• Genomics & Informatics
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• v.21 no.3
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• pp.37.1-37.11
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• 2023

Systemic lupus erythematosus (SLE) is an inflammatory-autoimmune disease with a complex multi-organ pathogenesis, and it is known to be associated with significant morbidity and mortality. Various genetic, immunological, endocrine, and environmental factors contribute to SLE. Genomic variants have been identified as potential contributors to SLE susceptibility across multiple continents. However, the specific pathogenic variants that drive SLE remain largely undefined. In this study, we sought to identify these pathogenic variants across various continents using genomic and bioinformatic-based methodologies. We found that the variants rs35677470, rs34536443, rs17849502, and rs13306575 are likely damaging in SLE. Furthermore, these four variants appear to affect the gene expression of NCF2, TYK2, and DNASE1L3 in whole blood tissue. Our findings suggest that these genomic variants warrant further research for validation in functional studies and clinical trials involving SLE patients. We conclude that the integration of genomic and bioinformatic-based databases could enhance our understanding of disease susceptibility, including that of SLE.

• Korean Journal of Ichthyology
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• v.19 no.4
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• pp.266-273
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• 2007

Heat shock proteins (HSPs) are a family of highly conserved proteins playing an important role in the functioning of unstressed and stressed cells. The HSP70 family, the most widely studied of the hsps, is constitutively expressed (hsc70) in unstressed cells and is also induced in response to stressors (hsp70), especially those affecting the protein machinery. The HSP/HSC70 proteins act as molecular chaperones and are crucial for protein functioning, including folding, intracellular localization, regulation, secretion, and protein degradation. Here, we report the identification and characterization of the putative amino acid sequence deduced from one cDNA clone identified as heat shock protein 70. The alignment showed that the putative sequence is 100% identical to the heat shock protein 70 cognate (HSC 70) of olive flounder. The 5'-flanking region sequence (approximately 1 kb) ahead of the hsc70 gene was cloned by genome walking and a putative core promoter region and transcription elements were identified. We characterized the promoter of the olive flounder hsc70 gene by examining the ability of 5'-upstream fragments to drive expression of green fluorescent protein (GFP) in live embryos.

• Reproductive and Developmental Biology
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• v.32 no.3
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• pp.159-166
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• 2008

We report here the generation of transgenic chickens that produce human Thrombopoietin (hTPO) using replication-defective Moloney murine leukemia virus (MoMLV)-based vectors packaged with vesicular stomatitis virus G glycoprotein (VSV-G). For the retrovirus vectors, we used hCMV (human Cytomegalovirus) internal promoter to drive the hTPO gene. After confirming the expression of the hTPO gene in various target cells, the concentrated solution of recombinant retrovirus was injected beneath the blastoderm of non-incubated chicken embryos (stage X). The biological activity of the recombinant hTPO in target cell was significantly higher than its commercially available counterpart. Out of 132 injected eggs, 11 chicks hatched after 21 days of incubation and 4 hatched chicks were found to express vector-encoded hTPO gene. However, 3 out of the 4 transgenics died within one month of hatching. The major significance of this study is that it is one of the very few successful reports on the production of transgenic chickens as bioreactors aiming mass production of commercially valuable and biological active human cytokine proteins.

• Journal of Plant Biotechnology
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• v.2 no.1
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• pp.43-49
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• 2000

An efficient and reliable Agrobacterium transformation procedure based on TDZ (thidiazuron)-induced organogenesis was established and applied to six Brazilian eggp1ant varieties. Optimum transgenic plants recovery was achieved upon the study of the following parameters affecting transformation efficiency, using F-100 variety as a model: i) explant source; ii) pre-culture period; iii) physical state of the pre-culture medium and iv) coculture conditions. The highest frequency of kanamycin-resistant calli derived from leaf explants (5%) was obtained without a pre-culture period and co-cultivation for 24 h in liquid medium followed by five days on solid RM (regeneration medium). For cotyledon explants, best results were achieved upon a pre-culture of 24 h in liquid RM and a co-cultivation period of 24 h in liquid RM followed by three days in solid RM, resulting in a transformation Sequency of 22.7%. Kanamycin-resistant organogenic calli were also obtained from cultivars Emb, Preta Comprida, Round nose Shaded, Campineira and Florida Market. The expression pattern of an epidermis-specific promoter was studied using transformants expressing a chimaeric construct comprised by the promoter Atgrp-5 transcriptionally fused to the coding region of the gus gene. The expression pattern was similar to that previously observed in tobacco and Arabidopsis thaliana, with preferential expression at the epidermis and the stem phloem. These results support the idea that the Atgrp-5 promoter can be used to drive defense genes in these tissues, which are sites of pathogen interaction and spread, in programs for the genetic improvement of eggplant.

