• Ocean Science Journal
• /
• 제41권4호
• /
• pp.315-318
• /
• 2006

Three Synechococcus strains were isolated from seawater near the Ieodo Ocean Research Station (IORS), and their 16S rDNA genes and the internal transcribed spacer (ITS) between the 16S and 23S rRNA genes were sequenced to investigate their phylogenetic relationships. Phylogenetic trees based on the 16S rDNA and ITS sequences showed that they clustered in the main MC-A Synechococcus group (subcluster 5.1), but formed branches differentiating them from the described clades. As the IORS is located in an area affected by diverse water masses, high Synechococcus diversity is expected in the area. Therefore, the IORS might be a good site to study the diversity, physiology, and distribution of the Synechococcus group.

• Journal of Microbiology and Biotechnology
• /
• 제24권12호
• /
• pp.1609-1621
• /
• 2014

The plant pathogen Burkholderia gladioli, which has a broad host range that includes rice and onion, causes bacterial panicle blight and sheath rot. Based on the complete genome sequence of B. gladioli BSR3 isolated from infected rice sheaths, the genome of B. gladioli BSR3 contains the luxI/luxR family of genes. Members of this family encode N-acyl-homoserine lactone (AHL) quorum sensing (QS) signal synthase and the LuxR-family AHL signal receptor, which are similar to B. glumae BGR1. In B. glumae, QS has been shown to play pivotal roles in many bacterial behaviors. In this study, we compared the QS-dependent gene expression between B. gladioli BSR3 and a QS-defective B. gladioli BSR3 mutant in two different culture states (10 and 24 h after incubation, corresponding to an exponential phase and a stationary phase) using RNA sequencing (RNA-seq). RNA-seq analyses including gene ontology and pathway enrichment revealed that the B. gladioli BSR3 QS system regulates genes related to motility, toxin production, and oxalogenesis, which were previously reported in B. glumae. Moreover, the uncharacterized polyketide biosynthesis is activated by QS, which was not detected in B. glumae. Thus, we observed not only common QS-dependent genes between B. glumae BGR1 and B. gladioli BSR3, but also unique QS-dependent genes in B. gladioli BSR3.

• Journal of Microbiology and Biotechnology
• /
• 제19권3호
• /
• pp.271-276
• /
• 2009

Functional gene studies in the cultivated white button mushroom Agaricus bisporus have been constrained by the absence of effective gene-silencing tools. Using two endogenous genes from A. bisporus, we have tested the utility of dsRNA hairpin constructs to mediate downregulation of specific genes. Hairpin constructs for genes encoding orotidine 5'-monophosphate decarboxylase (URA3) and carboxin resistance (CBX) were introduced into A. bisporus using Agrobacteriummediated transfection. Although predicted changes in phenotype were not observed in vitro, quantitative-PCR analyses indicated unambiguously that transcripts in several transformants were substantially reduced compared with the non-transformed controls. Interestingly, some hairpin transformants exhibited increased transcription of target genes. Our observations show that hairpin transgenic sequences can mediate downregulation of A. bisporus endogenous genes and that the technology has the potential to expedite functional genomics of the mushroom.

• Journal of mucopolysaccharidosis and rare diseases
• /
• 제1권2호
• /
• pp.54-59
• /
• 2015

Purpose: Growth hormone (GH) therapy substantially improves several cognitive functions in PWS. However, the molecular mechanisms underlying the beneficial effects of GH on cognition remain unclear in PWS. In this study, we investigated the effects of recombinant human GH on the gene expression of GABAB receptor subunits and GH/insulin-like growth factor (IGF) axis genes in the brain regions of PWS-mimicking mice (Snord116del). Methods: Snord116del mice were injected subcutaneously with 1.0 mg/kg GH or saline, once daily for 7 days. The collected brain tissues were analyzed for mRNA content using quantitative PCR (qPCR) in the cerebellum, hippocampus, and cerebral cortex. Results: GH increased the mRNA expression level of the $GABA_{B1}$ receptor subunit ($GABA_{BR1}$) and IGF-1R in the cerebellum. Furthermore, a significant positive correlation was found between the level of $GABA_{BR1}$ mRNA and the expression of the IGF-1R transcript. GH also induced an increase in the mRNA expression of IGF-2 and IGF-2R in the cerebellum. Conclusion: These data indicate that GH may provide beneficial effects on cognitive function through its influences on the expression of $GABA_{BR1}$ and GH/IGF-1 axis genes in PWS patients.

