• Journal of Life Science
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• v.29 no.1
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• pp.105-111
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• 2019

In recent years, progress has been made in the search for the development of new anti-cancer agents by employing specific inhibitors of histone deacetylase (HDAC)-6 to block signal transduction pathways in cancer cells. This study examined the effects of tubastatin A (TubA), an HDAC-6 inhibitor, on the growth and development of immature oocytes in murine ovaries using RNA sequencing analysis. The results from a gene set enrichment analysis (GSEA) indicated that the expression of most of the gene sets involved in the cell cycle and control and progression of meiosis decreased in the TubA-treated group as compared with that in germinal vesicle (GV) stage oocytes. In addition, an ingenuity pathway analysis (IPA) suggested that TubA not only caused increased expression of p53 and pRB and decreased expression of CDK4/6 and cyclin D but also caused elevated expression of genes involved in the control of the DNA check point in G2/M stage oocytes. These results suggest that TubA may induce cell cycle arrest and apoptosis through the induction of changes in the expression of genes involved in signal transduction pathways associated with DNA damage and the cell cycle of immature oocytes in the ovary.

• The Plant Pathology Journal
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• v.35 no.4
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• pp.389-392
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• 2019

The studies on detection of the Strawberry mottle virus (SMoV) have been conducted in Poland for breeding programme purpose and for producers of strawberry plant material. Leaf samples collected from infected strawberry plants were grafted on Fragaria sp. Indicators which were maintained in greenhouse for further study. Seven Fragaria vesca var. semperflorens 'Alpine' indicators infected by SMoV were used for the study aimed on molecular characterization of virus isolates. Partial RNA2 was amplified from total nucleic acids using the RT-PCR method. The obtained amplicons separately digested with BfaI, FauI, HaeIII, HincI, and TaqI enzymes showed different restriction profiles. The nucleotide sequences analysis of RNA2 fragment confirmed the genetic diversity of the SMoV isolates as their similarity ranged from 94.7 to 100%. Polish isolates shared 75.7-99.2% identity with sequence of the virus strains from the Czech Republic, the Netherlands, and Canada. Phylogenetic analysis resulted in grouping of the isolates found in Poland together with one of the Czech strain whereas two other from the Czech and the strains from the Netherlands and Canada created the separate cluster.

• Journal of Microbiology and Biotechnology
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• v.6 no.5
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• pp.364-365
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• 1996

A region encoding the 16S rRNA was cloned by PCR from Streptomyces melanosporofaciens 7489 and sequenced by the chain-termination dideoxy sequencing method. A phylogenetic tree constructed by sequence alignment of 24 Streptomyces species suggests that there is little evolutionary distance between this strain and Streptomyces rimosus.

• IMMUNE NETWORK
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• v.20 no.4
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• pp.34.1-34.8
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• 2020

Cryopreservation and thawing of PBMCs are inevitable processes in expanding the scale of experiments in human immunology. Here, we carried out a fundamental study to investigate the detailed effects of PBMC cryopreservation and thawing on transcriptomes. We sorted Tregs from fresh and cryopreserved/thawed PBMCs from an identical donor and performed single-cell RNA-sequencing (scRNA-seq). We found that the cryopreservation and thawing process minimally affects the key molecular features of Tregs, including FOXP3. However, the cryopreserved and thawed sample had a specific cluster with up-regulation of genes for heat shock proteins. Caution may be warranted in interpreting the character of any cluster of cells with heat shock-related properties when cryopreserved and thawed samples are used for scRNA-seq.

