• Genomics & Informatics
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• v.18 no.3
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• pp.29.1-29.11
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• 2020

Maize seed pigmentation is one of the important issue to develop maize seed breeding. The differently gene expression was characterized and compared for three inbred lines, such as the pigment accumulated seed (CM22) and non-pigmented seed (CM5 and CM19) at 10 days after pollination. We obtained a total of 63,870, 82,496, and 54,555 contigs by de novo assembly to identify gene expression in the CM22, CM5, and CM19, respectably. In differentially expressed gene analysis, it was revealed that 7,044 genes were differentially expressed by at least two-fold, with 4,067 upregulated in colored maize inbred lines and 2,977 upregulated in colorless maize inbred lines. Of them,18 genes were included to the anthocyanin biosynthesis pathways, while 15 genes were upregulated in both CM22/5 and CM22/19. Additionally, 37 genes were detected in the metabolic pathway concern to the seed pigmentation by BINs analysis using MAPMAN software. Finally, these differently expressed genes may aid in the research on seed pigmentation in maize breeding programs.

• BMB Reports
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• v.52 no.3
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• pp.163-164
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• 2019

The ribosomal synthesis of proteins in the eukaryotic cytosol has always been thought to start from the unformylated N-terminal (Nt) methionine (Met). In contrast, in virtually all nascent proteins in bacteria and eukaryotic organelles, such as mitochondria and chloroplasts, Nt-formyl-methionine (fMet) is the first building block of ribosomal synthesis. Through extensive approaches, including mass spectrometric analyses of the N-termini of proteins and molecular genetic techniques with an affinity-purified antibody for Nt-formylation, we investigated whether Nt-formylated proteins could also be produced and have their own metabolic fate in the cytosol of a eukaryote, such as yeast Saccharomyces cerevisiae. We discovered that Nt-formylated proteins could be generated in the cytosol by yeast mitochondrial formyltransferase (Fmt1). These Nt-formylated proteins were massively upregulated in the stationary phase or upon starvation for specific amino acids and were crucial for the adaptation to specific stresses. The stress-activated kinase Gcn2 was strictly required for the upregulation of Nt-formylated proteins by regulating the activity of Fmt1 and its retention in the cytosol. We also found that the Nt-fMet residues of Nt-formylated proteins could be distinct N-terminal degradation signals, termed fMet/N-degrons, and that Psh1 E3 ubiquitin ligase mediated the selective destruction of Nt-formylated proteins as the recognition component of a novel eukaryotic fMet/N-end rule pathway, termed fMet/N-recognin.

• Biomolecules & Therapeutics
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• v.29 no.1
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• pp.11-21
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• 2021

Adipose tissue secretes many adipokines which contribute to various metabolic processes, such as blood pressure, glucose homeostasis, inflammation and angiogenesis. The biology of adipose tissue in an obese individual is abnormally altered in a manner that increases the body's vulnerability to immune diseases, such as psoriasis. Psoriasis is considered a chronic inflammatory skin disease which is closely associated with being overweight and obese. Additionally, secretion of leptin, a type of adipokine, increases dependently on adipose cell size and adipose accumulation. Likewise, high leptin levels also aggravate obesity via development of leptin resistance, suggesting that leptin and obesity are closely related. Leptin induction in psoriatic patients is mainly driven by the interleukin (IL)-23/helper T (Th) 17 axis pathway. Furthermore, leptin can have an effect on various types of immune cells such as T cells and dendritic cells. Here, we discuss the relationship between obesity and leptin expression as well as the linkage between effect of leptin on immune cells and psoriasis progression.

• Genomics & Informatics
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• v.19 no.1
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• pp.2.1-2.10
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• 2021

BRAF inhibitors (e.g., vemurafenib) are widely used to treat metastatic melanoma with the BRAF V600E mutation. The initial response is often dramatic, but treatment resistance leads to disease progression in the majority of cases. Although secondary mutations in the mitogen-activated protein kinase signaling pathway are known to be responsible for this phenomenon, the molecular mechanisms governing acquired resistance are not known in more than half of patients. Here we report a genome- and transcriptome-wide study investigating the molecular mechanisms of acquired resistance to BRAF inhibitors. A microfluidic chip with a concentration gradient of vemurafenib was utilized to rapidly obtain therapy-resistant clones from two melanoma cell lines with the BRAF V600E mutation (A375 and SK-MEL-28). Exome and transcriptome data were produced from 13 resistant clones and analyzed to identify secondary mutations and gene expression changes. Various mechanisms, including phenotype switching and metabolic reprogramming, have been determined to contribute to resistance development differently for each clone. The roles of microphthalmia-associated transcription factor, the master transcription factor in melanocyte differentiation/dedifferentiation, were highlighted in terms of phenotype switching. Our study provides an omics-based comprehensive overview of the molecular mechanisms governing acquired resistance to BRAF inhibitor therapy.

