• Restorative Dentistry and Endodontics
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• v.40 no.3
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• pp.223-228
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• 2015

Objectives: The aim of this study was to investigate the expression of 7 different sirtuin genes (SIRT1-SIRT7) in human dental pulp cells (HDPCs), and to determine the role of SIRTs in the odontoblastic differentiation potential of HDPCs. Materials and Methods: HDPCs were isolated from freshly extracted third molar teeth of healthy patients and cultulred in odontoblastic differentiation inducing media. Osteocalcin (OCN) and dentin sialophosphoprotein (DSPP) expression was analyzed to evaluate the odontoblastic differentiation of HDPCs by reverse transcription-polymerase chain reaction (RT-PCR), while alizarin red staining was used for the mineralization assay. To investigate the expression of SIRTs during odontoblastic differentiation of HDPCs, real time PCR was also performed with RT-PCR. Results: During the culture of HDPCs in the differentiation inducing media, OCN, and DSPP mRNA expressions were increased. Mineralized nodule formation was also increased in the 14 days culture. All seven SIRT genes were expressed during the odontogenic induction period. SIRT4 expression was increased in a time-dependent manner. Conclusions: Our study identified the expression of seven different SIRT genes in HDPCs, and revealed that SIRT4 could exert an influence on the odontoblast differentiation process. Further studies are needed to determine the effects of other SIRTs on the odontogenic potential of HDPCs.

• Restorative Dentistry and Endodontics
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• v.34 no.5
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• pp.430-441
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• 2009

The purpose of this study was to characterize functional distinction between human dental pulp cells(PC) and periodontal ligament cells(PDLC) using cDNA micro array assay and to confirm the results of the microarray assay using RT-PCR. 3 genes out of 51 genes which were found to be more expressed(>2 fold) in PC were selected, and 3 genes out of 19 genes which were found to be more expressed(>2 fold) in PDLC were selected for RT-PCR as well. According to this study, the results were as follows: 1. From the micro array assay, 51 genes were more expressed (2 fold) from PC than PDLC. 2. RT-PCR confirmed that ITGA4 and TGF ${\beta}2$ were more expressed in PC than in PDLC 3. From the micro array assay, 19 genes were more expressed (2 fold) from PDLC than PC. 4. RT-PCR confirmed that LUM, WISP1. and MMP1 were more expressed in PDLC than in PC. From the present study, different expression of the genes between the PC and PDLC were characterized to show the genes which play an important role in dentinogenesis were more expressed from PC than PDLC, while the genes which were related with collagen synthesis were more expressed from PDLC than PC.

• Restorative Dentistry and Endodontics
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• v.35 no.3
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• pp.152-163
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• 2010

This study investigated the changes in gene expression when mineral trioxide aggregate (MTA) was applied in vitro to human dental pulp cells (HDPCs). MTA in a teflon tube (diameter 10 mm, height 2 mm) was applied to HDPCs. Empty tube-applied HDPCs were used as negative control. For microarray analysis, total RNA was extracted at 6, 24, and 72 hrs after MTA application. The results were confirmed selectively by performing reverse transcriptase polymerase chain reaction for genes that showed changes of more than two-fold or less than half. Of the 24,546 genes, 109 genes were up-regulated greater than twofold (e.g., FOSB, THBS1, BHLHB2, EDN1, IL11, FN1, COL10A1, and TUFT1) and 69 genes were down-regulated below 50% (e.g., SMAD6 and DCN). These results suggest that MTA, rather than being a bio-inert material, may have potential to affect the proliferation and differentiation of pulp cells in various ways.

• Restorative Dentistry and Endodontics
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• v.37 no.3
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• pp.142-148
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• 2012

Objectives: We analyzed gene-expression profiles after 14 day odontogenic induction of human dental pulp cells (DPCs) using a DNA microarray and sought candidate genes possibly associated with mineralization. Materials and Methods: Induced human dental pulp cells were obtained by culturing DPCs in odontogenic induction medium (OM) for 14 day. Cells exposed to normal culture medium were used as controls. Total RNA was extracted from cells and analyzed by microarray analysis and the key results were confirmed selectively by reverse-transcriptase polymerase chain reaction (RT-PCR). We also performed a gene set enrichment analysis (GSEA) of the microarray data. Results: Six hundred and five genes among the 47,320 probes on the BeadChip differed by a factor of more than two-fold in the induced cells. Of these, 217 genes were upregulated, and 388 were down-regulated. GSEA revealed that in the induced cells, genes implicated in Apoptosis and Signaling by wingless MMTV integration (Wnt) were significantly upregulated. Conclusions: Genes implicated in Apoptosis and Signaling by Wnt are highly connected to the differentiation of dental pulp cells into odontoblast.

