• Ocean and Polar Research
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• v.44 no.3
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• pp.209-220
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• 2022

Carbonic anhydrase (CA) is a key controller of the carbon concentrating mechanism (CCM), and is known to be affected by ambient pH and CO₂ compositions. Herein, we characterized three novel CAs genes (PmCA1, 2, and 3) from the marine dinoflagellate Prorocentrum minimum, and evaluated the relative expressions of the PmCAs and photosynthetic genes PmatpB and PmrbcL under different pH conditions. Each PmCA was predicted to have amino acid residues constituting the zinc binding site. With signal peptide, PmCA1 and PmCA2 were predicted to be intracellular CAs located in the cytoplasm and chloroplast membrane, respectively. On the other hand, PmCA3 was predicted to be extracellular CA located in the plasma membrane. Also, PmCA1 was classified into the beta family, and PmCA2 and PmCA3 were classified into the alpha family via phylogenic analysis. The photosynthesis efficiency of P. minimum was similar at pH 7 to 9, and decreased significantly at pH 6 and pH 10. Overall, relative gene expression levels of the three PmCAs decreased at low pH, and increased as pH increased. Photosynthesis related genes, PmatpB and PmrbcL, showed similar expression patterns to those of PmCAs. These results suggest that changes in seawater pH may affect photosynthesis and CO₂ metabolism in marine dinoflagellates.

• Research in Plant Disease
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• v.21 no.3
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• pp.186-192
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• 2015

Cucumber mosaic virus possesses 2b gene known as a suppressor of post-transcriptional gene silencing (PTGS). To investigate its function and effect in plant, transgenic Nicotiana benethamiana expressing 2b gene was developed and analyzed in phenotypic characteristics and differential gene expression (DEG) comparing with wild-type. Eight lines of transgenic plants ($T_0$) were obtained with difficulty and showed severe deformed phenotypes in leaves, flowers, petioles and etc. Moreover, transgenic plants were hardly able to set seeds, but small amounts of seeds were barely produced in some of transgene-hemizygous plants. DEG analysis showed that transgenic plant ectopically accumulated diverse RNA transcripts at higher levels than wild-type probably due to the disturbance in RNA metabolism, especially of RNA decay, caused by 2b-mediated inhibition of PTGS. These ectopic accumulations of RNAs disrupt protein and RNA homeostasis and then subsequently lead to abnormal phenotypes of transgenic plants.

• Environmental Analysis Health and Toxicology
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• v.18 no.2
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• pp.145-153
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• 2003

The goal of this study is to develop a biomarker used in monitoring abnormal behaviors of Japanese medaka (Oryzias latipes) as a model organism caused by hazardous chemicals. Japanese medaka was treated by copper of appropriate sublethal concentrations after starvation for 48 hr. The untreated individuals showed common behavioral characteristics (i.e. , smooth and linear movements). Locomotive activity of the fish was monitored using an image processing and automatic data acquisition system. When treated with copper (100 ppb), the fish showed shaking patterns more frequently. As the concentration of copper increased to 1,000 ppb, activity decreated, and the fish showed an erratic movement. Fish were exposed to copper at various concentrations (0,100 and 1,000 ppb) for 24 hrs, and acetylcholine esterase (AChE) activity was observed. When fish were exposed to 1,000 ppb of copper, the body AChE activities appeared to decrease but the head AChE activities showed little change. Expressions of tyrosine hydroxylase (TH) protein in the different organs from both head (brain) and body (kidney) portions affected by the copper treatment were analyzed using immunohistochemical technique compared with control. Five organs of the fish (olfactory bulb, hyothalamus, optic lobe, pons and myelencephalon regions) showed a relatively strong TH protein expression in the control experiment. A differential expression of TH, however, was observed in the treatment (100 ppb and 1,000 ppb). The treatment (1,000 ppb) significantly suppressed TH protein production in the brain regions. In kidney, however, the same treatment caused little suppression compared with the control. Copper appeared to be less effective in suppression of TH than diazinon, a known TH suppressor. It was concluded that TH could be used at a potential biomarker to monitor the acute copper toxicity in Japanese medaka.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.9
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• pp.3691-3696
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• 2015

