• Korean Journal of Microbiology
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• v.54 no.2
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• pp.167-168
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• 2018

Here we report the complete genome sequence of Staphylococcus xylosus S170, strong biofilm-producing strain, which comprised a single circular 2,910,005 bp chromosome and 32.97% G + C content. The genome included 2,674 protein-coding sequences, 22 rRNA genes, and 57 tRNA genes. Gene analysis of S. xylosus S170 could contribute to better understanding of biofilm-forming mechanisms.

• Animal Bioscience
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• v.36 no.2_spc
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• pp.364-373
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• 2023

The gastrointestinal (GI) tract of ruminants contains diverse microbes that ferment various feeds ingested by animals to produce various fermentation products, such as volatile fatty acids. Fermentation products can affect animal performance, health, and well-being. Within the GI microbes, the ruminal microbes are highly diverse, greatly contribute to fermentation, and are the most important in ruminant nutrition. Although traditional cultivation methods provided knowledge of the metabolism of GI microbes, most of the GI microbes could not be cultured on standard culture media. By contrast, amplicon sequencing of 16S rRNA genes can be used to detect unculturable microbes. Using this approach, ruminant nutritionists and microbiologists have conducted a plethora of nutritional studies, many including dietary interventions, to improve fermentation efficiency and nutrient utilization, which has greatly expanded knowledge of the GI microbiota. This review addresses the GI content sampling method, 16S rRNA gene amplicon sequencing, and bioinformatics analysis and then discusses recent studies on the various factors, such as diet, breed, gender, animal performance, and heat stress, that influence the GI microbiota and thereby ruminant nutrition.

• Fisheries and Aquatic Sciences
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• v.4 no.4
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• pp.186-191
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• 2001

Vitellogenin (VTG) and VTG mRNA induction by $estradiol-17\beta\;(E_2)$ were examined in the primary cultures of hepatocyte in the rainbow trout. Hepatocytes were precultured for 2 days, then $E_2$ was added and cultured for another 5 days. Media and hepatocytes were then analyzed by electrophoresis and Northern blotting for VTG and VTG mRNA, respectively. The hepatocytes were formed a few aggregates within 5 days without further spreading to a monolayer. Cell viability and high DNA content were maintained during the incubation. The hepatocyte culture with E2 induced a weak VTG band at a molecular weight of 175kDa on Day 2 after $E_2$ addition. The relative amount of VTG was expressed in percentage of total protein concentrations. VTG was gradually increased as $1.9\%$ on Day 2, $6.3\%$ on Day 4 and $7.3\%$ on Day 5. VTG mRNA band was detected at about 6.6 kb in the culture with $E_2$ at day 1 of culture. The level of VTG mRNA expression linearly increased with time until Day 5 (r=0.97).

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.283-285
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• 2019

The draft genome sequencing for Pelagicola sp. DSW4-44 (= KCTC 62762 = KCCM 43261), 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 4.85 Mbp with G + C content of 54.3%, and included a total of 4,566 protein-coding genes, 3 rRNA genes, 48 tRNA genes, 3 non-coding RNA genes, and 67 pseudo genes. In the draft genome, the strain DSW4-44 contained genes involved in the nitrogen metabolism of dissimilatory nitrate reduction to ammonium (DNRA) and denitrification, which were not found other strains in the genus Pelagicola.

• Korean Journal of Microbiology
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• v.55 no.2
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• pp.174-176
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• 2019

A novel bacterium, designated strain RR4-38 (= KCTC 52651 = DSM 108068), belonging to the family Flavobacteriaceae was isolated from a biofilter in the seawater recirculating aquaculture system in South Korea. A single complete genome contig which is 3,182,272 bp with 41.9% G+C content was generated using PacBio RS II platform. The genome includes 2,829 protein-coding genes, 6 rRNA genes, 38 tRNA genes, 4 non-coding RNA genes, and 9 pseudogenes. The results will provide insights for understanding microbial activity in the seawater recirculating aquaculture system.

• 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.

