• Korean Journal of Breeding Science
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• v.42 no.2
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• pp.163-168
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• 2010

This study was carried out to determine the chromosomal localization of the 5S and 18S-26S ribosomal DNA(rDNA) genes by means of fluorescence in situ hybridization(FISH) techniques, and the constitutive heterochromatin detected by means of Gimsa C-banding technique in rye(Secale cereale L.). The somatic chromosomes number was 2n=14. The karyotype consists of four pairs of metacentrics(chromosomes 1, 2, 3, and 7) and three pairs of submetacentrics(chromosomes 4, 5, and 6). Secondary constrictions appeared in the short arm of chromosome 1. The 5S rDNA genes have been located on two pairs of chromosomes 1 and 5, and 18S-26S rDNAs genes have been located on one pair of chromosome 1. 5S rDNA genes were detected on the distal region of the secondary constrictions in nucleolus organizer regions(NOR) in chromosome 1, and other detected on the intercalary region in the short arm of chromosome 5.

• Genomics & Informatics
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• v.21 no.4
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• pp.51.1-51.5
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• 2023

The genus Neoarius, known as marine catfish, is a group of the family Ariidae, composed of 10 species found in Oceania. None of the species in this genus have their mitochondrial genome described, which is highly valuable in phylogenetic and molecular evolution studies. For the present work, eight species from the Neoarius genus were selected: Neoarius utarus, Neoarius midgleyi, Neoarius graeffei, Neoarius leptaspis, Neoarius berenyi, Neoarius paucus, Neoarius pectoralis, and Neoarius aff. graeffei. DNA sequences of the eight species were obtained through the NCBI Sequence Read Archive (SRA) database, and the mitochondrial genomes were assembled using the NOVOplasty tool on the Galaxy platform, subsequently annotated with the MitoAnnotator tool. We then utilized the protein-coding genes from the mitogenomes to estimate the phylogenetic relationships within the group, including seven additional mitogenomes available in the NCBI. In all species, the mitochondrial genomes presented 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 D-loop.

• Animal cells and systems
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• v.6 no.2
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• pp.145-151
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• 2002

Phylogenetic signal present in the mitochondrial 16S ribosomal RNA gene (16S rDNA) and the nuclear large subunit ribosomal RNA gene (28S rDNA) was explored to assess their utility in resolving family level relationships of the superfamily Tephritoidea. These two genes were chosen because they appear to evolve at different rates, and might contribute to resolve both shallow and deeper phylogenetic branches within a highly diversified group. For the 16S rDNA data set, the number of aligned sites was 1,258 bp, but 1,204 bp were used for analysis after excluding sites of ambiguous alignment. Among these 1,204 sites, 662 sites were variable and 450 sites were informative for parsimony analysis. For the 28S rDNA data set, the number of aligned sites was 1,102 bp, but 1,000 bp were used for analysis after excluding sites of ambiguous alignment. Among these 1000 sites, 235 sites were variable and 95 sites were informative for parsimony analysis. Our analyses suggest that: (1) while 16S rDNA is useful for resolving more recent phylogenetic divergences, 28S rDNA can be used to define much deeper phylogenetic branches; (2) the combined analysis of the 16S and 28S rDNAs enhances the overall resolution without losing phylogenetic signal from either single gene analysis; and (3) additional genes that evolve at intermediate rates between the 16S and 28S rDNAs are needed to further resolve relationships among the tephritoid families.

• Parasites, Hosts and Diseases
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• v.53 no.4
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• pp.455-463
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• 2015

The present study was performed to compare the mitochondrial genomes between 2 Spirometra tapeworms, Spirometra erinaceieuropaei and Spirometra decipiens (Cestoidea: Diphyllobothriidae), which larval stages are important etiological agents of sparganosis in humans. For each species, the full mitochondrial genome was amplified in 8 overlapping fragments using total genomic DNA purified from a single worm as the template. The mitochondrial genomes were 13,643 bp (S. erinaceieuropaei) and 13,641 bp (S. decipiens) in length and contained 36 genes; 12 protein-coding genes, 2 ribosomal RNA (rRNA, small and large subunits), and 22 transfer RNAs (tRNAs). The 12 protein-coding genes constituted 10,083 bp (S. erinaceieuropaei) and 10,086 bp (S. decipiens) of their respective mitochondrial genomes. The tRNA genes, ranging in length from 56 to 70 bp, were identified based on putative secondary structures such as the typical cloverleaf shape. A total of 23 intergenic sequences, varying from 1 to 204 bp in size, were interspersed in S. erinaceieuropaei (total, 504 bp) and S. decipiens (total, 496 bp) mtDNA. The 12 protein-coding genes of S. erinaceieuropaei and S. decipiens differed by 12.4%, whereas the overall difference in mtDNA sequence between S. erinaceieuropaei and S. decipiens was 12.9%. Thus, from the standpoint of the mitochondrial genome, S. decipiens represents a valid species that can be distinguished from S. erinaceieuropaei.

