• Plant Breeding and Biotechnology
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• v.6 no.4
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• pp.413-425
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• 2018

A previous work developed and identified a new omega-5 gliadin deficient wheat line named O-free by crossing Keumkang and Olgeuru, which is nutritionally quite meaningful in that omega-5 gliadin is one of the known wheat allergens. To verify the characteristics of the O-free, we performed RNA sequencing (RNAseq) analysis of the O-free and the two parent lines (Keumkang and Olgeuru). The results of the similarity analysis with the ESTs for gliadins and glutenins showed that the O-free ESTs had no similarity with the omega-5 gliadin sequences but had similarity to other gliadins and glutenins. Furthermore, mapping results between the raw RNAseq data from the O-free and the omega-5 gliadin sequence showed a clear deletion of the N-terminal sequences which are an important signature of omega-5 gliadin. We also designed specific PCR primers that could identify omega-5 gliadin in the genomic DNA. The results showed that no omega-5 gliadin fragments were detected in the O-free. According to these results, we confirmed that the deficiency of omega-5 gliadin in the O-free is not caused by post-transcriptional or post-translational regulations such as epigenetic phenomena but by a simple deletion in the chromosome. Furthermore, we showed that the low-molecular weight glutenin subunit (LMW-GS) gene in the O-free had a single nucleotide polymorphism (SNP) causing a premature stop codon, resulting in a truncated polypeptide. We expect that the O-free line may serve as an excellent source of wheat that could prevail in the hypo-allergen wheat market, which has recently gained interest world-wide.

• Plant Breeding and Biotechnology
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• v.6 no.4
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• pp.354-362
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• 2018

Maize has high food and industrial value, whereas has difficulties in research because of their complex and huge size genome. Nested association mapping (NAM) was constructed to better understand maize genetics. However, most studies were conducted using the reference genome B73, and only a few studies were conducted on tropical maize. Ki3, one of the founder lines of the NAM population, is a tropical maize. We analyzed the genetic characteristics of Ki3 by using RNA sequencing and bioinformatics tools for various genetic studies. As results, a total of 30,526 genes were expressed, and expression profile were constructed. A total of 1,558 genes were differentially expressed in response to drought stress, and 513 contigs of them come from de novo assemblies. In addition, high-density polymorphisms including 464,930 single nucleotide polymorphisms (SNPs), 21,872 multiple nucleotide polymorphisms (MNPs) and 93,313 insertions and deletions (InDels) were found compared to reference genome. Among them, 15.0 % of polymorphisms (87,838) were passed non-synonymous test which could alter amino acid sequences. The variants have 66,550 SNPs, 5,853 MNPs, and 14,801 InDels, also proportion of homozygous type was higher than heterozygous. These variants were found in a total of 15,643 genes. Of these genes, 637 genes were found as differentially expressed genes (DEGs) under drought stress. Our results provide a genome-wide analysis of differentially expressed genes and information of variants on expressed genes of tropical maize under drought stress. Further characterization of these changes in genetic regulation and genetic traits will be of great value for improvement of maize genetics.

• 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 Life Science
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• v.29 no.1
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• pp.118-122
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• 2019

Oxytocin (Oxt) and vasopressin (Avp) are mainly synthesized in neuronal cells of the hypothalamus and are released from the posterior pituitary. The structure and sequences of Oxt and Avp genes imply that they are closely related and that they are the result of a duplication event during evolution. A previous study suggested that a small regulatory microRNA (miRNA), miR-24, regulated Oxt after binding. However, it is not clear whether this miRNA can modulate Avp simultaneously. The aim of the present study was to investigate putative targeting miRNAs of Avp, including miR-24. Targeted candidate miRNA oligonucleotides were transfected into COS-7 cells to elucidate the binding activity of miRNAs and Avp using dual-luciferase assays. The luciferase assay showed that only miR-24 displayed elevated binding activity with Avp as compared to a control and other candidate miRNAs. Transfection with seed mutants of Avp and miR-24 inhibitors clearly showed that miR-24 can directly bind to the Avp gene. These results provide new insight into the regulatory mechanism of neurohypophysial hormones by a single miRNA.