• Journal of Microbiology and Biotechnology
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• v.28 no.8
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• pp.1318-1331
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• 2018

Lettuce (Lactuca sativa L.) is a major ingredient used in many food recipes in South Korea. Lettuce samples were collected during their maximum production period between April and July in order to investigate the microbiota of lettuce during different seasons. 16S rRNA gene-based sequencing was conducted using Illumina MiSeq, and real-time PCR was performed for quantification. The number of total bacterial was greater in lettuce collected in July than in that collected in April, albeit with reduced diversity. The bacterial compositions varied according to the site and season of sample collection. Potential pathogenic species such as Bacillus spp., Enterococcus casseliflavus, Klebsiella pneumoniae, and Pseudomonas aeruginosa showed season-specific differences. Results of the network co-occurrence analysis with core genera correlations showed characteristics of bacterial species in lettuce, and provided clues regarding the role of different microbes, including potential pathogens, in this microbiota. Although further studies are needed to determine the specific effects of regional and seasonal characteristics on the lettuce microbiota, our results imply that the 16S rRNA gene-based sequencing approach can be used to detect pathogenic bacteria in lettuce.

• Journal of Microbiology and Biotechnology
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• v.22 no.3
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• pp.431-435
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• 2012

In this study, we describe a novel approach to achieve replicative selectivity of conditionally replicative adenovirus that is based upon trans-splicing ribozyme-mediated replacement of cancer-specific RNAs. We developed a specific ribozyme that can reprogram human telomerase reverse transcriptase (hTERT) RNA to induce adenoviral E1A gene expression selectively in cancer cells that express the RNA. Western blot analysis showed that the ribozyme highly selectively triggered E1A expression in hTERT-expressing cancer cells. RT-PCR and sequencing analysis indicated that the ribozyme-mediated E1A induction was caused via a high fidelity trans-splicing reaction with the targeted residue in the hTERT-expressing cells. Moreover, reporter activity under the control of an E1A-dependent E3 promoter was highly transactivated in hTERT-expressing cancer cells. Therefore, adenovirus containing the hTERT RNA-targeting trans-splicing ribozyme would be a promising anticancer agent through selective replication in cancer cells and thus specific destruction of the infected cells.

• Biomedical Science Letters
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• v.23 no.2
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• pp.96-103
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• 2017

Nocardia species (spp.) are opportunistic pathogen in immunocompromised hosts. The genus Nocardia contains more than 70 species. Nocardia takedensis has been recently reported as a new species of the genus Nocardia. In this study, we describes the first clinical isolate of N. takedensis from the skin lesion in Busan, Korea. For the identification of clinical isolate to the species level as N. takedensis, classical methods (colony morphology, biochemical characteristics, and antimicrobial susceptibility), molecular method (16S rRNA gene sequencing), and MS (mass spectrometry) analysis were conducted. Clinical isolates grew slowly on the culture media (5% sheep blood agar and chocolate agar) under 5% $CO_2$ condition. Especially, carotene pigmentation was detected well on the media. Using mass spectrometry, Nocardia isolate was not identified to the species level. However, molecular method based on 16S rRNA sequencing confirmed the isolate as N. takedensis correctly. N. takedensis isolate was partial positive for acid-fast bacilli on the Ziehl-Neelsen method. And it was observed to be resistance to amoxicillin/clavulanic acid and ciprofloxacin. Our results provide useful information to develop optimal identification protocol of N. takedensis in clinical diagnostic laboratories.

• Journal of Microbiology and Biotechnology
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• v.28 no.4
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• pp.652-662
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• 2018

Diarrhea is a global disease with a high morbidity and mortality rate in children. In this study, 25 fecal samples were collected from children under 5 years old. Seven samples had been taken from healthy children without diarrhea and marked as the healthy control group; eight samples had been sampled from children with diarrhea caused by dyspepsia and defined as the non-infectious group; and ten samples had been taken from children with diarrhea induced by intestinal infections and identified as the infectious group. We detected the microbial communities of samples by using high-throughput sequencing of 16S rRNA genes. The proportion of aerobic and facultative anaerobic microbes in samples of the infectious group was much higher than in the non-infectious group. In addition, the relative abundance of Enterococcus in the healthy control group was significantly higher than in the non-infectious group and infectious group. This can be used as a potential diagnostic biomarker for diarrhea.

• 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.

• 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.