• Journal of Microbiology and Biotechnology
• /
• v.11 no.3
• /
• pp.515-523
• /
• 2001

The dinoflagellates have some primitive nuclear features and are evolutionarily intermediate between prokaryotes and eukaryotes. The small subunit ribosomal RAN gene, the 5.8S ribosomal RNA gene, and the internal transcribed spacer (ITS) of Gonyaulax polyedra were cloned, and their sequences were analyzed to better understand their evolutionary position. The small subunit ribosomal RNA gene was 1,794 nt long, the large subunit ribosomal RNA gene was approximately 3,500 nt long, and the 5.8S ribosomal RNA gene was 159 nt long. The first internal transcribed spacer (ITS1) was 191 nt long, and the second internal transcribed spacer (ITS2) was 185 nt long. The intergenic spacer of the ribosomal RNA gene (IGS) was about 2,200 nt long, indicating that 5,800 nt of transcribed sequences were separated by roughly 2,200 nt of intergenic spacer. The ribosomal RNA genes were repeated many times and arranged in a head-to-tail, tandemly repeated manner. The repeating unit of ribosomal RNA gene of G. polyedra was proposed to be 8,000 nt long. Based on the lengths of ribosomal RNA, sequence alignments with representative organisms, and phylogenetic analysis on ribosomal RNA, G. polyedra appears to be one of the alveolates branched from the eukaryotic crown and, among dinoflagellates, it seems to not have emerged early.

• Asian-Australasian Journal of Animal Sciences
• /
• v.22 no.10
• /
• pp.1429-1436
• /
• 2009

Adiponectin is an adipocyte-derived protein that has a regulatory role in energy homeostasis and influences insulin sensitivity. Its effects on glucose utilization and lipid metabolism are mediated by AdipoR1 and AdipoR2. How insulin affects adiponectin gene expression and secretion is still controversial. This study was conducted to determine the expression of adiponectin, AdipRs and $PPAR-\gamma$ during the differentiation of bovine preadipocytes and the effect of insulin on expression of these genes in bovine adipocytes. The bovine preadipocytes started to accumulate lipids three days after differentiation was induced, with increased expression of adiponectin, AdipoR2 and $PPAR-\gamma$ mRNAs. Insulin decreased the expression of adiponectin mRNA in a dose- and time-dependent fashion, and the inhibition was detectable at insulin concentrations as low as 10 nM and as early as 2 h after addition of 100 nM insulin. Insulin also inhibited the expression of AdipoR2 mRNA at concentrations from 1 to 1,000 nM or 24 h after addition of 100 nM insulin, but did not affect the expression of AdipoR1 in bovine adipocytes. Inhibition of PI3K with LY294002 reversed the inhibition of adiponectin and AdipoR2 mRNA expression by insulin. These results suggest that insulin suppresses the expression of adiponectin and AdipoR2 at least partially via the PI3K signal pathway.

• Asian Pacific Journal of Cancer Prevention
• /
• v.16 no.17
• /
• pp.7589-7594
• /
• 2015

Background: MicroRNAs (miRNAs) are small non-coding RNA molecules, implicated in several activities like initiation, progression and prognosis of various cancers. Single nucleotide polymorphisms (SNPs) in miRNA genes can lead to alteration in mRNA expression, resulting in diverse functional consequences. The aim of our study was to investigate the association of miR-149C>T and miR-196a2C>T SNPs with susceptibility to development of oral squamous cell carcinoma (OSCC) in South Indian subjects. Materials and Methods: 100 OSCC patients and 102 healthy controls from the general population were recruited for the study. Genetic analysis was performed by polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP) as per a standard protocol. Results: The genotype frequencies in miR-196a2 polymorphism, of TT, CT and CC in the OSCC patients were 69%,10% and 22% respectively while for control group it was 80%, 15% and 5% respectively. The CC genotype of miR196a2 polymorphism was significantly associated with oral squamous cell carcinoma. The genotype frequencies in miR-149 polymorphisms of CC, CT and TT in the oral squamous cell carcinoma (OSCC) patients were 72%, 22% and 6% respectively and for control group 88%, 12% and 0% respectively. CT and TT genotypes of miR149 polymorphism were found to be significantly associated with OSCC (p = 0.05 and 0.07). Conclusions: Our study suggests that miR-196a2C>T and miR-149C>T polymorphisms may play crucial roles in the development of OSCC in South Indian subjects.