Background: Cancer loci comprise heterogeneous cell populations with diverse cellular secretions. Therefore, disseminating cancer-specific or cancer-associated protein antigens from tissue lysates could only be marginally correct, if otherwise not validated against precise standards. Materials and Methods: In this study, 2DE proteomic profiles were examined from lysates of 13 lung-adenocarcinoma tissue samples and matched against the A549 cell line proteome. A549 matched-cancer-specific hits were analyzed and characterized by MALDI-TOF/MS. Results: Comparative analysis identified a total of 13 protein spots with differential expression. These proteins were found to be involved in critical cellular functions regulating pyrimidine metabolism, pentose phosphate pathway and integrin signaling. Gene ontology based analysis classified majority of protein hits responsible for metabolic processes. Among these, only a single non-predictive protein spot was found to be a cancer cell specific hit, identified as Armadillo repeat-containing protein 8 (ARMC8). Pathway reconstruction studies showed that ARMC8 lies at the centre of cancer metabolic pathways. Conclusions: The findings in this report are suggestive of a regulatory role of ARMC8 in control of proliferation and differentiation in lung adenocarcinomas.

• Genomics & Informatics
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• v.16 no.4
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• pp.34.1-34.9
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• 2018

Cirsium japonicum belongs to the Asteraceae or Compositae family and is a medicinal plant in Asia that has a variety of effects, including tumour inhibition, improved immunity with flavones, and antidiabetic and hepatoprotective effects. Silymarin is synthesized by 4-coumaroyl-CoA via both the flavonoid and phenylpropanoid pathways to produce the immediate precursors taxifolin and coniferyl alcohol. Then, the oxidative radicalization of taxifolin and coniferyl alcohol produces silymarin. We identified the expression of genes related to the synthesis of silymarin in C. japonicum in three different tissues, namely, flowers, leaves, and roots, through RNA sequencing. We obtained 51,133 unigenes from transcriptome sequencing by de novo assembly using Trinity v2.1.1, TransDecoder v2.0.1, and CD-HIT v4.6 software. The differentially expressed gene analysis revealed that the expression of genes related to the flavonoid pathway was higher in the flowers, whereas the phenylpropanoid pathway was more highly expressed in the roots. In this study, we established a global transcriptome dataset for C. japonicum. The data shall not only be useful to focus more deeply on the genes related to product medicinal metabolite including flavolignan but also to study the functional genomics for genetic engineering of C. japonicum.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.25 no.11
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• pp.1512-1518
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• 2021

Since single cell RNA sequencing provides the expression profiles of individual cells, it provides higher cellular differential resolution than traditional bulk RNA sequencing. Using these single cell RNA sequencing data, clustering analysis is generally conducted to find cell types and understand high level biological processes. In order to effectively process the high-dimensional single cell RNA sequencing data fir the clustering analysis, this paper uses a variational autoencoder to transform a high dimensional data space into a lower dimensional latent space, expecting to produce a latent space that can give more accurate clustering results. By clustering the features in the transformed latent space, we compare the performance of various classical clustering methods for single cell RNA sequencing data. Experimental results demonstrate that the proposed framework outperforms many state-of-the-art methods under various clustering performance metrics.

• The Korean Journal of Physiology and Pharmacology
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• v.9 no.5
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• pp.275-282
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• 2005

By using differential display, we identified one of the genes encoding the multi-subunit complex protein V-ATPase, c subunit gene (ATP6L), and showed alterations of the gene expression by oxidative stresses. Expression of the ATP6L gene in Neuro-2A cells was increased by the treatment with $H_2O_2$ and incubation in hypoxic chamber, implying that the expression of the ATP6L gene is regulated by oxidative stresses. To examine mechanisms involved in the regulation of the gene expression by oxidative stresses, the transcriptional activity of the rat ATP6L promoter was studied. Transcription initiation site was determined by primer extension analysis and DNA sequencing, and promoter of the rat ATP6L and its deletion clones were constructed in reporter assay vector. Significant changes of the promoter activities in Neuro-2A cells were observed in two regions within the proximal 1 kbp promoter, and one containing a suppressor was in -195 to -220, which contains GC box that is activated by binding of Sp1 protein. The suppression of promoter activity was lost in mutants of the GC box. We confirmed by electrophoretic mobility shift and supershift assays that Sp1 protein specifically binds to the GC box. The promoter activity was not changed by the $H_2O_2$ treatment and incubation in hypoxic chamber, however, $H_2O_2$ increased the stability of ATP6L mRNA. These data suggest that the expression of the ATP6L gene by oxidative stresses is regulated at posttranscriptional level, whereas the GC box is important in basal activities of the promoter.

