• Microbiology and Biotechnology Letters
• /
• v.51 no.3
• /
• pp.303-305
• /
• 2023

In this study, we report the complete genome sequence of Priestia megaterium strain HyangYak-01, which was isolated from the rhizosphere soil of Centella asiatica. The genome consists of 5,086,279 bp of sequences with 38.2 percent GC content and 5,111 coding genes. The genome contains several important genes related to plant growth-promoting activities, which were also confirmed with in vitro media assays.

• Proceedings of the Korean Society of Applied Pharmacology
• /
• 1993.11a
• /
• pp.39-40
• /
• 1993

Hepatitis B virus (HBV)is a member of the Hepadna virus family whose members share a characteristic virion structure and genome size, around 3.2kb in a paritially double-stranded form. The genome of HBV contains four overlapping open reading frames designated as P(polymerase). C(core), S(surface antigen)and X. The X gene has potential to encode 154 amino acids protein.

• Genomics & Informatics
• /
• v.17 no.4
• /
• pp.43.1-43.5
• /
• 2019

Lactobacillus acidophilus UBLA-34, L. paracasei UBLPC-35, L. plantarum UBLP-40, and L. reuteri UBLRU-87 were isolated from different varieties of fermented foods. To determine the probiotic safety at the strain level, the whole genome of the respective strains was sequenced, assembled, and characterized. Both the core-genome and pan-genome phylogeny showed that L. reuteri was closest to L. plantarum than to L. acidophilus, which was closest to L. paracasei. The genomic analysis of all the strains confirmed the absence of genes encoding putative virulence factors, antibiotic resistance, and the plasmids.

• Plant Biotechnology Reports
• /
• v.5 no.4
• /
• pp.317-322
• /
• 2011

We determined the nuclear DNA content (genome size) of over 35 accessions each of bamboo and rattan species from Southeast Asia. The 2C DNA per nucleus was quantified by flow cytometry. The fluorescence of nuclei isolated from the leaves and stained with propidium iodide was measured. The genome size of the bamboo species examined was between 2.5 and 5.9 pg DNA per 2C nucleus. The genome size of the rattan species examined ranged from 1.8 to 10.5 pg DNA per 2C nucleus. This information will be useful for scientists working in diverse areas of plant biology such as biotechnology, biodiversity, genome analysis, plant breeding, physiology and molecular biology. Such data may be utilized to attempt to correlate the genome size with the ploidy status of bamboo species in cases where ploidy status has been reported.

• Genomics & Informatics
• /
• v.11 no.1
• /
• pp.38-45
• /
• 2013

In cancer genome studies, the annotation of newly detected oncogene/tumor suppressor gene candidates is a challenging process. We propose using concept lattice analysis for the annotation and interpretation of genes having candidate somatic mutations in whole-exome sequencing in acute myeloid leukemia (AML). We selected 45 highly mutated genes with whole-exome sequencing in 10 normal matched samples of the AML-M2 subtype. To evaluate these genes, we performed concept lattice analysis and annotated these genes with existing knowledge databases.

• Journal of Animal Science and Technology
• /
• v.63 no.6
• /
• pp.1411-1422
• /
• 2021

Lactobacillus acidophilus is a gram-positive, microaerophilic, and acidophilic bacterial species. L. acidophilus strains in the gastrointestinal tracts of humans and other animals have been profiled, but strains found in the canine gut have not been studied yet. Our study helps in understanding the genetic features of the L. acidophilus C5 strain found in the canine gut, determining its adaptive features evolved to survive in the canine gut environment, and in elucidating its probiotic functions. To examine the canine L. acidophilus C5 genome, we isolated the C5 strain from a Korean dog and sequenced it using PacBio SMRT sequencing technology. A comparative genomic approach was used to assess genetic relationships between C5 and six other strains and study the distinguishing features related to different hosts. We found that most genes in the C5 strain were related to carbohydrate transport and metabolism. The pan-genome of seven L. acidophilus strains contained 2,254 gene families, and the core genome contained 1,726 gene families. The phylogenetic tree of the core genes in the canine L. acidophilus C5 strain was very close to that of two strains (DSM20079 and NCFM) from humans. We identified 30 evolutionarily accelerated genes in the L. acidophilus C5 strain in the ratio of non-synonymous to synonymous substitutions (dN/dS) analysis. Five of these thirty genes were associated with carbohydrate transport and metabolism. This study provides insights into genetic features and adaptations of the L. acidophilus C5 strain to survive the canine intestinal environment. It also suggests that the evolution of the L. acidophilus genome is closely related to the host's evolutionary adaptation process.

