• Genomics & Informatics
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• v.21 no.3
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• pp.35.1-35.12
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• 2023

The Bacillus cereus group, also known as B. cereus sensu lato (B. cereus s.l.), is composed of various Bacillus species, some of which can cause diarrheal or emetic food poisoning. Several emerging highly heat-resistant Bacillus species have been identified, these include B. thermoamylovorans, B. sporothermodurans, and B. cytotoxicus NVH 391-98. Herein, we performed whole genome analysis of two thermotolerant Bacillus sp. isolates, Bacillus sp. B48 and Bacillus sp. B140, from an omelet with acacia leaves and fried rice, respectively. Phylogenomic analysis suggested that Bacillus sp. B48 and Bacillus sp. B140 are closely related to B. cereus and B. thuringiensis, respectively. Whole genome alignment of Bacillus sp. B48, Bacillus sp. B140, mesophilic strain B. cereus ATCC14579, and thermophilic strain B. cytotoxicus NVH 391-98 using the Mauve program revealed the presence of numerous homologous regions including genes responsible for heat shock in the dnaK gene cluster. However, the presence of a DUF4253 domain-containing protein was observed only in the genome of B. cereus ATCC14579 while the intracellular protease PfpI family was present only in the chromosome of B. cytotoxicus NVH 391-98. In addition, prophage Clp protease-like proteins were found in the genomes of both Bacillus sp. B48 and Bacillus sp. B140 but not in the genome of B. cereus ATCC14579. The genomic profiles of Bacillus sp. isolates were identified by using whole genome analysis especially those relating to heat-responsive gene clusters. The findings presented in this study lay the foundations for subsequent studies to reveal further insights into the molecular mechanisms of Bacillus species in terms of heat resistance mechanisms.

• Journal of Animal Science and Technology
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• v.66 no.4
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• pp.859-862
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• 2024

It has been reported that the administration of Limosilactobacillus fermentum alleviates diseases such as osteoporosis and colitis. In this study, we report the complete genome sequence of Limosilactobacillus fermentum KUFM407, a probiotic strain of LAB isolated from Korean traditional fermented food, Kimchi. Whole genome sequencing of L. fermentum KUFM407 was performed on the Illumina MiSeq and Oxford Nanopore MinION platform. The genome consisted of one circular chromosome (2,077,616 base pair [bp]) with a guanine cytosine (GC) content of 51.5% and one circular plasmid sequence (13,931 bp). Genome annotation identified 1,932 protein-coding genes, 15 rRNAs, and 58 tRNAs in the assembly. The function annotation of the predicted proteins revealed genes involved in the biosynthesis of bacteriocin and fatty acids. The complete genome of L. fermentum KUFM407 could provide valuable information for the development of new probiotic food and health supplements.

• Microbiology and Biotechnology Letters
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• v.52 no.1
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• pp.102-104
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• 2024

Massilia sp. KACC 81254BP, isolated from a landfill on Jeju Island, Republic of Korea, possesses the capability to degrade polyhydroxyalkanoates (PHAs). The genomic analysis of strain KACC 81254BP consists of a circular chromosome comprising 5,028,452 base pairs with a DNA G+C content of 64.6%. This complete genome consists of a total of 4,513 genes, including those encoding the PHA degradation enzyme (PhaZ). This study offers valuable genomic insights into the enzymes responsible for degrading polyester plastics.

• Development and Reproduction
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• v.4 no.1
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• pp.79-85
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• 2000

This study was made to optimize the conditions needed to produce two types of gynogenetic diploids in the sweet fish, Plecoglossus altivelis. Firstly, ultraviolet (UV) ray doses between 3,000 erg to 14,000 erg/$\textrm{mm}^2$ were tested to inactivate sperm genetically. Based on the appearance of the haploid syndromes in the embryo, a dose of UV ray 6000~7000 erg was required to inactivate sperm genetically. Then, cold shock treatment at 1~2$^{\circ}C$ for 15~30 min were conducted to retain the 2nd polar body in inseminated egg. The best elapsed time before the start of the cold shock was examined between 5~8 min. The experiments in which began 5 min after insemination at 1~2$^{\circ}C$ during 17.5 min gave 21.2％ survival rate and 89.7% normal eyed embryo rate. The gynogenetic diploid produced by suppression of the first cleavage, a considerably high number of heteroploids appeared and high mortality was observed at the metamorphosis stage, so further investigation is needed. The production of gynogenetic diploids were confirmed by GPI isozyme marker. The heterozygous type in Gpi-1 locus was observed in the meiotic-G2N as a result of gene-centromere recombination during meiosis. The heterozygous type was never observed in mitotic-G2N and showed segregation into two homozygous types at Gpi-1 locus.