• Journal of Embryo Transfer
• /
• v.25 no.2
• /
• pp.127-131
• /
• 2010

The objective of this study was to determine the mRNA expression patterns of several putative imprinted genes in in vivo and in vitro fertilized, parthenogenetic, and cloned porcine preimplantation embryos. Both maternally (Dlk1, IGF2, Peg1/Mest and Ndn) and paternally (IGF2r, H19 and Xist) imprinted genes were selected. We have used reverse transcription polymerase chain reaction (RT-PCR) to investigate gene expression patterns in the porcine embryos. IGF2 transcripts were detected in the most of embryos. In nuclear transfer (NT), Peg1/MEST transcripts showed fluctuating pattern. Dlk1 was only expressed partially from the morula and blastocyst stage of NT embryos. Ndn gene expression was started somewhat early for in vivo embryos. However, the expressions of maternally imprinted genes were similar in all types of blastocysts (NT, in vivo and in vitro fertilized, and parthenogenetic embryos). The IGF2R gene expression level was somewhat irregular and varied among samples. However, for the majority samples of all types of embryos, IGF2R expression was diminished after one- to two-cell stages and reappeared at the morulae or blastocyst stage embryos. H19 gene was only expressed early in parthenogenetic and in vivo embryos. For NT embryos, H19 was only expressed in blastocysts. Xist expression was detected in all blastocysts with the earliest being in vivo 8-cell stage embryos and the last one being NT blastocysts. These putative imprinted genes appeared to have stage specific expression patterns with a fluctuating pattern for some genes (Peg/Mest, IGF2r, H19). These results suggest that stage specific presence of imprinted genes can affect the embryo implantation and fetal development.

• Journal of Life Science
• /
• v.22 no.2
• /
• pp.232-238
• /
• 2012

Kumjungsansung-Makgeolli$^{(R)}$ is a traditional Korean rice wine that is fermented from traditional nuruk and rice. In this study, we performed the PCR-denaturing gradient gel electrophoresis (DGGE) analysis targeting the 16S and 28S rRNA genes to characterize bacterial and fungal diversity during Makgeolli fermentation. The predominant bacteria in the PCR-DGGE profile during Makgeolli fermentation were Lactobacillus spp. (Lactobacillus curvatus, L. kisonensis, L. plantarum, L. sakei, and L. gasseri), Pediococcus spp. (P. acidilactici, P. parvulus, P. agglomerans, and P. pentosaceus), Pantoea spp. (P. agglomerans and P. ananatis), and Citrobacter freundii; these were identified on the base of analysis of 16S rRNA gene sequences. The dominant bacterium during Makgeolli fermentation was L. curvatus. The predominant fungi in PCR-DGGE profile during Makgeolli fermentation were Pichia kudriavzevii, Saccharomyces cerevisiae, Asidia idahoensis, Kluyveromyces marxianus, Saccharomycopsis fibuligera, and Torulaspora delbrueckii, and these were identified on the basis of analysis of 28S rRNA gene sequences. The dominant fungal species during Makgeolli fermentation changed from P. kudriavzevii at 0-2 days incubation to S. cerevisiae at 3-6 days incubation. This study suggests that PCR-DGGE analysis could be a suitable tool for the understanding of microbial diversity and structure during Makgeolli fermentation.

• Korean Journal of Environmental Biology
• /
• v.21 no.1
• /
• pp.77-85
• /
• 2003

We have examined the 16S-23S rRNA intergenic spacer regions (ISR) of Vibrio fluvialis. ISRs were PCR amplified, cloned into a plasmid vector and then sequenced. As results of ISR nucleotide sequence analysis, total of 6 clones were isolated depending on the size. The clones were different in both the number and the composition of the tRNA genes, and were designated ISR-A, ISR-E, ISR-El, ISR-lA, ISR-EKV, ISR-EKAV. ISR-A contains $tRNA^{Ala}$; ISR-lA, $tRNA^{Ile}$-$tRNA^{Ala}$; ISR-EKV, $tRNA^{GIu}$-$tRNA^{Lys}$-$tRNA^{Val}$;ISE-EKAV, $tRNA^{GIu}$-$tRNA^{Lys}$-$tRNA^{Ala}$-$tRNA^{Val}$; ISR -E and E1, $tRNA^{GIu}$ clusters. ISR-EKV was shown to be a minor type out of the six ISR types and showed a very limited homology between ISR-EKV from V, fluvialis and ISRa from other Vibrio species. Therefore ISR-EKV sequence was used to design species-specific primers to detect V, fiuvialis from other Vibrio species by PCR reaction. The specificity of the primers was examined using genomic DNA of other Vibrios as templates for PCR reaction. The result showed that PCR can be a useful method to detect V. fluvialis among Vibrio species in a single PCR reaction.

