v.47 no.1
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• pp.15-25
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• 2020

Allium L. is one of the largest genera of the Amaryllidaceae family, with more than 920 species including many economically important species used as vegetables, spices, medicines, or ornamental plants. Currently, DNA barcoding tools are being successfully used for the molecular taxonomy of Allium. A total of 46 Allium species were collected from their native areas, and DNA was extracted using the IBRC DNA extraction kit. We used specific primers to PCR amplify matK. DNA sequences were edited and aligned for homology, and a phylogenetic tree was constructed using the neighbor-joining method. The results show thymine (38.5%) was the most frequent and guanine (13.9%) the least frequent nucleotide. The matK regions of the populations were quite highly conserved, and the amount of C and CT was calculated at 0.162 and 0.26, respectively. Analysis of the nucleotide substitution showed C-T (26.22%) and A-G (8.08%) to have the highest and lowest percent, respectively. The natural selection process dN/dS was 1.16, and the naturality test results were -1.5 for Tajima's D and -1.19 for Fu's Fs. The NJ dendrogram generated three distinct clades: the first contained Allium austroiranicum and A. ampeloprasum; the second contained A. iranshahrii, A. bisotunense, and A. cf assadi; and the third contained A. rubellum and other species. In this study, we tested the utility of the matK region as a DNA barcode for discriminating Allium. species.

• Bulletin of the Korean Chemical Society
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• v.12 no.5
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• pp.554-559
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• 1991

The photophysical and photochemical properties of khellin were compared with those of 8-methoxypsoralen (8-MOP). Quantum yields of fluorescence and triplet formation decreases as solvent polarity increases, which is opposite to 8-MOP, and photocycloadditivity of khellin to olefins is much lower than that of 8-MOP. Electron ejection from khellin by laser flash was not observed, but observed from 8-MOP. As models of 4',5'-monoadducts of khellin or 8-MOP with thymine base, khellin<>dimethylfumarate 4',5'-monoadduct (KDF) was also compared with 8-MOP<>thymidine 4',5'-monoadduct (F-2) in those properties to give some insight on the second-step biadduct formation resulting in cross-links of DNA duplex. KDF and F-2 were very similar to khellin and 8-MOP in photophysical properties, respectively. However, KDF did not form adducts with various olefins, and thus it is thought that 2,3-double bond of chromone moiety in khellin is hardly reactive in contrast with 3,4-double bond of coumarin moiety in 8-MOP. These results indicate that khellin is fairly photostable compound, a poor type Ⅰ photodynamic sensitizer and producer of ${O_2}^{-}$ which is some cause of phototoxic erythemal reactions and undesirable side effects. Therefore khellin is safer to use than 8-MOP in photochemotherapy of some skin diseases. Although khellin is much less reactive than 8-MOP, khellin must be also a monofunctional drug. Since khellin is, however, as effective as 8-MOP in photochemotherapy of some skin diseases, it is suggested that khellin may be different from 8-MOP in the action mechanism.

• International Journal of Industrial Entomology and Biomaterials
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• v.37 no.2
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• pp.82-89
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• 2018

This study was carried out to understand phylogenetic relationships of the 30 mulberry cultivars converved in Korea based on the ITS rDNA region, and they were compared to 40 reference sequences from GenBank. The size and the G+C content of the ITS rDNA gene regions from the 30 Korean mulberry cultivars and 40 reference sequences varied from 612-630 bp and 58.19-61.62%, respectively. Based on the results of the comparative phylogenetic analysis of the ITS rDNA regions of the 30 Korean mulberry cultivars and 40 reference sequences, they were divided into three groups (Group 1, 2, and 3) and two subgroups (Group 1A and 1B within Group 1). The sequence lengths of the Korean mulberry cultivar numbers 1-26 and 27-30 were 615 bp and 616 bp, respectively. At 205 bp location of ITS1 rDNA region, the cultivar numbers 1-26 contain the nucleotide thymine but the cultivar numbers 27-30 contain the nucleotide adenine. In addition, the insertion of the nucleotide adenine at 206 bp location was found only in the four Korean mulberry cultivars (numbers 27-30). Based on these sequence information and phylogenetic result, the 30 Korean mulberry cultivars were identified as M. alba and M. australis. This study will contribute to the construction of genetic database constructions and accurate variety identifications for unidentified mulberry varieties in Korea.

• Clinical and Experimental Pediatrics
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• v.62 no.2
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• pp.55-61
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• 2019

Purpose: Myotonic dystrophy, also known as dystrophia myotonica (DM), is an autosomal dominant disorder with 2 genetically distinct forms. DM type 1 (DM1) is the more common form and is caused by abnormal expansion of cytosine/thymine/guanine (CTG) repeats in the DM protein kinase (DMPK ) gene. Our study aimed to determine whether the age of onset is correlated with CTG repeat length in a population of pediatric patients with DM1. Methods: We retrospectively identified 30 pediatric patients with DM1 that underwent DMPK testing, of which the clinical data of 17 was sufficient. The cohort was divided into 2 subgroups based on the clinical phenotype (congenital-onset vs. late-onset) and number of CTG repeats (<1,000 vs. ${\geq}1,000$). Results: We found no significant difference between the age of onset and CTG repeat length in our pediatric patient population. Based on clinical subgrouping, we found that the congenital-onset subgroup was statistically different with respect to several variables, including prematurity, rate of admission to neonatal intensive care unit, need for respiratory support at birth, hypotonia, dysphagia, ventilator dependence, and functional status on last visit, compared to the late-onset subgroup. Based on genetic subgrouping, we found a single variable (poor feeding in neonate) that was significantly different in the large CTG subgroup than that in the small CTG subgroup. Conclusion: Clinical variables exhibiting statistically significant differences between the subgroups should be focused on prognosis and designing tailored management approaches for the patients; our findings will contribute to achieve this important goal for treating patients with DM1.