• Plant Biotechnology Reports
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• v.5 no.2
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• pp.169-175
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• 2011

In this study, the JIP test was exploited to assess drought-tolerance of transgenic rice overexpressing OsNAC10. Two types of promoters, RCc3 (root-specific) and GOS2 (constitutive), were used to drive the transcription factor OsNAC10, a gene involved in diverse functions including stress responses. Three-month-old plants were exposed to drought for 1 week and their fluorescence kinetics was evaluated. Our results showed that drought-treated non-transgenic plants (NT) have higher fluorescence intensity at the J phase (2 ms) compared to transgenic plants, indicating a decline in electron transport beyond the reduced plastoquinone ($Q_A^-$). As manifested by negative L bands, transgenic plants also showed higher energetic connectivity and stability over NT plants under drought conditions. Also, the pool size of the end electron acceptor at the photosystem I was reduced more in NT than in transgenic plants under drought conditions. Furthermore, the transgenic plants had higher $PI_{total}$, a combined parameter that reflects all the driving forces considered in JIP test, than NT plants under drought conditions. In particular, the $PI_{total}$ of the RCc3:OsNAC10 plants was higher than that of NT plants, which was in good agreement with their differences in grain yield. Thus, the JIP test proved to be practical for evaluating drought-tolerance of transgenic plants.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.18
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• pp.7547-7552
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• 2014

The mir-155 family is not only involved in a diversity of cancers, but also as a regulator of the immune system. However, the evolutionary history of this family is still unclear. The present study indicates that mir-155 evolved independently with lineage-specific gain of miRNAs. In addition, arm switching has occurred in the mir-155 family, and alternative splicing could produce two different lengths of ancestral sequences, implying the alternative splicing can also drive evolution for intragenic miRNAs. Here we screened validated target genes and immunity-related proteins, followed by analyzation of the mir-155 family function by high-throughput methods like the gene ontology (GO) and Kyoto Eneyclopedin of Genes and Genemes (KEGG) pathway enrichment analysis. The high-throughput analysis showed that the CCND1 and EGFR genes were outstanding in being significantly enriched, and the target genes cebpb and VCAM1 and the protein SMAD2 were also vital in mir-155-related immune reponse activities. Therefore, we conclude that the mir-155 family is highly conserved in evolution, and CCND1 and EGFR genes might be potential targets of mir-155 with regard to progress of cancers, while the cebpb and VCAM1 genes and the protein SMAD2 might be key factors in the mir-155 regulated immune activities.

• Bulletin of the Korean Chemical Society
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• v.31 no.6
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• pp.1479-1484
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• 2010

Photosynthesis uses light energy to drive the oxidation of water at an oxygen-evolving catalytic site within photosystem II (PSII). Chlorophyll binding by the photosystem II subunit S protein, PsbS, was found to be necessary for energy-dependent quenching (qE), the major energy-dependent component of non-photochemical quenching (NPQ) in Arabidopsis thaliana. It is proposed that PsbS acts as a trigger of the conformational change that leads to the establishment of nonphotochemical quenching. However, the exact structure and function of PsbS in PSII are still unknown. Here, we clone and express the recombinant PsbS gene from Arabidopsis thaliana in E. coli and purify the resulting homogeneous protein. We used various biochemical and biophysical techniques to elucidate PsbS structure and function, including circular dichroism (CD), fluorescence, and DSC. The protein shows optimal stability at $4^{\circ}C$ and pH 7.5. The CD spectra of PsbS show that the conformational changes of the protein were strongly dependent on pH conditions. The CD curve for PsbS at pH 10.5 curve had the deepest negative peak and the peak of PsbS at pH 4.5 was the least negative. The fluorescence emission spectrum of the purified PsbS protein was also measured, and the ${\lambda}_{max}$ was found to be at 328 nm. PsbS revealed some structural changes under varying temperature and oxygen gas condition.