• Genomics & Informatics
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• v.21 no.1
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• pp.5.1-5.13
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• 2023

Neisseria gonorrhoeae is a Gram-negative aerobic diplococcus bacterium that primarily causes sexually transmitted infections through direct human sexual contact. It is a major public health threat due to its impact on reproductive health, the widespread presence of antimicrobial resistance, and the lack of a vaccine. In this study, we used a bioinformatics approach and performed subtractive genomic methods to identify potential drug targets against the core proteome of N. gonorrhoeae (12 strains). In total, 12,300 protein sequences were retrieved, and paralogous proteins were removed using CD-HIT. The remaining sequences were analyzed for non-homology against the human proteome and gut microbiota, and screened for broad-spectrum analysis, druggability, and anti-target analysis. The proteins were also characterized for unique interactions between the host and pathogen through metabolic pathway analysis. Based on the subtractive genomic approach and subcellular localization, we identified one cytoplasmic protein, 2Fe-2S iron-sulfur cluster binding domain-containing protein (NGFG RS03485), as a potential drug target. This protein could be further exploited for drug development to create new medications and therapeutic agents for the treatment of N. gonorrhoeae infections.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.254-254
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• 2022

Astragalus membranaceus (A. membranaceus) has traditionally been used as a medicinal plant in East Asia for the treatment ofvarious diseases. A. membranaceus belongs to the legume family and is known to be rich in substances such as flavonoids and saponins. Recent pharmacological studies of A. membranaceus have shown that the plant has immunomodulatory, anti-oxidant, anti-cancer, and anti-inflammatory effects. However, knowledge of major biosynthetic pathways in A. membranaceu is still lacking. Recently developed sequencing techniques enable high-quality transcriptome analysis in plants, which is recognized as an important part in elucidating the regulatory mechanisms of many plant secondary metabolic pathways. However, it is difficult to predict the number of transcripts because plant transcripts contain a large number of isoforms due to alternative splicing events, which can vary depending on the assembly platform used. In this study, we constructed three unigene sets using Pac-Bio isoform sequencing, Trinity and rnaSPAdes assembly for detailed transcriptome analysis mA. membranaceus. Furthermore, all genes involved in the flavonoid biosynthetic pathway were searched from three unigene sets, and structural comparisons and expression profiles between these genes were analyzed. The isoflavone synthesis was active in most tissues. Flavonol synthesis was mainly active in leaves and flowers, and anthocyanin synthesis was specific in flowers. Gene structural analysis revealed structural differences in the flavonoid-related genes derived from the three unigene sets. This study suggests the need for the application of multiple unigene sets for the analysis of key biosynthetic pathways in plants.

• Journal of Microbiology and Biotechnology
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• v.33 no.10
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• pp.1268-1280
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• 2023

Echinacoside (ECH) is a naturally occurring phenylethanoid glycoside, isolated from Echinacea angustifolia, and this study aimed to analyze its effect on thermogenesis and its interaction with dopaminergic receptors 1 and 5 (DRD1 and DRD5) in 3T3-L1 white adipocytes and mice models. We employed RT-PCR, immunoblot, immunofluorescence, a staining method, and an assay kit to determine its impact. ECH showed a substantial increase in browning signals in vitro and a decrease in adipogenic signals in vivo. Additionally, analysis of the iWAT showed that the key genes involved in beiging, mitochondrial biogenesis, and ATP-dependent thermogenesis were upregulated while adipogenesis and lipogenesis genes were downregulated. OXPHOS complexes, Ca²⁺ signaling proteins as well as intracellular Ca²⁺ levelswere also upregulated in 3T3-L1 adipocytes following ECH treatment. This was collectively explained by mechanistic studies which showed that ECH mediated the beiging process via the DRD1/5-cAMP-PKA and subsequent downstream molecules, whereas it co-mediated the α1-AR-signaling thermogenesis via the DRD1/5/SERCA2b/RyR2/CKmt pathway in 3T3-L1 adipocytes. Animal experiments revealed that there was a 12.28% reduction in body weight gain after the ECH treatment for six weeks. The effects of ECH treatment on adipose tissue can offer more insights into the treatment of obesity and metabolic syndrome.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2021.04a
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• pp.5-5
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• 2021