• The Plant Pathology Journal
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• v.33 no.5
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• pp.522-527
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• 2017

We determined the effects of atmospheric temperature ($10-30{\pm}2^{\circ}C$ in $5^{\circ}C$ increments) and carbon dioxide ($CO_2$) levels ($400{\pm}50ppm$, $540{\pm}50ppm$, and $940{\pm}50ppm$) on the infection of Solanum tuberosum cv. Chubaek by Potato leafroll virus (PLRV). Below $CO_2$ levels of $400{\pm}50ppm$, the PLRV infection rate and RNA content in plant tissues increased as the temperature increased to $20{\pm}2^{\circ}C$, but declined at higher temperatures. At high $CO_2$ levels ($940{\pm}50ppm$), more plants were infected by PLRV at $30{\pm}2^{\circ}C$ than at 20 or $25{\pm}2^{\circ}C$, whereas PLRV RNA content was unchanged in the $20-30{\pm}2^{\circ}C$ temperature range. The effects of atmospheric $CO_2$ concentration on the acquisition of PLRV by Myzus persicae and accumulation of PLRV RNA in plant tissues were investigated using a growth chamber at $20{\pm}2^{\circ}C$. The M. persicae PLRV RNA content slightly increased at elevated $CO_2$ levels ($940{\pm}50ppm$), but this increase was not statistically significant. Transmission rates of PLRV by Physalis floridana increased as $CO_2$ concentration increased. More PLRV RNA accumulated in potato plants maintained at 540 or $940{\pm}50ppm$ $CO_2$, than in plants maintained at $400{\pm}50ppm$. This is the first evidence of greater PLRV RNA accumulation and larger numbers of S. tuberosum plants infected by PLRV under conditions of combined high $CO_2$ levels ($940{\pm}50ppm$) and high temperature ($30{\pm}2^{\circ}C$).

• 한국생물공학회:학술대회논문집
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• 2003.04a
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• pp.686-689
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• 2003

A Gene content phylogenetic tree and a 16S rRNA based phylogenetic tree were compared for 9 Archaea and 15 Proteobacteria, whole-genome sequenced, by neighbor joining and bootstrap methods (n=1000). Ratio of conserved COG (clusters of orthologous groups of proteins) to ortholog revealed that they were within the range of 4.60% (Mezorhizobium loti) or 56.57% (Mycoplasma genitalium), The diversity of ratio meant the Possibility of searching for useful genes, as they possess peculiar genes. The gene content tree and the 16S rDNA tree showed coincidence and discordance in Archaea and Proteobacteria.

• Food Science and Biotechnology
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• v.18 no.6
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• pp.1500-1504
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• 2009

Effects of methanol extract from turmeric (Curcuma longa L.) (CME) on underlying mechanisms of lipolysis were investigated in 3T3-L1 adipocytes. Compared to the control, lipid accumulation with 72 hr treatment of CME at the concentration $20\;{\mu}g/mL$ was significantly decreased by 19.9% as quantified by Oil red O dye. Intracellular triglyceride (TG) content was also lowered by 19.3%. To determine the mechanism for TG content reduction, glycerol release level was measured. Incubation of 3T3-L1 adipocytes with 15 and $20\;{\mu}g/mL$ of CME significantly elevated the level of free glycerol released into the cultured medium by 20.4 and 28.6%, respectively. In subsequent measurements using quantitative real-time polymerase chain reaction (PCR), mRNA levels of hormone-sensitive lipase (HSL) and adipose triglyceride lipase (ATGL) were significantly increased by 21.2 and 24.9%, respectively, at the concentration $20\;{\mu}g/mL$. Results indicated that CME stimulated lipolysis through induction of HSL and ATGL mRNA expressions, resulting in increased glycerol release.

• The Korean Journal of Zoology
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• v.35 no.1
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• pp.80-86
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• 1992

The nucleotide sequences of 185 rRNAs of the five Korean decapods were partially determined by the direct sequencing method using the reverse transcriptase. ne average GC content of five species was 51.1% which is higher than that of yeast(45.0%) and lower than those of frog (53.0%) and rat (55.6%). This result follows the general patterns of the GC content in the nucleotides of the nucleic acid shown among the various phylogenetic groups. The average ratio of transrional/transversional nucleotide substitution of pairwise comparison among six species (including Anemia salina) was 1.200 $\pm$ 0.310 when whole region alas examined. However, the ratio showed some differences when the conservative regions and variable regions frere separatelv examined. The molecular phylogenies of the five species were constructed by using two different tree making methods. In general the results support the previously reported molecular phylogeny of the decapod crustaceans. However, our results indicate thats in the analysis of the sequence dat3, the UPGMA clustering method of the distance matrix method should be carefully employed after considering the rate of nucneotide substitution in the different regions of the molecule.