• Journal of Microbiology and Biotechnology
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• v.29 no.3
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• pp.410-418
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• 2019

To investigate a novel ${\beta}$-glucosidase from Bifidobacterium breve ATCC 15700 (BbBgl) to produce compound K (CK) via ginsenoside $F_2$ by highly selective and efficient hydrolysis of the C-3 glycoside from ginsenoside Rd, the BbBgl gene was cloned and expressed in E. coli BL21. The recombinant BbBgl was purified by Ni-NTA magnetic beads to obtain an enzyme with specific activity of 37 U/mg protein using pNP-Glc as substrate. The enzyme activity was optimized at pH 5.0, $35^{\circ}C$, 2 or 6 U/ml, and its activity was enhanced by $Mn^{2+}$ significantly. Under the optimal conditions, the half-life of the BbBgl is 180 h, much longer than the characterized ${\beta}$-glycosidases, and the $K_m$ and $V_{max}$ values are 2.7 mM and $39.8{\mu}mol/mg/min$ for ginsenoside Rd. Moreover, the enzyme exhibits strong tolerance against high substrate concentration (up to 40 g/l ginsenoside Rd) with a molar biotransformation rate of 96% within 12 h. The good enzymatic properties and gram-scale conversion capacity of BbBgl provide an attractive method for large-scale production of rare ginsenoside CK using a single enzyme or a combination of enzymes.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.54 no.5
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• pp.698-702
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• 2021

Yellow head virus (YHV) is a rod-shaped positive-sense single-stranded RNA virus, classified into the genus Okavirus, family Roniviridae, and order Nidovirales. In this study, 200 fleshy prawns (Fenneropenaeus chinensis) collected from the vicinity of Narodo in Goheung-gun, Korea, were screened for the presence of yellow head complex viruses and related genotype such as YHV genotype 8. The detection rate of YHV genotype 8 among the 200 fleshy prawns, determined using nested RT-PCR (reverse transcription polymerase chain reation), was 39.0%. Phylogenetic analysis of the ORF1b gene of YHV showed that eight distinct genetic lineages were detected. The four strains of YHV genotype 8 obtained in this study formed a robust clade with the YHV genotype 8 group that was first isolated from fleshy prawns in China suspected to have acute hepatopancreatic necrosis disease (AHPND).

• Parasites, Hosts and Diseases
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• v.59 no.2
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• pp.179-182
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• 2021

Human infection with Taenia asiatica or a hybrid between Taenia saginata and T. asiatica has not been reported in Cambodia. We detected for the first time a hybrid form between T. saginata and T. asiatica in Preah Vihear Province, Cambodia. An adult tapeworm specimen, i.e., 75 cm long strobila without scolex, was expelled from a 27-year-old man after praziquantel medication and purging. It was morphologically indistinguishable between T. saginata and T. asiatica. Several proglottids were molecularly analyzed to confirm the tapeworm species. The mitochondrial gene encoding cytochrome c oxidase subunit 1 (cox1) and nuclear genes encoding elongation factor-1α (ef1) and ezrin-radixin-moesin (ERM)-like protein (elp) were sequenced, and a single-allele analysis was performed to confirm the haploid genotype. The results revealed that our sample showed a discrepancy between the mitochondrial and 2 nuclear genes. It possessed homozygous sequences typical of T. saginata at cox1 and ef1 loci. However, it was heterozygous at the elp locus, with 1 allele in T. asiatica (elpA) and 1 in T. saginata (elpC), which indicates that it is a hybrid between T. saginata and T. asiatica. The present results confirmed the presence of a hybrid between T. saginata and T. asiatica in Cambodia and strongly suggest the existence of also 'pure' T. asiatica in Cambodia.