• Journal of Embryo Transfer
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• v.31 no.4
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• pp.335-347
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• 2016

Multiple interferon tau (IFNT) genes exist in bovine. An antiluteolytic substance secreted by the bovine conceptus and primarily responsible for maternal recognition of pregnancy is bovine trophoblast protein 1 (bIFNT1), a new type I interferon tau (IFNT) genes. The objectives of this research were to investigate whether multiple, distinct gene encode bIFNT1 and other type I bIFNT gene in the bovine genome and to examine expression of bIFNT1 and other bIFNTc1 mRNAs during conceptus development. These transcrips could be regulated through caudal-related homeobox-2 (CDX2) and ETS2 and/or AP1 (JUN) expression, a transcription factor implicated in the control of cell differentiation in the trophectoderm. The presence of mRNAs encoded by bIFNT1 and type I bIFNTc1 genes were examined quantitatively via reverse transcription-polymerase chain reaction (RT-PCR) analysis of total cellular RNA (tcRNA) extracted from on day 17, 20 and 22 bovine conceptuses. The expression level of bIFNT1 was higher on day 17 transcripts were gradually weakly detectable on day 20 and 22. However, the other bIFNTc1 gene examined transcripts was highly expressed on day 20 and transcripts were weakly detectable on day 17 and 22 bovine conceptuses. Furthermore, human choriocarcinoma JEG3 was co-transfected with an -1kb-bIFNT1/c1-Luc constructs and several transcription factor expression plasmids. Compared to each -1kb-bIFNT1/c1-Luc increased when this constructs were co-transfected with, ETS2, AP1(JUN), CREBBP and/or CDX2. Also, bIFNTc1 gene was had very effect on activity by alone ETS2, and AP1 (JUN) expression factors in choriocarcinoma JEG3 cell. However, bIFNT1 gene expression of the upstream region was not identified. We demonstrated that the activities of bIFN genes are regulated by differential, tissue-specific and developmental competence during pregnancy.

• Clinical and Experimental Reproductive Medicine
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• v.32 no.3
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• pp.207-216
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• 2005

Objective: To understand the crucial requirement for the normal early folliculogenesis, we evaluated molecular as well as physiological differences during in vitro ovarian culture. Among the important regulators for follicle development, anti-Müllerian hormone (AMH) and FSH Receptor (FSHR) have been known to be expressed in the cuboidal granulosa cells. Meanwhile, it is known that c-kit is germ cell-specific and GDF-9 is also oocyte-specific regulator. To evaluate the functional requirement for the competence of normal follicular development, we investigated the differential mRNA expression of several factors secreted from granulosa cells and oocytes between in vivo and in vitro developed ovaries. Materials and Methods: Ovaries from ICR neonates (the day of birth) were cultured for 4 days (for primordial to primary transition) or 8 days (for secondary follicle formation) in ${\alpha}$-MEM glutamax supplemented with 3 mg/ml BSA without serum or growth factors. The mRNA levels of the several factors were investigated by quantitative real-time PCR analysis. Freshly isolated 0-, 4-, and 8-day-old ovaries were used as control. Results: The mRNA of AMH and FSHR as granulosa cell factors was highly increased according to the ovarian development in both of 4- and 8-day-old control. However, the mRNA expression was not induced in both of 4- and 8-day in vitro cultured ovaries. The mRNA expression of GDF-9 known to regulate follicle growth as an oocyte factor was different between in vivo and in vitro developed ovaries. In addition, the transcript of GDF-9 was expressed in the primordial follicles of mouse ovaries. The mRNA expression of c-kit was not significantly different during the early folliculogenesis in vitro. Conclusion: This is the first report regarding endogenous AMH and FSHR expression during the early folliculogenesis in vitro. In conclusion, it will be very valuable to evaluate cuboidal granulosa cell factors as functional marker(s) for normal early folliculogenesis in vitro.

• The Plant Pathology Journal
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• v.18 no.2
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• pp.63-67
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• 2002

To understand plant-pathogen interactions, a complete set of hot pepper genes differentially expressed against pathogen attack was isolated. As an initial step, hundreds of differentially expressed cDNAS were isolated from hot pepper leaves showing non-host resistance against bacterial plant pathogens (Xanthomonas campestris pv. glycines and Pseudomonas syringae pv. syringae) using differential display reverse transcription polymerase chain reaction (DDDRT-PCR) technique. Reverse Northern and Northern blot analyses revealed that 50% of those genes were differentially expressed in pepper loaves during non-host resistance response. Among them, independent genes without redundancy were micro-arrayed for further analysis. Random EST sequence database were also generated from various CDNA libraries including pepper tissue specific libraries and leaves showing non-host hypersensitive response against X. campestris pv. glycines. As a primary stage, thousands of cDNA clones were sequenced and EST data were analyzed. These clones are being spotted on glass slide to study the expression profiling. Results of this study may further broaden knowledge on plant-pathogen interactions.