• Journal of Microbiology and Biotechnology
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• v.34 no.8
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• pp.1627-1635
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• 2024

The inhabitation and parasitism of root-knot nematodes (RKNs) can be difficult to control, as its symptoms can be easily confused with other plant diseases; hence, identifying and controlling the occurrence of RKNs in plants remains an ongoing challenge. Moreover, there are only a few biological agents for controlling these harmful nematodes. In this study, Xenorhabdus sp. SCG isolated from entomopathogenic nematodes of genus Steinernema was evaluated for nematicidal effects under in vitro and greenhouse conditions. The cell-free filtrates of strain SCG showed nematicidal activity against Meloidogyne species J2s, with mortalities of > 88% at a final concentration of 10%, as well as significant nematicidal activity against the three other genera of plant-parasitic nematodes in a dose-dependent manner. Thymine was isolated as active compounds by assay-guided fractionation and showed high nematicidal activity against M. incognita. Greenhouse experiments suggested that cell-free filtrates of strain SCG efficiently controlled the nematode population in M. incognita-infested tomatoes (Solanum lycopersicum L., cv. Rutgers). In addition, a significant increase in host plant growth was observed after 45 days of treatment. To our knowledge, this is the first to demonstrate the nematicidal activity spectrum of isolated Xenorhabdus species and their application to S. lycopersicum L., cv. Rutgers under greenhouse conditions. Xenorhabdus sp. SCG could be a promising biological nematicidal agent with plant growth-enhancing properties.

• Tuberculosis and Respiratory Diseases
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• v.45 no.3
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• pp.529-535
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• 1998

Background: Interleukin-4 plays an important role in pathogenesis of asthma, especially in developing atopy by means of switching B lymphocytes to produce IgE. It has been shown that there is polymorphism in the Interleukin-4 promoter region, transversion of cytosine to thymine at-598 from translation initiation site of IL-4 gene. There has also been quite a few works to reveal the role of the polymorphism of IL-4 gene in patients with asthma. We performed this investigation to determine the role of the polymorphism in the severity of symptoms of patients with asthma. We also examined the frequency and the type of the polymorphism in asthmatics compared with non-asthmatics as well. Method: The subjects enrolled in this study were 49 asthmatics and 33 non-asthmatics. All the asthmatics were classified as mild and moderate to severe by the NHLBI/WHO Workshop. DNA from both asthmatics and non-asthmatics was extracted, then performed ARMS(Amplification Refractory Mutation System) as well as RFLP using BsmFl restriction enzyme in order to confirm the polymorphism of Il-4 gene. Results: There was no significant difference in the occurrence of polymorphism of the IL-4 promoter sequence between asthm and non-asthma groups(P=0.7). Among those with polymorphisms, the number of C/C type was slightly more than C/T type in both asthmatics and non-asthmatics, 26 vs 21 in asthmatics and 18 vs 15 in non-asthmatics, which was, however, insignificant statistically. No significant relationship between the severity of asthma and the polymorphism was found(P=0.7). Conclusion: There was no significant difference between the severity of asthma and the IL-4 promoter polymorphism(P=0.709). Interestingly, the frequency of the polymorphism in both asthmatics as well as non-asthmatics was found to be even higher than that occurred in Caucasians. However, no significant difference in the frequency of the polymorphism was found in both groups.

• Tuberculosis and Respiratory Diseases
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• v.58 no.4
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• pp.367-374
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• 2005

Background : The fact that only 10-20% of chronic cigarette smokers develop chronic obstructive pulmonary disease (COPD) reflects the presence of genetic factors associated with the susceptibility to COPD. Recently, it was reported that the surfactant protein A increases the secretion of matrix metalloprotease 9, which degrades extracellular matrices of the lung, through a Toll-like receptor 2 (TLR2). In this context, possible role of TLR2 in the pathogenesis of COPD was postulated, and a functional dinucleotide repeat polymorphism in intron II of TLR2 was evaluated for any association with COPD. Method : Male patients with COPD and male smokers with a normal pulmonary function were enrolled in this study. The number of Guanine-Thymine repeats in intron II of the TLR2 gene were counted. Because the distributions of the repeats were trimodal, the alleles were classified into three subclasses, 12-16 repeats: short (S) alleles; 17-22 repeats: medium length (M) alleles; and 23-27 repeats: long (L) alleles. Result : 125 male patients with COPD and 144 age- and gender-matched blood donors with a normal lung function were enrolled. There were no differences in the distribution of each allele subclass (S, M and L) between the COPD and control group (p=0.75). The frequencies of the genotypes with and without each allele subclass in the COPD and control group were similar. Conclusion : A microsatellite polymorphism in intron II of TLR2 gene was not associated with the development of COPD in Koreans.