• Journal of Embryo Transfer
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• v.23 no.4
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• pp.269-274
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• 2008

The purpose of this study was to determine the effects of Taxol pre-treatment to in vitro matured bovine oocytes, and sucrose and trehalose added to vitrification solution on spindle morphology and embryonic development following cryopreservation. Bovine oocytes were collected from ovaries and matured in tissue culture medium 199 (TCM 199) supplemented with 10% Fetal Bovine Serum (FBS), 0.05ng/ml epidermal growth factor, 0.01 IU/ml luteinizing hormone and $1{\mu}g/ml$ estradiol for 22h in $39^{\circ}C$, 5% $CO_2$, TCM 199-HEPES containing 20% FBS was used as basic medium (BM) to prepare vitrification solution. Oocytes were pre-treated with $1\;{\mu}M$ Taxol in maturation medium for 15 min prior to vitrification. Oocytes were exposed to 1.6 M ethylene glycol (EG) and 1.3M dimethyl sulfoxide (DMSO) in BM and then were exposed to 3.2 M EG, 2.6 M DMSO and 0.5 M sucrose in BM or 3.2 M EG, 2.6 M DMSO and 0.5 M trehalose in BM. Oocytes with cumulus cells and oocytes without cumulus cells were considered as control 1 and control 2, respectively and held in TCM 199-HEPES at $39^{\circ}C$. Oocytes were frozen using modified solid surface vitrification and were stored in cryotubes in liquid nitrogen for more than 1 week. Frozen oocytes were thawed in TCM 199-HEPES containing 0.5 M, 0.25 M and 0.1 M sucrose in BM for 2 min, respectively or 0.5 M, 0.25 M and 0.1 M trehalose in BM for 2 min, respectively. Immunoflurorescence staining of oocytes was performed to assess spindle morphology and chromosome configuration of oocytes. The rates of cleavage and blastocyst were examined following in vitro fertilization. Normal spindle morphology rate of oocytes pre-treated with Taxol prior to vitrification was not higher than that of other vitrified groups. Taxol pre-treatment did not increase cleavage and blastocyst formation rates, although control groups showed significantly higher rates (p<0.05). Percentages of normal spindle and embryonic development were not significantly different among vitrified groups regardless of type of sugar. In conclusion, Taxol pre-treatment of oocytes before cryopreservation did not reduce the damage induced by vitrification and subsequently did not improve embryonic development following vitrification. Trehalose may be used as an alternative non-permeating cryoprotectant in vitrification solution.

• Toxicological Research
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• v.24 no.1
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• pp.69-78
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• 2008

Mutant mouse which show dwarfism has been developed by N-ethyl-N-nitrosourea (ENU) mutagenesis using BALB/c mice. The mutant mouse was inherited as autosomal recessive trait and named Small Body Size (SBS) mouse. The phenotype of SBS mouse was not apparent at birth, but it was possible to distinguish mutant phenotype from normal mice 1 week after birth. In this study, we examined body weight changes and bone mineral density (BMD), and we also carried out genetic linkage analysis to map the causative gene(s) of SBS mouse. Body weight changes were observed from birth to 14 weeks of age in both affected (n = 30) and normal mice (n = 24). BMD was examined in each five SBS and normal mice between 3 and 6 weeks of age, respectively. For the linkage analysis, we produced backcross progeny [(SBS${\times}$C57BL/6J) $F_1{\times}$ SBS] $N_2$ mice (n = 142), and seventy-four microsatellite markers were used for primary linkage analysis. Body weight of affected mice was consistently lower than that of the normal mice, and was 43.7% less than that of normal mice at 3 weeks of age (P < 0.001). As compared with normal mice at 3 and 6 weeks of age, BMD of the SBS mice was significantly low. The results showed 15.5% and 14.1 % lower in total body BMD, 15.3% and 8.7% lower in forearm BMD, and 29.7% and 20.1% lower in femur BMD, respectively. The causative gene was mapped on chromosome 10. The map order and the distance between markers were D10Mit248 - 2.1 cM - D10Mit51 - 4.2 cM - sbs - 0.7 cM - D10Mit283 - 1.4cM - D10Mit106 - 11.2cM - D10Mit170.

• Korean Journal of Plant Tissue Culture
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• v.22 no.5
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• pp.261-266
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• 1995

This study was carried out to develop new varieties which are dwarf and tolerant to winter cold in the Aurantioideae by intergeneric crossing. to do that, the reciprocal crosses of Hwanggeumyooza and trifoliate orange, yooza and trifoliate orange were done and in vitro immature ovule culture of their hybrid was carried out .The callus formation from immature ovule was good in order of Hwanggeumyooza, Hwanggeumyooza $\times$ tifoliate orange, yooza, and trifoliate orange and best at 1 to 3 mg/L NAA+0.5mg/L zeatin on MT medium. In vitro germination percentage of 20week old hybrid of Hwanggeumyooza $\times$ tifoliate orange and trifoliate orange $\times$ Hwanggeumyooza were 41.3% and 37.7, respectively. The phenotype of hybrid (95%) of Hwanggeumyooza $\times$ trifoliate orange and that (100%) of trifoliate orange $\times$ Hwanggeumyooza were similar to that of trifoliate orange. After Hwanggeumyooza was pollinated by pollens of trifoliate orange, the pollen tubes grew on stigma after 3h of pollination and entered into micropyle after about 24~28 h. One gamete in pollen was fused with polar nuclei after 2 days and other one fused with egg nucleus at 3days after pollination. The fruit set percentage by intergeneric crossing was 14.0% in Hwanggeumyooza $\times$ trtfoliate orange and 17.5% in trifoliate orange $\times$ Hwanggeumyooza. The fruit set percentages of Hwanggeumyooza. and trifoliate orange were 34.2% and 39.5% by artificial self-fertilization, 34.2% and 39.5% by artificial cross fertilization, 3.1% and 1.4% by parthenocarpy and 13.0% and 3.0% by natural fertilization, respectively. The somatic and gametic chromosome numbers of Hwanggeumyooza, yooza, and trifoliate orange were 2n=18 and n=9.