• KSBB Journal
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• v.20 no.5 s.94
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• pp.387-391
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• 2005

Totally 16,299 conservative genes, commonly found in 13 thermophilic and hyperthermophilic bacteria, were analyzed. All genes were belong to W 67 COGs (clusters of orthologous groups of proteins). COGs related to protein metabolism were 80 among 167 COGs. Conservative genes were not limited only thermophiles and hyperthermophiles, meaning thermal stability is independent of specific protein. However reverse gyrase was only found in all hyperthermophilic archaebacteria and eubacteria, meaning DNA stability is important in hyperthermophiles. Hyperthermophilic eubacteria and thermophilic archaebacteria had different position between phylogenetic tree of gene content and 165 rRNA gene. Thermophilic archaebacteria hyperthermophilic eubacteria and archaebacteria had similar values by the statistical analysis of distance values with 167 COGs in each organism.

• Restorative Dentistry and Endodontics
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• v.34 no.6
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• pp.537-550
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• 2009

During the last two decades, there has been an increasing interest in the impact of oral health on atherosclerosis and subsequent cardiovascular disease (CVD). To date, some periodontal pathogens including Porphyromonas gingivalis (P. gingivalis) have been reported to be relevant to CVD. Porphyromonas endodontalis (P. endodontalis), which shares approximately 87% sequence homology with P. gingivalis, is mostly found within infected root canals. However, recent studies reveal that this pathogen also resides in the dental plaque or periodontal pocket in patients with periodontitis. It has been shown that P. endodontalis invades human coronary artery endothelial cells (HCAEC) and coronary artery smooth muscle cells (CASMC). To evaluate whether P. endodontalis can participate in the progression of atherosclerosis and CVD, we examined the changes in transcriptional gene expression profiles of HCAEC responding to invaion by P. endodontalis in this study. The following results were obtained. 1. Porphyromonas endodontalis was invasive of HCAEC. 2. According to the microarray analysis, there were 625 genes upregulated more than two-folds, while there were 154 genes downregulated by half. 3. Upregulated genes were relevant to inflammatory cytokines, apoptosis, coagulation and immune response. Enhanced expression of MMP-1 was also noticeable. 4. The transcription profiles of the 10 selected genes examined by real-time PCR agreed well with those observed in the microarray analysis. Thus, these results show that P. endodontalis presents the potential to trigger and augment atherosclerosis leading to CVD.

• Journal of Life Science
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• v.30 no.9
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• pp.813-818
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• 2020

The archaeal clusters of orthologous genes (arCOG) algorithm, which identifies common genes among archaebacterial genomes, was used to identify conservative genes among 168 archaebacterial strains. The numbers of conserved orthologs were 14, 10, 9, and 8 arCOGs in 168, 167, 166, and 165 strains, respectively. Among 41 conserved arCOGs, 13 were related to function J (translation, ribosomal structure, and biogenesis), and 10 were related to function L (replication, recombination, and repair). Among the 14 conserved arCOGs in all 168 strains, 6 arCOGs of tRNA synthetase comprised the highest proportion. Of the remaining 8 arCOGs, 2 are involved in reactions with ribosomes, 2 for tRNA synthesis, 2 for DNA replication, and 2 for transcription. These results showed the importance of protein expression in archaea. For the classes or orders having 3 or more members, genomic analysis was performed by averaging the distance values of the conservative arCOGs. Classes Archaeoglobi and Thermoplasmata of the phylum Euryarchaeota showed the lowest and the highest average of distance value, respectively. This study can provides data necessary for basic scientific research and the development of antibacterial agents and tumor control.