• International Journal of Industrial Entomology and Biomaterials
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• v.27 no.1
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• pp.185-202
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• 2013

In this study, we present the nearly complete mitogenome sequences of the garden chafer, Polyphylla laticollis manchurica, which is listed as an endangered species in Korea. The P. l. manchurica mitogenome, which includes unfinished whole A+T-rich region and a partial srRNA was 14,473-bp long, possessing typical sets of genes (13 PCGs, 22 tRNA genes, and 2 rRNA genes). Gene arrangement of the P. l. manchurica mitogenome was identical to the common one found in the majority of insects. The 5 bp-long motif sequence (TAGTA) that has been suggested to be the possible binding site for the transcription termination peptide for the major-strand was also found in the P. l. manchurica mitogenome between $tRNA^{Ser}$(UCN) and ND1. The start codon for COI gene and ATPase8 was designated as a typical TTG. All tRNAs of the P. l. manchurica showed a stable canonical clover-leaf structure of other mt tRNAs, except for $tRNA^{Ser}$(AGN), DHU arm of which could not form stable stemloop structure. As has been previously determined, the high A/T content was unanimously observed in P. l. manchurica in terms of A/T bias in the third codon position (73.5%) compared with the first (66.4%) and second codon position (66.2%). The PCGs encoded in major-strands are slightly T-skewed, whereas those of the minor-strand are A-skewed, indicating strand asymmetry in nucleotide composition in the Coleoptera including P. l. manchurica.

• Korean Journal of Microbiology
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• v.44 no.2
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• pp.98-104
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• 2008

We constructed the null mutants of fission yeast Schizosaccharomyces pombe rsml gene that is thought to be involved in mRNA export. Though rsm1 gene is not essential for growth, the null mutant strain constructed by replacing the rsm1-coding region with an $kan^{r}$ gene showed growth retardation and mRNA export defects compared to wild type strain. We constructed double mutants which harbor rsm1 null allele and mutant allele of genes involved in mRNA export. The mex67 or npp106 null allele, when combined with rsm1 null allele, showed an additive effect on growth retardation and mRNA export defects. On the other hand, the thp1 null allele restored the defects of growth and mRNA export of rsm1 null mutant. These results suggest that rsm1 plays a role in mRNA export from the nucleus.

• Journal of Microbiology and Biotechnology
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• v.15 no.2
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• pp.376-383
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• 2005

Alcaligenes sp. JMP228 carrying 2,4­dichlorophenoxyacetic acid (2,4-D) degradative plasmid pJP4 was inoculated into natural soil, and transfer of the plasmid pJP4 to indigenous soil bacteria was investigated with and without 2,4-D amendment. Plasmid pJP4 transfer was enhanced in the soils treated with 2,4-D, compared to the soils not amended with 2,4-D. Several different transconjugants were isolated from the soils treated with 2,4-D, while no indigenous transconjugants were obtained from the unamended soils. Inoculation of the soils with both the donor Alcaligenes sp. JMP228/pJP4 and a recipient Burkholderia cepacia DBO 1 produced less diverse transconjugants than the soils inoculated with the donor alone. Repetitive extragenic palindromic-polymerase chain reaction (REP-PCR) analysis of the transconjugants exhibited seven distinct genomic DNA fingerprints. Analysis of 16S rDNA sequences indicated that the transconjugants were related to members of the genera Burkholderia and Pandoraea. Denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA genes revealed that inoculation of the donor caused clear changes in the bacterial community structure of the 2,4-D­amended soils. The new 16S rRNA gene bands in the DGGE profile corresponded with the 16S rRNA genes of 2,4-D­degrading transconjugants isolated from the soil. The results indicate that introduction of the 2,4-D degradative plasmid as Alcaligenes sp. JMP228/pJP4 has a substantial impact on the bacterial community structure in the 2,4-D-amended soil.