• Korean Journal of Fisheries and Aquatic Sciences
• /
• v.48 no.5
• /
• pp.731-738
• /
• 2015

Nematode infection in the epithelial tissue of cultured rockfish Sebastes schlegeli was first reported in 2012. Since then, nematode infections have caused serious economic losses in rockfish aquaculture on the west coast of Korea. Taxonomic and life cycle information for this parasite are currently unknown. In this study, 18S rRNA and cytochrome c oxidase subunit I (COI) genes were used for molecular identification and polymerase chain reaction (PCR) to detect the invisible stages of this parasite. Nucleotide sequences of the 18S rRNA of the rockfish nematode showed 98% identity with that of Philometra morii. Therefore, this rockfish nematode was classified to the Philometridae family. However, we could not identify it to genus level using 18S rRNA. Its COI nucleotide sequences shared 85% and 82% identities with those of Bursaphelenchus sinensis and Philometra overstreeti, respectively. In addition, two gene-specific primer sets were designed based on the 18S rRNA gene to detect the intermediate host and nematode larvae. These primers were specific to this rockfish nematode without cross-reacting to other pathogens. The detection limit of the PCR assay using these primers was 1,000 copies of nematoda plasmid DNA. Therefore, the PCR assay described here is suitable for the detection of nematode DNA within rockfish. In addition, this PCR assay could be used to detect nematode larvae and the intermediate host.

• Journal of Microbiology and Biotechnology
• /
• v.27 no.7
• /
• pp.1288-1299
• /
• 2017

Composting is widely used to transform waste into valuable agricultural organic fertilizer. Anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the global nitrogen cycle, but their role in composting remains poorly understood. In the present study, the community structure, diversity, and abundance of anammox bacteria were analyzed using cloning and sequencing methods by targeting the 16S rRNA gene and the hydrazine oxidase gene (hzo) in samples isolated from compost produced from cow manure and rice straw. A total of 25 operational taxonomic units were classified based on 16S rRNA gene clone libraries, and 14 operational taxonomic units were classified based on hzo gene clone libraries. The phylogenetic tree analysis of the 16S rRNA gene and deduced HZO protein sequences from the corresponding encoding genes indicated that the majority of the obtained clones were related to the known anammox bacteria Candidatus "Brocadia," Candidatus "Kuenenia," and Candidatus "Scalindua." The abundances of anammox bacteria were determined by quantitative PCR, and between $2.13{\times}10^5$ and $1.15{\times}10^6$ 16S rRNA gene copies per gram of compost were found. This study provides the first demonstration of the existence of anammox bacteria with limited diversity in cow manure composting.

• Parasites, Hosts and Diseases
• /
• v.59 no.4
• /
• pp.341-353
• /
• 2021

Acanthoparyphium shinanense n. sp. (Digenea: Echinostomatidae) is described from chicks experimentally infected with the metacercariae encysted in 2 brackish water clam species, Ruditapes philippinarum and Coecella chinensis, in the Republic of Korea. The metacercariae were round to oval, armed with 23 collar spines, and 0.216 (0.203-0.226) mm in diameter. From 5 chicks experimentally infected each with 200 metacercariae, 34 juvenile (5-day-old worms) and 104 adult flukes (7-day-old worms) were harvested from their small intestines, with the average worm recovery rate of 13.8%. The adult flukes were 3.18 (2.89-3.55) mm long and 0.68 (0.61-0.85) mm wide, with an elongated, posteriorly tapering body, and a prominent head collar armed with 23 collar spines arranged in a single uninterrupted row. The posterior testis of A. shinanense was longitudinally elongated, which is similar to Acanthoparyphium spinulosum Johnston, 1917 but unique from the other closely related species, including Acanthoparyphium tyosenense Yamaguti, 1939, Acanthoparyphium kurogamo Yamaguti, 1939, and Acanthoparyphium marilae Yamaguti, 1934. The eggs of A. shinanense were larger than those of A. spinulosum, and the anterior extent of 2 lateral groups of vitellaria was slightly more limited in A. shinanense than in A. spinulosum. Molecular analysis of nuclear and mitochondrial genes revealed low homology with A. spinulosum from USA (96.1% in 5.8S rRNA) and Ukraine (97.9% in 28S rRNA), Acanthoparyphium n. sp. from USA (98.0% in 28S rRNA), and Acanthoparyphium sp. from Australia, Kuwait, and New Zealand. Biological characteristics, including its first intermediate host and natural definitive hosts, as well as its zoonotic capability, should be elucidated.

• Korean Journal of Microbiology
• /
• v.54 no.3
• /
• pp.302-304
• /
• 2018

We, for the first time, isolated and identified a Vibrio splendidus KCTC 11899BP producing hyaluronate lyase from seawater. This enzyme is produced only when hyaluronic acid (HA) is added to the basal medium. Hyaluronate lyases are produced by microorganisms, which degrade the ${\beta}$-(1, 4) bond of HA to produce disaccharide. The genome of KCTC 11899BP, which consist of two circular contigs that are 3,522 kb (contig 1) long and 1,986 kb (contig 2) long respectively, as like other Vibrio sp. that contained 2 chromosomes. The genome included 4,700 predicted open reading frames, G + C content 44.12%, 137 tRNA genes, and 46 rRNA genes.