• 생명과학회지
• /
• 제29권1호
• /
• pp.118-122
• /
• 2019

옥시토신(Oxt)과 바소프레신(Avp)은 주로 시상하부의 신경세포에서 생성이 되어 뇌하수체 후엽에서 온 몸으로 분비된다. 유전자 구조와 염기서열 연구를 통해 옥시토신과 바소프레신이 진화적으로 발달되는 단계에서 유전자가 염색체 내에 중복된 것으로 추정되어져 왔다. 이전 연구에서 작은 조절자로 알려진 마이크로RNA 중 하나인 miR-24가 옥시토신과 직접 결합한 후 조절할 수 있다는 사실을 본 연구실에서 발표한 바가 있지만, 바소프레신을 동시에 조절할 수 있는지는 확실치 않았다. 본 연구에서 바소프레신을 조절할 수 있는 후보 마이크로RNA를 생물정보학적 방법으로 탐색하였다. 여러 후보 중 miR-24만이 바소프레신과 직접 결합할 수 있음을 형광 리포터 분석과 바소프레신 결합부위의 돌연변이 cDNA 제작을 통해 밝혀내었다. 바소프레신의 miR-24 결합 필수 부위인 "seed" 부분을 돌연변이 시킨 바소프레신의 경우 miR-24와의 결합능이 현저히 떨어지고 miR-24의 저해제 역시 결합능을 감소시키는 것을 보아 miR-24가 바소프레신에 결합하여 조절할 수 있음을 명확히 할 수 있었다. 이러한 결과를 종합해 볼 때 단일 마이크로RNA가 두 주요한 뇌하수체 호르몬의 조절에 관여한다는 새로운 조절 기전을 제시하여 준다.

• 한국식품저장유통학회지
• /
• 제14권6호
• /
• pp.688-694
• /
• 2007

To evaluate the human risk of long-term intake of genetically modified (GM) rice, we carried out RT-PCR of housekeeping genes. Housekeeping genes, which show highly uniform expression in living organisms during various stages of development and under different environmental conditions, were normalized by RT-PCR. We assessed the expression of 10 common housekeeping genes (18s rRNA, 25S rRNA, UBC, UBQ5, UBQ10, ACT11, GAPDH, eEF-$1{\alpha}$, ${\beta}$-TUB, GAPDH, ${\beta}$-actin, B2m, G6pd2, Gyk, Gus, Hprt, Cyclophlin A, Tfrc, ${\alpha}$-tubulin and RPL13A) in the liver, stomach, small intestine, large intestine, kidney and spleen of mice fed GM or non-GM rice. We found no significant differences in the expression of housekeeping genes between the two groups of mice.

• Journal of Microbiology and Biotechnology
• /
• 제33권4호
• /
• pp.471-484
• /
• 2023

Compost is widely used as an organic additive to improve the bioremediation of diesel-contaminated soil. In this study, the effects of compost amendment on the remediation performance, functional genes, and bacterial community are evaluated during the bioremediation of diesel-contaminated soils with various ratios of compost (0-20%, w/w). The study reveals that the diesel removal efficiency, soil enzyme (dehydrogenase and urease) activity, soil CH₄ oxidation potential, and soil N₂O reduction potential have a positive correlation with the compost amendment (p < 0.05). The ratios of denitrifying genes (nosZI, cnorB and qnorB) to 16S rRNA genes each show a positive correlation with compost amendment, whereas the ratio of the CH₄-oxidizing gene (pmoA) to the 16S rRNA genes shows a negative correlation. Interestingly, the genera Acidibacter, Blastochloris, Erythrobacter, Hyphomicrobium, Marinobacter, Parvibaculum, Pseudoxanthomonas, and Terrimonas are strongly associated with diesel degradation, and have a strong positive correlation with soil CH₄ oxidation potential. Meanwhile, the genera Atopostipes, Bacillus, Halomonas, Oblitimonas, Pusillimonas, Truepera, and Wenahouziangella are found to be strongly associated with soil N₂O reduction potential. These results provide useful data for developing technologies that improve diesel removal efficiency while minimizing greenhouse gas emissions in the bioremediation process of diesel-contaminated soil.