• Journal of Korean Society of Forest Science
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• v.101 no.2
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• pp.291-296
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• 2012

Triploids are a useful tool for biomass production and molecular breeding of trees with a long life span. Triploids of the poplar 'Hyunsasi' (Populus alba ${\times}$ P. glandulosa) have been developed by crossing between female diploids and a male tetraploid. The tetraploid was developed around the 1970s at Korea Forest Research Institute by colchicine-induced chromosome doubling. Seedlings of the $F_1$ generation were analyzed using flow cytometry to verify their ploidy status. The mean relative fluorescence index of 3 F1 poplars, labeled as Line- 1, Line-17, Line-18, were approximately 1.5 times higher than those of diploid poplars, and the results clearly indicated that they were triploids. The phenotype of the F1 poplars included larger leaves and thicker stem than diploids, and abnormal leaf morphology, especially in the triploid 'Line-18'. Three triploid lines developed roots more slowly and had less roots than diploid. However, 3 poplar cytotypes (2x, Line-1, Line-17) rooted within 10 days on MS medium. In contrast, compared with the 3 cytotypes, the Line-18 showed about 80% and 70% in the rooting rate and the number of roots. The triploid poplars could be directly utilized for biomass production and with their sterility, they could serve as basic material for genetic transformation. In addition, flow cytometric analysis proved to be an effective and reliable method for screening forest trees for their ploidy level.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.10
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• pp.1565-1574
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• 2018

Objective: The aim of the present study was to identify genetic variants based on RNA-seq data, obtained via transcriptome sequencing of muscle tissue of pigs differing in muscle histological structure, and to verify the variants' effect on histological microstructure and production traits in a larger pig population. Methods: RNA-seq data was used to identify the panel of single nucleotide polymorphisms (SNPs) significantly related with percentage and diameter of each fiber type (I, IIA, IIB). Detected polymorphisms were mapped to quantitative trait loci (QTLs) regions. Next, the association study was performed on 944 animals representing five breeds (Landrace, Large White, Pietrain, Duroc, and native Puławska breed) in order to evaluate the relationship of selected SNPs and histological characteristics, meat quality and carcasses traits. Results: Mapping of detected genetic variants to QTL regions showed that chromosome 14 was the most overrepresented with the identification of four QTLs related to percentage of fiber types I and IIA. The association study performed on a 293 longissimus muscle samples confirmed a significant positive effect of transforming acidic coiled-coil-containing protein 2 (TACC2) polymorphisms on fiber diameter, while SNP within forkhead box O1 (FOXO1) locus was associated with decrease of diameter of fiber types IIA and IIB. Moreover, subsequent general linear model analysis showed significant relationship of FOXO1, delta 4-desaturase, sphingolipid 1 (DEGS1), and troponin T2 (TNNT2) genes with loin 'eye' area, FOXO1 with loin weight, as well as FOXO1 and TACC2 with lean meat percentage. Furthermore, the intramuscular fat content was positively associated (p<0.01) with occurrence of polymorphisms within DEGS1, TNNT2 genes and negatively with occurrence of TACC2 polymorphism. Conclusion: This study's results indicate that the SNP calling analysis based on RNA-seq data can be used to search candidate genes and establish the genetic basis of phenotypic traits. The presented results can be used for future studies evaluating the use of selected SNPs as genetic markers related to muscle histological profile and production traits in pig breeding.

• Journal of Life Science
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• v.15 no.4 s.71
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• pp.513-521
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• 2005

A bacterium producing five fibrinolytic isozymes was isolated from black bean chung kuk. The bacterium was identified as Bacillus subtilis BB-1 by 16s rDNA sequence homology search. A gene out of five fibrinolytic genes in the Bacillus subtilis BB-1 was cloned by shot-gun method. A Cla I DNA fragment of B. subtilis BB-1 chromosome was cloned in to pBluescript II SK(-) and showed the fibrinolytic activity to bacterial cells. The Cla I DNA fragment was sequenced and the sequences did not show homology with gene for protease or fibrinolytic enzyme genes in other organisms. The Cla I DNA fragment was reduced to 2,142 bp by activity-guided PCR cloning method. The optimum pH and temperature of the enzyme were 5.0 and $35^{\circ}C$, respectively. Substrate specificity of the fibrinolytic enzyme was detected in skim milk, casein, gelatin and blood agar plates. The activity of the enzyme was not detected with these substrates. Taken together, this enzyme is a new fibrinolytic enzyme and may be used to prevent thrombosis and arteriosclerosis.