• Genomics & Informatics
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• v.10 no.3
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• pp.153-166
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• 2012

A variety of ligands differ in their capacity to bind the receptor, elicit gene expression, and modulate physiological responses. Such receptors include Toll-like receptors (TLRs), which recognize various patterns of pathogens and lead to primary innate immune activation against invaders, and G-protein coupled receptors (GPCRs), whose interaction with their cognate ligands activates heterotrimeric G proteins and regulates specific downstream effectors, including immuno-stimulating molecules. Once TLRs are activated, they lead to the expression of hundreds of genes together and bridge the arm of innate and adaptive immune responses. We characterized the gene expression profile of Toll-like receptor 4 (TLR4) in RAW 264.7 cells when it bound with its ligand, 2-keto-3-deoxyoctonate (KDO), the active part of lipopolysaccharide. In addition, to determine the network communications among the TLR, Janus kinase (JAK)/signal transducer and activator of transcription (STAT), and GPCR, we tested RAW 264.7 cells with KDO, interferon-${\beta}$, or cAMP analog 8-Br. The ligands were also administered as a pair of double and triple combinations.

• BMB Reports
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• v.41 no.8
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• pp.609-614
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• 2008

The concentrations and catalytic activities of enzymes control metabolic rates. Previous studies have focused on enzyme concentrations because there are no genome-wide techniques used for the measurement of enzyme activity. We propose a method for evaluating the significance of enzyme activity by integrating metabolic network topologies and genome-wide microarray gene expression profiles. We quantified the enzymatic activity of reactions and report the 388 significant reactions in five perturbation datasets. For the 388 enzymatic reactions, we identified 70 that were significantly regulated (P-value < 0.001). Thirty-one of these reactions were part of anaerobic metabolism, 23 were part of low-pH aerobic metabolism, 8 were part of high-pH anaerobic metabolism, 3 were part of low-pH aerobic reactions, and 5 were part of high-pH anaerobic metabolism.

• Environmental Mutagens and Carcinogens
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• v.26 no.4
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• pp.97-112
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• 2006

Heme oxygenase(HO)-1 is an important antioxidant enzyme that plays a pivotal role in cellular adaptation and protection in response to a wide array of noxious stimuli. Thus, HO-1 induction has been associated with prevention or mitigation of pathogenesis of various diseases, including acute inflammation, atherosclerosis, degenerative diseases, and carcinogenesis. Recent progress in our understanding of the function of molecules in the cellular signaling network as key modulators of gene transcription sheds light on the molecular mechanisms underlyuing HO-1 gene expression. A panel of redox-sensitive transcription factors such as activator protein-1, nuclear factor-kB, and nuclear factor E2-related factor-2, and some of the upstream kinases have been identified as prime regulators of HO-1 gene induction. This review summarizes molecular mechanisms underlying HO-1 expression and the significance of targeted induction of HO-1 as a potential chemopreventive or chemoprotective strategy.

• Microbiology and Biotechnology Letters
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• v.47 no.2
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• pp.296-302
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• 2019

In this study, the effects of ammonium concentration ($117.5-1155.0mg-N{\cdot}l^{-1}$), nitrite concentration ($0-50.0mg-N{\cdot}l^{-1}$), and temperature ($15-35^{\circ}C$) on nitrification performance and its functional genes (amoA-arc, amoA-bac, hao) in an enriched consortium inoculated with humic acid were determined. Notably, the maximum nitrification rate value was observed at $315mg-N{\cdot}l^{-1}$ of ammonium, but the highest functional gene copy numbers were obtained at $630mg-N{\cdot}l^{-1}$ of ammonium. No inhibition of the nitrification rate and functional gene copy numbers was observed via the added nitrites. The optimum temperature for maximum nitrification performance was observed to be $30^{\circ}C$. The amoA-bac copy numbers were also greater than those of amoA-arc under all test conditions. Notably, amoA-arc copy numbers and nitrification efficiency showed a positive relationship in network analysis. These results indicate that ammonium-oxidizing archaea and bacteria play important roles in the nitrification process.

• Molecules and Cells
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• v.45 no.7
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• pp.435-443
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• 2022

In response to environmental changes, signaling pathways rewire gene expression programs through transcription factors. Epigenetic modification of the transcribed RNA can be another layer of gene expression regulation. N⁶-adenosine methylation (m⁶A) is one of the most common modifications on mRNA. It is a reversible chemical mark catalyzed by the enzymes that deposit and remove methyl groups. m⁶A recruits effector proteins that determine the fate of mRNAs through changes in splicing, cellular localization, stability, and translation efficiency. Emerging evidence shows that key signal transduction pathways including TGFβ (transforming growth factor-β), ERK (extracellular signal-regulated kinase), and mTORC1 (mechanistic target of rapamycin complex 1) regulate downstream gene expression through m⁶A processing. Conversely, m⁶A can modulate the activity of signal transduction networks via m⁶A modification of signaling pathway genes or by acting as a ligand for receptors. In this review, we discuss the current understanding of the crosstalk between m⁶A and signaling pathways and its implication for biological systems.