Alcoholic and nonalcoholic steaohepatitis is a leading form of chronic liver disease with few biomakers ad treatment options currently available. a progressive disease of NAFLD may lead to fibrosis, cirrhosis, and hepatocellular carcinoma. Recently, we extracted HIMH0021, which is an active flavonoid component in the Acer tegmentosum extract, has been shown to protect against liver damage caused by hepatic dysfunction. Therefore, in this study, we aimed to investigate whether HIMH0021 could regulate steatohepatitis and liver fibrosis during alcoholic or nonalcoholic metabolic process. HIMH0021, which was isolated from the active methanol extract of A. tegmentosum, inhibited alcohol-induced steatosis and attenuated the serum levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) during hepatocellular alcohol metabolism, both of which promote lipogenesis as well as liver inflammation. Treatment with HIMH0021 conferred protection against lipogenesis and liver injury, inhibited the expression of cytochrome P4502E1, and increased serum adiponectin levels in the mice subjected to chronic-plus-binge feeding. Furthermore, in hepatocytes, HIMH0021 activated fatty acid oxidation by activating pAMPK, which comprises pACC and CPT1a. These findings suggested that HIMH0021 could be used to target a TNFα-related pathway for treating patients with alcoholic hepatitis.

• Journal of Yeungnam Medical Science
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• v.40 no.4
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• pp.328-334
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• 2023

An aging population and changes in dietary habits have increased the incidence of diabetes, resulting in complications such as diabetic foot ulcers (DFUs). DFUs can lead to serious disabilities, substantial reductions in patient quality of life, and high financial costs for society. By understanding the etiology and pathophysiology of DFUs, their occurrence can be prevented and managed more effectively. The pathophysiology of DFUs involves metabolic dysfunction, diabetic immunopathy, diabetic neuropathy, and angiopathy. The processes by which hyperglycemia causes peripheral nerve damage are related to adenosine triphosphate deficiency, the polyol pathway, oxidative stress, protein kinase C activity, and proinflammatory processes. In the context of hyperglycemia, the suppression of endothelial nitric oxide production leads to microcirculation atherosclerosis, heightened inflammation, and abnormal intimal growth. Diabetic neuropathy involves sensory, motor, and autonomic neuropathies. The interaction between these neuropathies forms a callus that leads to subcutaneous hemorrhage and skin ulcers. Hyperglycemia causes peripheral vascular changes that result in endothelial cell dysfunction and decreased vasodilator secretion, leading to ischemia. The interplay among these four preceding pathophysiological factors fosters the development and progression of infections in individuals with diabetes. Charcot neuroarthropathy is a chronic and progressive degenerative arthropathy characterized by heightened blood flow, increased calcium dissolution, and repeated minor trauma to insensate joints. Directly and comprehensively addressing the pathogenesis of DFUs could pave the way for the development of innovative treatment approaches with the potential to avoid the most serious complications, including major amputations.

• Journal of Pharmacopuncture
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• v.27 no.2
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• pp.101-109
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• 2024

Objectives: Dyslipidemia has currently become a major health challenge that still opens for safer and more effective modes of treatment. The plant Pandanus amaryllifolius Roxb. (pandan) has been indicated to contain active ingredients that interfere with the pathological pathway of dyslipidemia. The aim of the study was to test the effects of pandan leaves ethanol extract on lipid and proinflammatory profiles in a rat dyslipidemic model. Methods: Dyslipidemia was induced by administration of high-fat feed for 8 weeks. Treatments (vehicle, the reference drug simvastatin at 1.8 mg/kg, and extract at 200, 300 or 600 mg/kg) were given for 4 weeks following the completion of induction. Results: Significant post-treatment decreases in total cholesterol, low density lipoprotein (LDL), and triglyceride levels in groups receiving all doses of extract and simvastatin were observed. Similar results were also found in regards to proinflammatory cytokines levels. Pandan extracts significantly lowered the concentrations of IL-6, TNF-α, and NFκB p65. Characterization of metabolite contents of the extract confirmed the presence of the previously suggested active alkaloids pandamarilactonine-A and B. Conclusion: Taken together, results of the present study implied the ameliorating effects of pandan leaves ethanol extract in dyslipidemic condition which is potential for opening an avenue in combating this essential component of metabolic disorder.