• Korean Journal of Microbiology
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• v.54 no.4
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• pp.471-473
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• 2018

Variovorax sp. PMC12 is a rhizobacterium isolated from tomato rhizosphere and enhanced the plant resistance to abiotic and biotic stresses. Here we present the complete genome sequence of strain PMC12. The genome is comprised of two circular chromosomes harboring 5,873,297 bp and 1,141,940 bp, respectively. A total of 6,436 protein-coding genes, 9 rRNAs, 64 tRNAs, 3 ncRNAs, and 80 pseudogenes were identified. We found genes involved in 1-aminocyclopropane-1-carboxylate (ACC) deaminase, antioxidant activity, phosphate solubilization, and biosynthesis of proline and siderophore. Those genes may be related to capability of improving plant resistance to various stresses including salinity, cold temperature, and phytopathogen.

• Journal of Nutrition and Health
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• v.54 no.5
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• pp.448-458
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• 2021

Purpose: Mulberry (Morus alba L.) fruit is widely grown in Asia and consumed as fresh fruit, jam, and juices. The fruit has beneficial health effects, including anti-diabetic, anti-tumor, and anti-obesity properties. However, the mechanisms by which mulberry fruit juice powder (MJ) regulates inflammatory microRNAs (miRs) are not yet known. This study investigated the effect of mulberry fruit juice powder on the regulation of inflammation and miR-132/143 during 3T3-L1 adipocyte differentiation. Methods: The 3T3-L1 cells were induced to differentiate for 2 days and then treated with various concentrations of MJ for 7 days. Cytotoxicity was determined by evaluating cell viability using a water-soluble tetrazolium salt-8 assay kit. Intracellular lipid accumulation was evaluated by oil-red O staining. The levels of the expression of genes involved in adipogenesis and inflammation, and miR-132/143 were measured by quantitative real-time polymerase chain reactions. Results: MJ showed no cytotoxic effect on 3T3-L1 adipocytes at concentrations below 100 ng/mL. Intracellular lipid accumulation was reduced by MJ treatment at concentrations of 100 ng/mL. The messenger RNA (mRNA) levels of proliferator-activated receptor-γ, cytosine-cytosine-adenosine-adenosine-thymidine/enhancer-binding protein-α, and adipocyte protein 2, which are involved in adipogenesis, were suppressed by MJ. A reduction was also seen in mRNA levels of genes related to the inflammatory response, such as tumor necrosis factor-α, interleukin-6, monocyte chemoattractant protein-1, and inducible nitric oxide synthase. The expression of the inflammatory miR-132 and miR-143 was also decreased by MJ. Conclusion: These results suggest that MJ may suppress adipogenesis and inflammation through the regulation of miR-132/143 expression in 3T3-L1 adipocytes. Thus, MJ may be useful as a food agent that prevents obesity-associated inflammation.

• International Journal of Industrial Entomology and Biomaterials
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• v.2 no.1
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• pp.37-53
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• 2001

Two regions of mtDNA genome, cytochrome oxidase subunit I (COI) and 165 ribosomal RNA (165 rRNA) genes, were sequenced for 15 species of the long-horned beetle belonging to four subfamilies and geographic samples of mulberry longicorn beetle, Apriona germari, from two localities in Korea. Ten samples of A. germari collected from Suwon and Busan revealed three COI haplotypes ranging in nucleotide divergence of 0.3% to 0.5%, and the two populations shared one common COI haplotype (80%). The sequence divergence among 15 species of the long-horned beetle was much higher in COI gene (12.3%∼39.4%) than 16S rRNA gene (7.2% to 23.1), and the maximum value in the COI gene is exceptional compared with other relevant studies, including that of Coleoptera. The greatly increased divergence in the COI gene, in facto was stemmed from a peculiar sequence of Prionus insularis belonging to Prioninne, divergence of which ranges from 31.2% to 39.3% from other species. We discussed possible reason of the divergence in this species. Due to the abnormality of COI gene divergence, decrease in phylogenetic signal was severe in COI nucleotide and, subsequently, the converted amino acid sequences, rendering us to put more confidence on the 16S5 rRNA gene data. Although the molecular phylogeny confidently supports the monophyletic origin of Lepturinae, the presence of discrepancy between molecular data and traditional taxonomic views also is a testable hyothesis. One such discrepancy includes taxonomic position of Sophronica obrioides and Theophilea cylindricollis belonging to Lamiinae.