• Journal of Microbiology and Biotechnology
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• v.34 no.9
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• pp.1836-1847
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• 2024

Polyethylene terephthalate (PET), one of the most widely used plastics in the world, causes serious environmental problems. Recently, scientists have been focused on the enzymatic degradation of PET, an environmentally friendly method that offers an attractive approach to the degradation and recycling of PET. In this work, PET hydrolase from Streptomyces sp. W2061 was biochemically characterized, and the biodegradation of PET was performed using the PET model substrate bis (2-hydroxyethyl terephthalate) (BHET). PET hydrolase has an isoelectric point of 5.84, and a molecular mass of about 50.31 kDa. The optimum pH and temperature were 7.0 and 40℃, respectively. LC-MS analysis of the enzymatic products showed that the PET hydrolase successfully degraded a single ester bond of BHET, leading to the formation of MHET. Furthermore, in silico characterization of the PET hydrolase protein sequence and its predicted three-dimensional structure was designed and compared with the well-characterized IsPETase from Ideonella sakaiensis. The structural analysis showed that the (Gly-x1-Ser-x2-Gly) serine hydrolase motif and the catalytic triad (Ser, Asp, and His) were conserved in all sequences. In addition, we integrated molecular dynamics (MD) simulations to analyze the variation in the structural stability of the PET hydrolase in the absence and presence of BHET. These simulations showed the formation of a stable complex between the PET hydrolase and BHET. To the best of our knowledge, this is the first study on Streptomyces sp. W2061 to investigate the BHET degradation activity of PET hydrolase, which has potential application in the biodegradation of plastics in the environment.

• Journal of the Korean Society of Food Science and Nutrition
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• v.29 no.1
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• pp.174-179
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• 2000

The nitrogenous compounds in the muscle extracts of cultured and wild olive flounder, Paralichthys olivaceous, were analyzed. The analyzed coumpounds were extractive nitrogen, free amino acids, oligopeptides, ATP and its related ompounds, quaternary ammonium bases, and guanidino compounds. The distribution pattern of these compounds in cultured and wild fish was found to be very similar. Although the ATP and its related compounds and creatine in the muscle of cultured fish were slightly abundant than those in the muscle of wild one, the extractive nitrogen, total free amino acid, oligopeptides, and TMAO were found to be slightly rich in the muscle of wild fish than those in the muscle of cultrued one. The moisture content of cultured fish was relatively lower but the protein and fat contents of cultured one were higher than those of wild fish. However the differences in the proximate composition, extractive nitrogen and nitrogenous compounds between two fishes were not significantly different.

• Analytical Science and Technology
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• v.32 no.6
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• pp.262-270
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• 2019

The stable isotopic composition of bone collagen plays an important role in reconstructing palaeodiet, nutrition, palaeoenvironment and their lifestyle. This is the first case in extracting palaeodietary information and breastfeeding pattern of Goryeo people using stable isotope analysis due to the lack of human remains in this period. We analyzed human bone collagen excavated from Gyeongju Donggung palace and Wolji pond No.3. The average values of δ¹³C and δ¹⁵N are as follows: (δ¹³C(‰) = -19.5 ± 0.9‰, δ¹⁵N(‰) = 11.1 ± 1.1 ‰, (n = 4). Stable carbon isotope values shows a mainly C₃ based diet such as rice and barley. Stable nitrogen isotope results implies the protein sources attributed to terrestrial animals. There are various age groups in this study, which are adult, child and infant. Two individuals within early childhood age ranges (< 3 years) shows more elevated δ¹⁵N values than that of adult and this result implies the continuation of breastfeeding in this group until the age of 3. The results provide new insight into the breastfeeding pattern of Goryeo people, where breastfeeding and weaning practices have important implication for fertility, population dynamics, migration pattern and disease.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.6
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• pp.807-817
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• 2008

