• Asian-Australasian Journal of Animal Sciences
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• v.26 no.3
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• pp.309-315
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• 2013

MicroRNAs are a class of endogenous small RNAs that play important roles in post-transcriptional gene regulation by directing degradation of mRNAs or facilitating repression of target gene translation. In this study, three small RNA cDNA libraries from the mammary gland tissues of Laoshan dairy goats (Capra hircus) were constructed and sequenced, individually. Through Solexa high-throughput sequencing and bioinformatics analysis, we obtained 50 presumptive novel miRNAs candidates, and 55,448 putative target genes were predicted. GO annotations and KEGG pathway analyses showed the majority of target genes were involved in various biological processes and metabolic pathways. Our results discovered more information about the regulation network between miRNAs and mRNAs and paved a foundation for the molecular genetics of mammary gland development in goats.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
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• 2012.10a
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• pp.991-993
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• 2012

We analyzed RNA polymerase beta subunit gene (rpoB) mutation of rifampin-resistant Mycobacteria through analysis of nucleotide sequence of rpoB DNA (351 bp) containing rifampin resistant region, $rif^r$. For this study, we collected rifampin-resistant Mycobacteria that were identified by conventional culture methods from Masan National Hospital and The Korean Institute of Tuberculosis. We performed sequencing of DNA nucleotides and analyzed rpoB gene of those rifampin-resistant Mycobacteria. From this analysis, we invcestigated diverse mutations of rpoB gene included rifampin-resistant gene, which were not reported, from those rifampin-resistant Mycobacteria.

• Molecules and Cells
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• v.41 no.10
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• pp.917-922
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• 2018

The CRISPR-Cas system is a well-established RNA-guided DNA editing technique widely used to modify genomic DNA sequences. I used the CRISPR-Cas9 system to change the second and third nucleotides of the triplet $T{\underline{CT}}$ of human TNSFSF9 in HepG2 cells to $T{\underline{AG}}$ to create an amber stop codon. The $T{\underline{CT}}$ triplet is the codon for Ser at the $172^{nd}$ position of TNSFSF9. The two substituted nucleotides, AG, were confirmed by DNA sequencing of the PCR product followed by PCR amplification of the genomic TNFSF9 gene. Interestingly, sequencing of the cDNA of transcripts of the edited TNFSF9 gene revealed that the $T{\underline{AG}}$ had been re-edited to the wild type triplet $T{\underline{CT}}$, and 1 or 2 bases just before the triplet had been deleted. These observations indicate that CRISPR-Cas9-mediated editing of bases in target genomic DNA can be followed by spontaneous re-editing (correcting) of the bases during transcription.

• Food Science and Biotechnology
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• v.17 no.4
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• pp.892-894
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• 2008

During dongchimi fermentation at 5 and $25^{\circ}C$, the pH lowered slowly and reached 4.03 at $5^{\circ}C$ after 30 days, whereas it lowered dramatically and reached 3.59 at $25^{\circ}C$ after 2 days. The predominant bacteria were Leuconostoc (Leu.) mesenteroides at $25^{\circ}C$ until day 2 which changed into Lactobacillus (Lb.) plantarum at day 3, analyzed by a culture dependent method with partial 16S rRNA gene sequencing, whereas Leu. mesenteroides occupied predominantly at $5^{\circ}C$ until day 7. In a culture-independent method using a polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) with partial 16S rRNA gene sequencing, Lb. algidus was predominant at $5^{\circ}C$ until day 7 and Lb. plantarum occupied predominantly at $25^{\circ}C$ until day 3, which is different from the results of the culture based method, indicating the both methods need to be combined for accuracy. Based on the culture-dependent method, Leu. mesenteroides might be responsible for the early and mid-phase of dongchimi fermentation.

• Molecules and Cells
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• v.42 no.2
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• pp.104-112
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• 2019

Tracking the fate of individual cells and their progeny through lineage tracing has been widely used to investigate various biological processes including embryonic development, homeostatic tissue turnover, and stem cell function in regeneration and disease. Conventional lineage tracing involves the marking of cells either with dyes or nucleoside analogues or genetic marking with fluorescent and/or colorimetric protein reporters. Both are imaging-based approaches that have played a crucial role in the field of developmental biology as well as adult stem cell biology. However, imaging-based lineage tracing approaches are limited by their scalability and the lack of molecular information underlying fate transitions. Recently, computational biology approaches have been combined with diverse tracing methods to overcome these limitations and so provide high-order scalability and a wealth of molecular information. In this review, we will introduce such novel computational methods, starting from single-cell RNA sequencing-based lineage analysis to DNA barcoding or genetic scar analysis. These novel approaches are complementary to conventional imaging-based approaches and enable us to study the lineage relationships of numerous cell types during vertebrate, and in particular human, development and disease.

• Journal of Species Research
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• v.8 no.3
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• pp.313-317
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• 2019

Bats influence overall ecosystem health by regulating species diversity and being a major source of zoonotic viruses. Hence, there is a need to elucidate their migration, population structure, and phylogenetic relationship. The complete mitochondrial genome is widely used for studying the genome-level characteristics and phylogenetic relationship of various animals due to its high mutation rate, simple structure, and maternal inheritance. In this study, we determined the complete mitogenome sequence of the bird-like noctule (Nyctalus aviator) by Illumina next-generation sequencing. The sequences obtained were used to reconstruct a phylogenic tree of Vespertilionidae to elucidate the phylogenetic relationship among its members. The mitogenome of N. aviator is 16,863-bp long with a typical vertebrate gene arrangement, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 putative control region. Overall, the nucleotide composition is as follows: 32.3% A, 24.2% C, 14.3% G, and 29.2% T, with a slight AT bias (61.5%). The base composition of the 13 PCGs is as follows: 30.3% A, 13.4% G, 31.0% T, and 25.2% C. The phylogenetic analysis, based on 13 concatenated PCG sequences, infers that N. aviator is closely related to N. noctula with a high bootstrap value (100%).