• Journal of Microbiology and Biotechnology
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• v.31 no.10
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• pp.1420-1429
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• 2021

The safety of the probiotic strain Q180, which exerts postprandial lipid-lowering effects, was bioinformatically and phenotypically evaluated. The genome of strain Q180 was completely sequenced, and single circular chromosome of 3,197,263 bp without any plasmid was generated. Phylogenetic and related analyses using16S rRNA gene and whole-genome sequences revealed that strain Q180 is a member of Lactiplantibacillus (Lp., formerly Lactobacillus) plantarum. Antimicrobial resistance (AMR) genes were bioinformatically analyzed using all Lp. plantarum genomes available in GenBank, which showed that AMR genes are present differently depending on Lp. plantarum strains. Bioinformatic analysis demonstrated that some mobile genetic elements such as prophages and insertion sequences were identified in the genome of strain Q180, but because they did not contain harmful genes such as AMR genes and virulence factor (VF)- and toxin-related genes, it was suggested that there is no transferability of harmful genes. The minimum inhibition concentrations of seven tested antibiotics suggested by the European Food Safety Authority guidelines were slightly lower than or equal to the microbiological cut-off values for Lp. plantarum. Strain Q180 did not show hemolytic and gelatinase activities and biogenic amine-producing ability. Taken together, this study demonstrated the safety of strain Q180 in terms of absence of AMR genes and VF- and toxin-related genes as a probiotic strain.

• Animal Bioscience
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• v.34 no.8
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• pp.1253-1270
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• 2021

Assessment of male fertility is based on the evaluation of sperm. Semen evaluation measures various sperm quality parameters as fertility indicators. However, semen evaluation has limitations, and it requires the advancement and application of strict quality control methods to interpret the results. This article reviews the recent advances in evaluating various sperm-specific quality characteristics and methodologies, with the help of different assays to assess sperm-fertility status. Sperm evaluation methods that include conventional microscopic methods, computer-assisted sperm analyzers (CASA), and flow cytometric analysis, provide precise information related to sperm morphology and function. Moreover, profiling fertility-related biomarkers in sperm or seminal plasma can be helpful in predicting fertility. Identification of different sperm proteins and diagnosis of DNA damage has positively contributed to the existing pool of knowledge about sperm physiology and molecular anomalies associated with different infertility issues in males. Advances in methods and sperm-specific evaluation has subsequently resulted in a better understanding of sperm biology that has improved the diagnosis and clinical management of male factor infertility. Accurate sperm evaluation is of paramount importance in the application of artificial insemination and assisted reproductive technology. However, no single test can precisely determine fertility; the selection of an appropriate test or a set of tests and parameters is required to accurately determine the fertility of specific animal species. Therefore, a need to further calibrate the CASA and advance the gene expression tests is recommended for faster and field-level applications.

• Journal of Ginseng Research
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• v.45 no.1
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• pp.149-155
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• 2021

Background: We have reported that internal deletions in the nef, gag, and pol genes in HIV-1-infected patients are induced in those treated with Korean Red Ginseng (KRG). KRG delays the development of resistance mutations to antiretroviral drugs. Methods: The vif-vpr genes over 26 years in 20 hemophiliacs infected with HIV-1 from a single source were sequenced to investigate whether vif-vpr genes were affected by KRG and KRG plus highly active antiretroviral therapy (ART) (hereafter called GCT) and compared the results with our previous data. Results: A significantly higher number of in-frame small deletions were found in the vif-vpr genes of KRG-treated patients than at the baseline, in control patients, and in ART-alone patients (p < 0.001). These were significantly reduced in GCT patients (p < 0.05). In contrast, sequences harboring a premature stop codon (SC) were more significant in GCT patients (10.1%) than in KRG-alone patients, control (p < 0.01), and ART-alone patients (p = 0.078 for peripheral blood mononuclear cells). The proportion of SC in Vpr was similar to that in Vif, whereas the proportion of sequences revealing SC in the env-nef genes was significantly lower than that in the pol-vif-vpr genes (p < 0.01). The genetic distance was 1.8 times higher in the sequences harboring SC than in the sequences without SC (p < 0.001). Q135P in the vif gene is significantly associated with rapid progression to AIDS (p < 0.01). Conclusion: Our data show that KRG might induce sD in the vif-vpr genes and that vif-vpr genes are similarly affected by lethal mutations.