Steers with ad libitum access to rice straw were assigned to four diets to evaluate the effects of maize or soybean hull supplementation on intake, in vivo digestibility, ruminal pH, VFA, ammonia-nitrogen ($NH_3-N$) and in situ ruminal disappearance of feed nutrients by cattle consuming rice straw. Supplement treatments were: no supplement (RS); soybean meal at 0.127% BW (SBM); cracked maize at 0.415% BW plus 0.044% BW soybean meal (MAIZE); or soybean hulls at 0.415% BW plus 0.044% BW soybean meal (HULLS). The MAIZE and HULLS diets were formulated to provide approximately 4 MJ of $NE_m$ per kg of diet. Rice straw DMI was not affected (p = 0.34) by supplement. Apparent dry matter (DM) digestibility was greater (p<0.001) for MAIZE and HULLS (56.6 and 60.0%, respectively) than for steers consuming SBM or RS (51.8 and 44.4%, respectively). Apparent NDF digestibility was greater (p<0.0004) for HULLS than MAIZE (61.7 vs. 58.0%, respectively) and apparent ADF digestibility was greater (p<0.0008) for HULLS than MAIZE (61.1 vs. 49.2%, respectively). There was no difference in apparent hemicellulose digestibility (p = 0.43). Analysis of ruminal fluid collected 0, 2, 4, 6, and 8 h post-feeding revealed ammonia-nitrogen was greatest (p<0.05) for steers on SBM and HULLS diets at 2 h (24.08 and 22.57 mg/dl, respectively) and total volatile fatty acids was greatest (p<0.05) for HULLS at 4 h (230 mM/L). In situ disappearance, measured at 0, 2, 4, 6, 8, 16 and 24 h, indicated that SBM, MAIZE and HULLS tended to enhance the digestibility of DM and fiber components of rice straw. In situ disappearance of rice straw DM was greatest for SBM and/or HULLS from 4 to 24 h (p = 0.03). Rice straw NDF and ADF disappearance was enhanced by supplementation from 16 to 24 h (p<0.02). Rice straw DM, NDF and ADF disappearances at 24 h were similar for MAIZE and HULLS treatments. When feeding cattle rice straw diets, energy and protein-based supplements are essential. This study showed that fiber-based supplements are just as, if not more, effective as starch-based supplements in rice straw utilization. This study shows that soybean hulls, in spite of their high fiber content, are as efficient as maize for supplementing rice straw primarily because fiber in soybean hulls is highly digestible as shown by in vivo digestibility and in situ disappearance.

• Applied Microscopy
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• v.41 no.4
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• pp.249-255
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• 2011

Neurons utilize a large quantity of energy for their survival and function, and thereby require active mitochondrial function. Mitochondrial morphology shows dynamic changes, depending on the cellular condition, and mitochondrial dynamics are required for neuronal development and function. In this study, we found that the length of mitochondria in the distal axon is significantly shorter than that of mitochondria in dendrites or proximal axons of cerebral cortical neurons, and the reason for this difference is the local fission within the axon. We also found that suppression of Drp1, a key regulator of mitochondrial fission, resulted in significant elongation of mitochondria in axons. Collectively, these results suggest that local mitochondrial fission within the axon contributes to region-dependent mitochondrial length differences in the axons of cortical neurons.

• The Korean Journal of Malacology
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• v.22 no.2
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• pp.109-113
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• 2006

Subcellular localization of a protein containing nuclear localization signals (NLS) has been well studied in many organisms ranging from invertebrates to vertebrates. However, no systematic analysis of NLS-containing proteins available from Mollusks has been reported. Here, we describe in silico screening of NLS-containing proteins using the mollusks database that contains 22,138 amino acids. To screen putative proteins with NLS-motif, we used both predict NLS and perl script. As a result, we have found 266 proteins containing NLS sequences which are about 1.2% out of the entire proteins. On the basis of KOG (The eukaryotic orthologous groups) analysis, we can't predict the precise functions of the NLS-containing proteins. However, we found out that these proteins belong to several types of proteins such as chromatin structure and dynamics, translation, ribosomal structure, biogenesis, and signal transduction mechanism. In addition, we have analysed these sequences based on the classes of mollusks. We could not find many from the species that are the main subjects of phylogenetic studies. In contrast, we noticed that cephalopods has the highest number of NLS-containing proteins. Thus, we have constructed mollusks NLS database and added these information and data to the mollusks database by constructing web interface. Taken together, these information will be very useful for those who are or will be studying NLS-containing proteins from mollusks.

• Experimental and Molecular Medicine
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• v.50 no.11
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• pp.5.1-5.14
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• 2018

Oxidative stress-induced mitochondrial dysfunction is implicated in the pathogenesis of intervertebral disc degeneration (IVDD). Sirtuin 3 (SIRT3), a sirtuin family protein located in mitochondria, is essential for mitochondrial homeostasis; however, the role of SIRT3 in the process of IVDD has remained elusive. Here, we explored the expression of SIRT3 in IVDD in vivo and in vitro; we also explored the role of SIRT3 in senescence, apoptosis, and mitochondrial homeostasis under oxidative stress. We subsequently activated SIRT3 using honokiol to evaluate its therapeutic potential for IVDD. We assessed SIRT3 expression in degenerative nucleus pulposus (NP) tissues and oxidative stress-induced nucleus pulposus cells (NPCs). SIRT3 was knocked down by lentivirus and activated by honokiol to determine its role in oxidative stress-induced NPCs. The mechanism by which honokiol affected SIRT3 regulation was investigated in vitro, and the therapeutic potential of honokiol was assessed in vitro and in vivo. We found that the expression of SIRT3 decreased with IVDD, and SIRT3 knockdown reduced the tolerance of NPCs to oxidative stress. Honokiol ($10{\mu}M$) improved the viability of NPCs under oxidative stress and promoted their properties of anti-oxidation, mitochondrial dynamics and mitophagy in a SIRT3-dependent manner. Furthermore, honokiol activated SIRT3 through the AMPK-PGC-$1{\alpha}$ signaling pathway. Moreover, honokiol treatment ameliorated IVDD in rats. Our study indicated that SIRT3 is involved in IVDD and showed the potential of the SIRT3 agonist honokiol for the treatment of IVDD.