• Journal of Life Science
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• v.32 no.6
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• pp.463-467
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• 2022

As a result of applying the COG (Cluster of Orthologous Groups of Protein) algorithm to 1,309 species to confirm the conserved genes of prokaryotes, ribosomal protein S11 (COG0100) was identified. The numbers of conservative genes were 2, 5, 5, and 6 in 1,308, 1,307, 1,306, and 1,305 species, respectively. Twenty-nine genes were conserved in over 1,302 species, and they encoded 23 ribosomal proteins, 3 tRNA synthetases, 2 translation factors, and 1 RNA polymerase subunit. Most of them were related to protein production, suggesting the importance of protein expression in prokaryotes. The highest conservative COG was COG0048 (ribosomal protein S12) among the 29 COGs. The 29 conserved genes usually have one protein for each prokaryote. COG0090 (ribosomal protein L2) had not only the lowest conservation value but also the largest standard deviation of phylogenetic distance value. As COG0090 is not only a member of the ribosome, but also a regulator of replication and transcription, it could be inferred that prokaryotes have large variations in COG0090 to survive in various environments. This study could provide data necessary for basic science, tumor control, and development of antibacterial agents.

• Restorative Dentistry and Endodontics
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• v.36 no.5
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• pp.397-408
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• 2011

Objectives: This study investigated changes in gene expressions concerning of differentiation, proliferation, mineralization and inflammation using Human-8 expression bead arrays when white Mineral Trioxide Aggregate and calcium hydroxide-containing cement were applied in vitro to human dental pulp cells (HDPCs). Materials and Methods: wMTA (white ProRoot MTA, Dentsply) and Dycal (Dentsply Caulk) in a Teflon tube (inner diameter 10 mm, height 1 mm) were applied to HDPCs. Empty tube-applied HDPCs were used as negative control. Total RNA was extracted at 3, 6, 9 and 24 hr after wMTA and Dycal application. The results of microarray were confirmed by reverse transcriptase polymerase chain reaction. Results: Out of the 24,546 genes, 43 genes (e.g., BMP2, FOSB, THBS1, EDN1, IL11, COL10A1, TUFT1, HMOX1) were up-regulated greater than two-fold and 25 genes (e.g., SMAD6, TIMP2, DCN, SOCS2, CEBPD, KIAA1199) were down-regulated below 50% by wMTA. Two hundred thirty nine genes (e.g., BMP2, BMP6, SMAD6, IL11, FOS, VEGFA, PlGF, HMOX1, SOCS2, CEBPD, KIAA1199) were up-regulated greater than two-fold and 358 genes (e.g., EDN1, FGF) were down-regulated below 50% by Dycal. Conclusions: Both wMTA and Dycal induced changes in gene expressions related with differentiation and proliferation of pulp cells. wMTA induced changes in gene expressions related with mineralization, and Dycal induced those related with angiogenesis. The genes related with inflammation were more expressed by Dycal than by wMTA. It was confirmed that both wMTA and Dycal were able to induce gene expression changes concerned with the pulp repair in different ways.

• Journal of Life Science
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• v.27 no.6
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• pp.694-701
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• 2017

Mycoplasma genitalium represents the smallest genome among mono-cultivable prokaryotes. To discover and compare the orthologs (conservative genes) among M. genitalium and 14 prokaryotes that are uncultivable and have less orthologs than M. genitalium, COG (clusters of orthologous groups of protein) analyses were applied. The analyzed prokaryotes were M. genitalium, one hyperthermophilic exosymbiotic archaeon Nanoarchaeum equitans, four intracellular plant pathogenic eubacteria of Candidatus Phytoplasma genus, and nine endosymbiotic eubacteria of phloem- and xylem-feeding insects. Among 367 orthologs of M. genitalium, 284 orthologs were conservative between M. genitalium and at least one other prokaryote. All 15 prokaryotes commonly have 29 orthologs, representing the significance of proteins in life. They belong to 25 translation-related, including 22 ribosomal proteins, 3 subunits of RNA polymerase, and 1 protein-folding-related. Among the 15 prokaryotes, 40 orthologs were only found in all four Candidatus Phytoplasma. The other nine Candidatus, all endosymbionts with insects, showed only a single common COG0539 (ribosomal protein S1), representing the diversity of orthologs among them. These results might provide clues to understand conservative genes in uncultivable prokaryotes, and may be helpful in industrial areas, such as handling prokaryotes producing amino acids and antibiotics, and as precursors of organic synthesis.