• Korean Journal of Plant Resources
• /
• v.33 no.5
• /
• pp.536-549
• /
• 2020

Soybean (Glycine max (L.) Merrill) is one of the most important crops of the world. With the completion of the soybean genome sequence, the Korean soybean core collection consisted of 430 accessions with genetic and phenotypic diversity was constructed in recent year. The availability of genome sequences and core collection will result in the crop improvement by molecular breeding using the various accessions and genome editing approaches. Efficient tissue culture techniques, such as haploid production, protoplast culture and plant regeneration from various organs are essential for the successful molecular biological approach and crop improvement. However, soybean is still considered to be recalcitrant in tissue culture because of the low frequency of regeneration and limitation of available responsive cultivars. In this study, we discuss the recent studies of tissue culture technology and methodology for efficient tissue culture to genetic improvement and application of molecular biotechnology in soybean.

• Microbiology and Biotechnology Letters
• /
• v.52 no.3
• /
• pp.328-330
• /
• 2024

Listeriosis is one of serious foodborne disease caused mainly by consumption of food contaminated with Listeria monocytogenes. In this study, we isolated L. monocytogenes strain IJPL9-1 from pork in Korea and conducted whole-genome sequencing (WGS). WGS data revealed a single chromosome of 2,913,085 bp. The strain was identified as sequence type (ST) 224, clonal complex (CC) 224, lineage I, and sub-lineage (SL) 6178 based on multilocus sequence typing (MLST) and core genome MLST (cgMLST). The average nucleotide identity was 95.15% with the reference genome EGD-e and 99.99% with FSCNU_000110, the outbreak strain in Korea in 2018. The serogroup was determined to be IIb, and the presence of antimicrobial resistance genes fosX, vga(G), mprF, norB, and sul was determined.

• International Journal of Industrial Entomology and Biomaterials
• /
• v.2 no.1
• /
• pp.87-89
• /
• 2001

The nucleotide sequence of the domestic silkworm (Bombyx mori) mitochondrial (mt) control region and its flanking genes was determined from PCR clones. The control region of the silkworm mt genome was located between the small ribosomal RNA gene and transfer RN $A^{Met}$. This 499 bp control region hale 95.4% A+T content. Extensive comparative analysis studies performed with similar control region of other insect genomes could not reveal a highly conserved region containing conserved motifs of animal mito-chondrial genome. The remarkable feature that found in this control region was the presence of tandem motifs containing nine repetitive sequences. The potential usefulness of this motif sequences for Bombyx species or their taxonomically related species is enhanced by its unique localization in the maternally inheritance mitochondrial molecule.e.

• Genomics & Informatics
• /
• v.8 no.1
• /
• pp.28-33
• /
• 2010

Increased exposure of human to RF fields has raised concerns for its potential adverse effects on our health. To address the biological effects of RF radiation, we used genome wide gene expression as the indicator. We exposed normal WI-38 human fibroblast cells to 1763 MHz mobile phone RF radiation at a specific absorption rate (SAR) of 60 W/kg with an operating cooling system for 24 h. There were no alterations in cell numbers or morphology after RF exposure. Through microarray analysis, we identified no differentially expressed genes (DEGs) at the 0.05 significance level after controlling for multiple testing errors with the Benjaminiochberg false discovery rate (BH FDR) method. Meanwhile, 82 genes were differentially expressed between RF-exposed cells and controls when the significance level was set at 0.01 without correction for multiple comparisons. We found that 24 genes (0.08% of the total genes examined) were changed by more than 1.5-fold on RF exposure. However, significant enrichment of any gene set or pathway was not observed from the functional annotation analysis. From these results, we did not find any evidence that non-thermal RF radiation at a 60-W/kg SAR significantly affects cell proliferation or gene expression in WI-38 cells.