• Biomolecules & Therapeutics
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• v.28 no.1
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• pp.98-103
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• 2020

Marfan syndrome (MFS), a connective tissue disorder caused by mutations in the fibrillin-1 (Fbn1) gene, has vascular manifestations including aortic aneurysm, dissection, and rupture. Its vascular pathogenesis is assumed to be attributed to increased transforming growth factor β (TGFβ) signaling and blockade of excessive TGFβ signaling has been thought to prevent dissection and aneurysm formation. Here, we investigated whether galunisertib, a potent small-molecule inhibitor of TGFβ receptor I (TβRI), attenuates aneurysmal disease in a murine model of MFS (Fbn1^C1039G/+) and compared the impact of galuninsertib on the MFS-related vascular pathogenesis with that of losartan, a prophylactic agent routinely used for patients with MFS. Fbn1^C1039G/+ mice were administered galunisertib or losartan for 8 weeks, and their ascending aortas were assessed for histopathological changes and phosphorylation of Smad2 and extracellular signal-regulated kinase 1/2 (Erk1/2). Mice treated with galunisertib or losartan barely exhibited phosphorylated Smad2, suggesting that both drugs effectively blocked overactivated canonical TGFβ signaling in Fbn1^C1039G/+ mice. However, galunisertib treatment did not attenuate disrupted medial wall architecture and only partially decreased Erk1/2 phosphorylation, whereas losartan significantly inhibited MFS-associated aortopathy and markedly decreased Erk1/2 phosphorylation in Fbn1^C1039G/+ mice. These data unexpectedly revealed that galunisertib, a TβRI inhibitor, showed no benefits in aneurysmal disease in MFS mice although it completely blocked Smad2 phosphorylation. The significant losartan-induced inhibition of both aortic vascular pathogenesis and Smad2 phosphorylation implied that canonical TGFβ signaling might not prominently drive aneurysmal diseases in MFS mice.

• Journal of Cancer Prevention
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• v.22 no.4
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• pp.234-240
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• 2017

Background: Lung cancer is the leading cause of cancer-related death worldwide, for which smoking is considered as the primary risk factor. The present study was conducted to determine whether genetic alterations induced by radon exposure are associated with the susceptible risk of lung cancer in never smokers. Methods: To accurately identify mutations within individual tumors, next generation sequencing was conduct for 19 pairs of lung cancer tissue. The associations of germline and somatic variations with radon exposure were visualized using OncoPrint and heatmap graphs. Bioinformatic analysis was performed using various tools. Results: Alterations in several genes were implicated in lung cancer resulting from exposure to radon indoors, namely those in epidermal growth factor receptor (EGFR), tumor protein p53 (TP53), NK2 homeobox 1 (NKX2.1), phosphatase and tensin homolog (PTEN), chromodomain helicase DNA binding protein 7 (CHD7), discoidin domain receptor tyrosine kinase 2 (DDR2), lysine methyltransferase 2C (MLL3), chromodomain helicase DNA binding protein 5 (CHD5), FAT atypical cadherin 1 (FAT1), and dual specificity phosphatase 27 (putative) (DUSP27). Conclusions: While these genes might regulate the carcinogenic pathways of radioactivity, further analysis is needed to determine whether the genes are indeed completely responsible for causing lung cancer in never smokers exposed to residential radon.

• ALGAE
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• v.38 no.4
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• pp.253-264
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• 2023

The Ceramiales is the most diverse and species-rich group (2,669 spp.) of red algae, and it is widely distributed from tropical to polar oceans. Mitochondrial genomes (mitogenomes) and other genes have contributed to our knowledge regarding the classification and phylogeny of this diverse red algal group; however, the mitogenome architecture remains understudied. Here, we compared 42 mitogenomes, including 19 newly generated in this study, to expand our knowledge. The number of genes in mitogenome varied from 43 to 68 due to gene duplication. The mitogenome architecture was also variable, categorized into four types (A-D): type A = ancestral type with a basic composition; type B = those with inverse transpositions; type C = those with inverted duplications; and type D = those with both inversion and duplication. The palindromic and inverted repeats were consistently found in flanking regions of the rearrangement, especially near the cob and nad6 genes. The three rearranged mitogenome architectures (types B, C, D) are the first report of these in red algae. Phylogenetic analyses of 23 protein-coding genes supported the current familial classification of the Ceramiales, implying that the diversity of mitogenome architecture preceded the phylogenetic relationships. Our study suggests that palindromic and inverted repeats may drive mitogenome architectural variation.