• Korean Journal of Microbiology
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• v.54 no.4
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• pp.480-482
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• 2018

The draft genome sequencing for Zhongshania marina $DSW25-10^T$, isolated from deep seawater of East Sea in Korea, was performed using Illumina HiSeq platform. As a result, the draft genome was comprised of a total length of approximately 4.08 Mbp with G + C content of 49.0%, and included a total of 3,702 protein-coding genes, 3 rRNA genes, 39 tRNA genes, 4 non-coding RNA genes, and 36 pseudogenes. In addition, the metabolic pathways of aliphatic and aromatic compounds were identified. In light of these metabolic pathways, Zhongshania marina $DSW25-10^T$ is expected to be a useful bioremediation resource.

• Journal of Veterinary Science
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• v.24 no.5
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• pp.73.1-73.16
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• 2023

Background: Highly pathogenic avian influenza virus (HPAIV) is considered a global threat to both human health and the poultry industry. MicroRNAs (miRNA) can modulate the immune system by affecting gene expression patterns in HPAIV-infected chickens. Objectives: To gain further insights into the role of miRNAs in immune responses against H5N1 infection, as well as the development of strategies for breeding disease-resistant chickens, we characterized miRNA expression patterns in tracheal tissues from H5N1-infected Ri chickens. Methods: miRNAs expression was analyzed from two H5N1-infected Ri chicken lines using small RNA sequencing. The target genes of differentially expressed (DE) miRNAs were predicted using miRDB. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis were then conducted. Furthermore, using quantitative real-time polymerase chain reaction, we validated the expression levels of DE miRNAs (miR-22-3p, miR-146b-3p, miR27b-3p, miR-128-3p, miR-2188-5p, miR-451, miR-205a, miR-203a, miR-21-3p, and miR-200a3p) from all comparisons and their immune-related target genes. Results: A total of 53 miRNAs were significantly expressed in the infection samples of the resistant compared to the susceptible line. Network analyses between the DE miRNAs and target genes revealed that DE miRNAs may regulate the expression of target genes involved in the transforming growth factor-beta, mitogen-activated protein kinase, and Toll-like receptor signaling pathways, all of which are related to influenza A virus progression. Conclusions: Collectively, our results provided novel insights into the miRNA expression patterns of tracheal tissues from H5N1-infected Ri chickens. More importantly, our findings offer insights into the relationship between miRNA and immune-related target genes and the role of miRNA in HPAIV infections in chickens.

• Animal Bioscience
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• v.36 no.3
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• pp.404-416
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• 2023

Objective: Daweizi (DWZ) is a famous indigenous pig breed in China and characterized by tender meat and high fat percentage. However, the expression profiles and functions of transcripts in DWZ pigs is still in infancy. The object of this study was to depict the transcript profiles in DWZ pigs and screen the potential pathway influence adipogenesis and fat deposition, Methods: Histological analysis of backfat tissue was firstly performed between DWZ and lean-type Yorkshire pigs, and then RNA sequencing technology was utilized to explore miRNAs, lncRNAs and mRNAs profiles in backfat tissue. 18 differentially expressed (DE) transcripts were randomly selected for quantitative real-time polymerase chain reaction (QPCR) to validate the reliability of the sequencing results. Finally, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis were conducted to investigate the potential pathways influence adipocyte differentiation, adipogenesis and lipid metabolism, and a schematic model was further proposed. Results: A total of 1,625 differentially expressed transcripts were identified in DWZ pigs, including 27 upregulated and 45 downregulated miRNAs, 64 upregulated and 119 down-regulated lncRNA, 814 upregulated and 556 downregulated mRNAs. QPCR analysis exhibited strong consistency with the sequencing data. GO and KEGG analysis elucidated that the differentially expressed transcripts were mainly associated with cell growth and death, signal transduction, peroxisome proliferator-activated receptors (PPAR), AMP-activated protein kinase (AMPK), PI3K-Akt, adipocytokine and foxo signaling pathways, all of which are strongly involved in cell development, lipid metabolism and adipogenesis. Further analysis indicated that the BGIR9823_87926/miR-194a-5p/AQP7 network may be effective in the process of adipocyte differentiation or adipogenesis. Conclusion: Our study provides comprehensive insights into the regulatory network of backfat deposition and lipid metabolism in pigs from the point of view of miRNAs, lncRNAs and mRNAs.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.60 no.2
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• pp.224-230
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• 2015

Next generation sequencing technologies provide opportunities to reveal the genetic variants and differentially expressedgenes. The genetic variants are closely relevance to understanding of genes and phenotypic differences related to agronomic characteristics among cultivars. In this study, we conducted RNA-seq using two Korean soybean accessions, including Daewon and Hwangkeum, by using next generation sequencing against Williams 82 genome as reference. A number of variants such assingle nucleotide variants (SNV), multiple nucleotide variants (MNV), insertion/deletion (InDel) and replacement, was 34,411 and 55,544 in Daewon and Hwangkeum, respectively. Among these variants, 9,611 nonsynonymous variants were detected within 4,290 genes in Daewon and 13,225 non-synonymous variants were located on 5,672 genes in Hwangkeum. The distribution of nonsynonymous variants and expression values of genes can serve as invaluable resource for genotyping and study of traits within genes for soybean improvements.