• Parasites, Hosts and Diseases
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• v.59 no.1
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• pp.67-76
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• 2021

Legionella pneumophila is an opportunistic pathogen that survives and proliferates within protists such as Acanthamoeba spp. in environment. However, intracellular pathogenic endosymbiosis and its implications within Acanthamoeba spp. remain poorly understood. In this study, RNA sequencing analysis was used to investigate transcriptional changes in A. castellanii in response to L. pneumophila infection. Based on RNA sequencing data, we identified 1,211 upregulated genes and 1,131 downregulated genes in A. castellanii infected with L. pneumophila for 12 hr. After 24 hr, 1,321 upregulated genes and 1,379 downregulated genes were identified. Gene ontology (GO) analysis revealed that L. pneumophila endosymbiosis enhanced hydrolase activity, catalytic activity, and DNA binding while reducing oxidoreductase activity in the molecular function (MF) domain. In particular, multiple genes associated with the GO term 'integral component of membrane' were downregulated during endosymbiosis. The endosymbiont also induced differential expression of various methyltransferases and acetyltransferases in A. castellanii. Findings herein are may significantly contribute to understanding endosymbiosis of L. pneumophila within A. castellanii.

• The Plant Pathology Journal
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• v.39 no.3
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• pp.303-308
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• 2023

The global climate change and international trade have facilitated the movement of plants across borders, increasing the risk of introducing novel plant viruses in new territories. Ixora coccinea exhibited virus-like foliar symptoms, including mosaic and mild mottle. An Oxford Nanopore Technologies-based compact and portable MinION platform was used to identify the causal viral pathogen. The complete genome sequence of jasmine virus H (JaVH; 3867 nt, JaVH-CNU) was determined and found to share 88.4-90.3% nucleotide identity with that of Jasminum sambac JaVH isolate in China. Phylogenetic analysis based on the complete amino acid sequences of RNA-dependent RNA polymerase and coat protein revealed that JaVH-CNU was grouped separately with other JaVH isolates. This is the first report of a natural JaVH infection of I. coccinea. The application of rapid nanopore sequencing for plant virus identification was demonstrated and is expected to provide accurate and rapid diagnosis for virus surveillance.

• Journal of Dairy Science and Biotechnology
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• v.41 no.4
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• pp.211-218
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• 2023

This study aimed to identify lactic acid bacteria isolated from eight fermented milk products in Iran. We enumerated Lactobacillus species using De Man-Rogosa-Sharpe (MRS)-maltose and MRS agar with pH adjusted to 5.2, as well as assessment at 37℃ for 48 hr, studied Streptococcus spp. using M17 agar at 43℃ for 24 hr, and assessed Bifidobacterium species using nalidixic acid, paromomycin sulfate, neomycin sulfate, and lithium chloride (BL-NPNL) agar at 37℃ for 48 hr. The total viable Streptococcus spp. cell in fermented milk varied at 4.73-8.83 log CFU/mL. However, Bifidobacterium spp. were not detected in any of the tested samples. Lactobacilli were not detected in four of the eight samples, and viable Lactobacilli cells in the remaining four samples ranged 2.48-3.85 log CFU/mL. The pH of the tested samples ranged 3.53-4.19, and soluble solids (Brix measurement) ranged 7.5%-17.9%. A total of 130 isolates of gram-positive catalase-positive bacteria were characterized at the species level using 16S rRNA sequencing. Sequence analysis identified six species: Streptococcus thermophilus, Lactobacillus delbrueckii subsp. sunkii, Lactobacillus delbrueckii subsp. indicus, Lactiplantibacillus plantarum, Lacticaseibacillus rhamnosus, and Levilactobacillus brevis.

• Bulletin of the Korean Chemical Society
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• v.27 no.5
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• pp.657-662
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• 2006

Identification of accessible sites in targeted RNAs is a major limitation to the effectiveness of antisense oligonucleotides. A class of antisense oligodeoxynucleotides, known as the “10-23” DNA enzyme or DNAzyme, which is a small catalytic DNA, has been shown to efficiently cleave target RNA at purine-pyrimidine junctions in vitro. We have designed a strategy to identify accessible cleavage sites in the target RNA, which is hepatitis C virus nonstructural gene 3 (HCV NS3) RNA that encodes viral helicase and protease, from a pool of random DNAzyme library. A pool of DNAzymes of 58 nucleotides-length that possess randomized annealing arms, catalytic core sequence, and fixed 5'/3'-end flanking sequences was designed and screened for their ability to cleave the target RNA. The screening procedure, which includes binding of DNAzyme pool to the target RNA under inactive condition, selection and amplification of active DNAzymes, incubation of the selected DNAzymes with the target RNA, and target site identification on sequencing gels, identified 16 potential cleavage sites in the target RNA. Corresponding DNAzymes were constructed for the selected target sites and were tested for RNA-cleavage in terms of kinetics and accessibility. These selected DNAzymes were effective in cleaving the target RNA in the presence of $Mg^{2+}$. This strategy can be applicable to identify accessible sites in any target RNA for antisense oligonucleotides-based gene inactivation methods.