• Computers and Concrete
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• v.30 no.3
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• pp.225-236
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• 2022

In this article, Multi-Gene Genetic Programming (MGGP) is proposed for the estimation of the compressive strength of concrete. MGGP is known to be a powerful algorithm able to find a relationship between certain input space features and a desired output vector. With respect to most conventional machine learning algorithms, which are often used as "black boxes" that do not provide a mathematical formulation of the output-input relationship, MGGP is able to identify a closed-form formula for the input-output relationship. In the study presented in this article, MGPP was used to predict the compressive strength of plain concrete, concrete with fly ash, and concrete with furnace slag. A formula was extracted for each mixture and the performance and the accuracy of the predictions were compared to the results of Artificial Neural Network (ANN) and Extreme Learning Machine (ELM) algorithms, which are conventional and well-established machine learning techniques. The results of the study showed that MGGP can achieve a desirable performance, as the coefficients of determination for plain concrete, concrete with ash, and concrete with slag from the testing phase were equal to 0.928, 0.906, 0.890, respectively. In addition, it was found that MGGP outperforms ELM in all cases and its' accuracy is slightly less than ANN's accuracy. However, MGGP models are practical and easy-to-use since they extract closed-form formulas that may be implemented and used for the prediction of compressive strength.

• ALGAE
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• v.37 no.2
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• pp.135-147
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• 2022

The red algal genus Chondrus have long been used as raw materials for carrageenan and dietary fiber in health foods. Despite the importance of genetic information in safeguarding natural seaweed resources, knowledge of the population genetics of Chondrus in the northwest Pacific is limited. In this study, genetic diversity and phylogeographic structure of 45 populations (777 specimens) of Chondrus from Korea, China, and Japan were evaluated based on mitochondrial COI-5P gene sequences, and phylogenetic relationships were confirmed based on plastid rbcL gene sequences. Molecular analyses assigned the specimens in this study to three Chondrus species: C. nipponicus, C. ocellatus, and C. giganteus; phenotype-based species classification was impossible owing to their high morphological plasticity. We found moderate intraspecific genetic diversity and a shallow phylogeographic structure in both for C. nipponicus and C. ocellatus, and low intraspecific genetic diversity in C. giganteus. Each of the three species exhibited high-level intraspecific gene flow among regions based on the most common haplotypes (CN1 for C. nipponicus, CO1 for C. ocellatus, and CG1 for C. giganteus). Our comprehensive genetic information provides insights into the phylogeographic patterns and intraspecific diversity of the economically important Chondrus species. It also highlights the need to conserve existing natural Chondrus resources through continuous monitoring of genetic diversity and phylogeographic pattern.

• IMMUNE NETWORK
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• v.13 no.5
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• pp.222-226
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• 2013

Translocations involving chromosome 21q22 are frequently observed in hematologic malignancies including acute myeloid leukemia (AML), most of which have been known to be involved in malignant transformation through transcriptional dysregulation of Runt-related transcription factor 1 (RUNX1) target genes. Nineteen RUNX1 translocational partner genes, at least, have been identified, but not Homeobox A (HOXA) genes so far. We report a novel translocation of RUNX1 into the HOXA gene cluster in a 57-year-old female AML patient who had been diagnosed with myelofibrosis 39 months ahead. G-banding showed 46,XX,t(7;21)(p15;q22). The involvement of RUNX1 and HOXA genes was confirmed by fluorescence in situ hybridization.

• IMMUNE NETWORK
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• v.9 no.5
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• pp.169-178
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• 2009

DNA immunization induces B and T cell responses to various pathogens and tumors. However, these responses are known to be relatively weak and often transient. Thus, novel strategies are necessary for enhancing immune responses induced by DNA immunization. Here, we demonstrated that co-immunization of influenza virus nucleoprotein (NP) gene significantly enhances humoral and cell-mediated responses to codelivered antigens in mice. We also found that NP DNA coimmunization augments in vivo proliferation of adoptively transferred antigen-specific CD4 and CD8 T cells, which enhanced protective immunity against tumor challenge. Our results suggest that NP DNA can serve as a novel genetic adjuvant in cocktail DNA vaccination.

• ALGAE
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• v.26 no.1
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• pp.33-40
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• 2011

Porphyroglossum is the last one of nine genera within the family Gelidiaceae that has yet to be analyzed by molecular markers. We analyzed rbcL and cox1 genes from P. zollingeri specimens collected near the type locality in Indonesia and compared them with other gelidioid algae. Thalli are cartilaginous, complanate, and up to 15 cm high. Abundant rhizoidal filaments are concentrated in the medullary layer. Tetrasporangial sori are on small, determinate ramuli. In all gene analyses, P. zollingeri consistently nested within Gelidium. The sister relationship of P. zollingeri to G. floridanum was well resolved. Because Gelidium has priority over Porphyroglossum, a new combination is proposed, viz. Gelidium zollingeri. Network analysis of the four cox1 haplotypes revealed many missing haplotypes, indicating high genetic diversity in the species.