• Advances in environmental research
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• v.9 no.3
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• pp.215-232
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• 2020

Crude oils are essential source of energy. It is majorly found in geographical locations beneath the earth's surface and crude oil is the main factor for the economic developments in the world. Natural crude oil contains unrefined petroleum composed of hydrocarbons of various molecular weights and it contains other organic materials like aromatic compounds, sulphur compounds, and many other organic compounds. These hydrocarbons are rapidly getting degraded by biosurfactant producing microorganisms. The present study deals with the isolation, purification, and characterization of biosurfactant producing microorganism from oil-contaminated soil. The ability of the microorganism producing biosurfactant was investigated by well diffusion method, drop collapse test, emulsification test, oil displacement activity, and blue agar plate method. The isolate obtained from the oil contaminated soil was identified as Bacillus subtilis. The identification was done by microscopic examinations and further characterization was done by Biochemical tests and 16SrRNA gene sequencing. Purification of the biosurfactant was performed by simple liquid-liquid extraction, and characterization of extracted biosurfactants was done using Fourier transform infrared spectroscopy (FTIR). The degradation of crude oil upon treatment with the partially purified biosurfactant was analyzed by FTIR spectroscopy and Gas-chromatography mass spectroscopy (GC-MS).

• 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 Marine Bioscience and Biotechnology
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• v.12 no.1
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• pp.50-58
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• 2020

Sphacelaria is a filamentous brown algal genus that can be epibiotic on macroalgae, marine plants, and sea turtles. Its important role in benthic ecosystems, exposure to different stressors (e.g., grazing), and use as a model organism make Sphacelaria ideal for assessing physiological responses of organisms to environmental inputs. Single-cell RNA sequencing is a powerful new probe for understanding environmental responses of organisms at the molecular (transcriptome) level, capable of delineating gene regulation in different cell types. In the case of plants, this technique requires protoplasts ("naked" plant cells). The existing protoplast isolation protocols for Sphacelaria use non-commercial enzymes and are low-yielding. This study is the first to report the production of protoplasts from Sphacelaria fusca (Hudson) S.F. Gray, using a combination of commercial enzymes, chelation, and osmolarity treatment. A simple combination of commercial enzymes (cellulase Onozuka RS, alginate lyase, and driselase) with chelation pretreatment and an increased osmolarity (2512 mOsm/L H₂O) gave a protoplast yield of 15.08 ± 5.31 × 10⁴ protoplasts/g fresh weight, with all the Sphacelaria cell types represented. Driselase had no crucial effect on the protoplast isolation. However, the increased osmolarity had a highly significant and positive effect on the protoplast isolation, and chelation pretreatment was essential for optimal protoplast yield. The protocol represents a significant step forward for studies on Sphacelaria by efficiently generating protoplasts suitable for cellular studies, including single-cell RNA sequencing and expression profiling.

• Journal of Microbiology and Biotechnology
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• v.25 no.9
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• pp.1537-1541
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• 2015

Previous detection methods for Citrobacter are considered time consuming and laborious. In this study, we have developed a rapid and accurate detection method for Citrobacter species in pork products, using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). A total of 35 Citrobacter strains were isolated from 30 pork products and identified by both MALDI-TOF MS and 16S rRNA gene sequencing approaches. All isolates were identified to the species level by the MALDI-TOF MS, while 16S rRNA gene sequencing results could not discriminate them clearly. These results confirmed that MALDITOF MS is a more accurate and rapid detection method for the identification of Citrobacter species.

• 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.

• Korean Journal of Soil Science and Fertilizer
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• v.44 no.1
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• pp.127-145
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• 2011

Various environmental ecosystems are valuable sources for microbial ecology studies, and their analyses using recently developed molecular ecological approaches have drawn significant attention within the scientific community. Changes in the microbial community structures due to various anthropogenic activities can be evaluated by various culture-independent methods e.g. ARISA, DGGE, SSCP, T-RFLP, clone library, pyrosequencing, etc. Direct amplification of total community DNA and amplification of most conserved region (16S rRNA) are common initial steps, followed by either fingerprinting or sequencing analysis. Fingerprinting methods are relatively quicker than sequencing analysis in evaluating the changes in the microbial community. Being an efficient, sensitive and time- and cost effective method, T-RFLP is regularly used by many researchers to access the microbial diversity. Among various fingerprinting methods T-RFLP became an important tool in studying the microbial community structure because of its sensitivity and reproducibility. In this present review, we will discuss the important developments in T-RFLP methodology to distinguish the total microbial diversity and community composition in the various ecosystems.