• Toxicological Research
• /
• 제21권3호
• /
• pp.209-218
• /
• 2005

We investigated effects of recombinant human erythropoietin (rHuEPO) on profiles of mRNA transcripts in 6 male cynomolgus (M. fascicularis) monkey's spleen for 4 weeks. Six monkeys, composed of control and treatment group (Control : M1, M2, M3: Treatment : M4, M5, M6) were intravenously administered 3 times per week without or with a dose of rHuEPO 2730 IU/0.1 ml/kg. After 4 weeks rHuEPO treatment, spleen was removed for RNA isolation. Splenic gene expression was assessed using Affymetrix U133A 2.0 arrays containing 18,400 transcripts and variants, including 14,500 well-characterized human genes. Gene expression pattern was very different between individuals even in same treatment. In rHuEPO treated groups showed number of genes were up- or down-regulated (M4: 79: M5: 48; M6: 73 genes). Six genes (epidermal growth factor receptor, calgranulin A, estrogen receptor binding site associated antigen, matrix metalloproteinase 19, zinc finger and BTB domain containing 16, progestin and adipoQ receptor) were commonly expressed in rHuEPO treated group. The different individual response could be major considering factor in monkey experiment. Further study is needed to clarify the different individual response to rHuEPO in molecular level. This study will be valuable in the fundamental understanding and validation of molecular toxicology for bio-generic drugs including rHuEPO in cynomolgus monkey.

• Animal Bioscience
• /
• 제36권1호
• /
• pp.144-155
• /
• 2023

Objective: Adipocyte differentiation is regulated by a variety of functional genes and noncoding RNAs. However, the role of miRNAs in lipid deposition of goat white adipose tissue is still unclear. Therefore, this study revealed the miRNA expression profile in goat subcutaneous adipocytes by sRNA-seq. Methods: The miRNA expressed in goat subcutaneous preadipocytes and the mature adipocytes were sequenced by sRNA-seq. The differentially expressed miRNAs (DEm) were screened and gene ontology (GO) and Kyoto encyclopedia for genes and genomes (KEGG) analyses were performed. Gain-of-function and loss-of-function combined with oil red O staining, Bodipy staining, and quantitative reverse-transcription polymerase chain reaction (qPCR) were utilized to determine the effect of miR-133a-3p on adipocyte differentiation. Results: A total of 218 DEm were screened out. The target genes of these DEm were significantly enriched in GO items such as biological regulation and in KEGG terms such as FAK signaling pathway and MAPK signaling pathway. qPCR verified that the expression trend of miRNA was consistent with miRNA-seq. The gain-of-function or loss-of-function of miR-133a-3p showed that it promoted or inhibited the accumulation of lipid droplets, and CCAAT enhancer binding protein α (C/EBPα) and C/EBPβ were extremely significantly up-regulated or down-regulated respectively (p<0.01), the loss-of-function also led to a significant down-regulation of peroxisome proliferator activated receptor gamma (PPARγ) (p<0.01). Conclusion: This study successfully identified miRNAs expression patterns in goat subcutaneous adipocytes, and functional identification indicates that miR-133a-3p is a positive regulator of the differentiation process of goat subcutaneous adipocytes. Our results lay the foundation for the molecular mechanism of lipid deposition in meat-source goats from the perspective of miRNA.

• Molecules and Cells
• /
• 제27권2호
• /
• pp.205-209
• /
• 2009

The loci of the 5S and 45S rRNA genes were localized on chromosomes in five species of Capsicum, namely, annuum, chacoense, frutescens, baccatum, and chinense by FISH. The 5S rDNA was localized to the distal region of one chromosome in all species observed. The number of 45S rDNA loci varied among species; one in annuum, two in chacoense and frutescens, and chinense, and four in baccatum, with the exceptions that 'CM334' of annuum had three loci and 'tabasco' of frutescens gad one locus. 'CM334'-derived BAC clones, 384B09 and 365P05, were screened with 5S rDNA as a probe, and BACs 278M03 and 262A23 were screened with 25S rDNA as a probe. Both ends of these BAC clones were sequenced. FISH with these BAC probes on pachytenes from 'CM334' plant showed one 5S rDNA locus and three 45S rDNA loci, consistent with the patterns on the somatic chromosomes. The 5S rDNA probe was also applied on extended DNA fibers to reveal that its coverage measured as long as 0.439 Mb in the pepper genome. FISH techniques applied on somatic and meiotic chromosomes and fibers have been established for chili to provide valuable information about the copy number variation of 45S rDNA and the actual physical size of the 5S rDNA in chili.