• Journal of Ginseng Research
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• v.46 no.1
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• pp.156-166
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• 2022

Background: Panax ginseng Meyer (P. ginseng), a herb distributed in Korea, China and Japan, exerts benefits on diverse inflammatory conditions. However, the underlying mechanism and active ingredients remains largely unclear. Herein, we aimed to explore the active ingredients of P. ginseng against inflammation and elucidate underlying mechanisms. Methods: Inflammation model was constructed by lipopolysaccharide (LPS) in C57BL/6 mice and RAW264.7 macrophages. Molecular docking, molecular dynamics, surface plasmon resonance imaging (SPRi) and immunofluorescence were utilized to predict active component. Results: P. ginseng significantly inhibited LPS-induced lung injury and the expression of proinflammatory factors, including TNF-α, IL-6 and IL-1β. Additionally, P. ginseng blocked fluorescencelabeled LPS (LPS488) binding to the membranes of RAW264.7 macrophages, the phosphorylation of nuclear factor-κB (NF-κB) and mitogen-activated protein kinases (MAPKs). Furthermore, molecular docking demonstrated that ginsenoside Ro (GRo) docked into the LPS binding site of toll like receptor 4 (TLR4)/myeloid differentiation factor 2 (MD2) complex. Molecular dynamic simulations showed that the MD2-GRo binding conformation was stable. SPRi demonstrated an excellent interaction between TLR4/ MD2 complex and GRo (K_D value of 1.16 × 10^-9 M). GRo significantly inhibited LPS488 binding to cell membranes. Further studies showed that GRo markedly suppressed LPS-triggered lung injury, the transcription and secretion levels of TNF-α, IL-6 and IL-1β. Moreover, the phosphorylation of NF-κB and MAPKs as well as the p65 subunit nuclear translocation were inhibited by GRo dose-dependently. Conclusion: Our results suggest that GRo exerts anti-inflammation actions by direct inhibition of TLR4 signaling pathway.

• Journal of Life Science
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• v.33 no.8
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• pp.651-662
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• 2023

Peroxisomes, known as microbodies, are a class of morphologically similar subcellular organelles commonly found in most eukaryotic cells. They are 0.2~1.8 ㎛ in diameter and are bound by a single membrane. The matrix is usually finely granular, but occasionally crystalline or fibrillary inclusions are observed. They characteristically contain hydrogen peroxide (H₂O₂) generating oxidases and contain the enzyme catalase, thus confining the metabolism of the poisonous H₂O₂ within these organelles. Therefore, the eukaryotic organelles are greatly dynamic both in morphology and metabolism. Plant peroxisomes, in particular, are associated with numerous metabolic processes, including β-oxidation, the glyoxylate cycle and photorespiration. Furthermore, plant peroxisomes are involved in development, along with responses to stresses such as the synthesis of important phytohormones of auxins, salicylic acid and jasmonic acids. In the past few decades substantial progress has been made in the study of peroxisome biogenesis in eukaryotic organisms, mainly in animals and yeasts. Advancement of sophisticated techniques in molecular biology and widening of the range of genomic applications have led to the identification of most peroxisomal genes and proteins (peroxins, PEXs). Furthermore, recent applications of proteome study have produced fundamental information on biogenesis in plant peroxisomes, together with improving our understanding of peroxisomal protein targeting, regulation, and degradation. Nonetheless, despite this progress in peroxisome development, much remains to be explained about how peroxisomes originate from the endoplasmic reticulum (ER), then assemble and divide. Peroxisomes perform dynamic roles in many phases of plant development, and in this review, we focus on the latest progress in furthering our understanding of plant peroxisome functions, biogenesis, and dynamics.

• The Korean Journal of Physiology and Pharmacology
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• v.16 no.4
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• pp.255-264
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• 2012

The structures of the intact synaptosomal plasma membrane vesicles (SPMVs) isolated from bovine cerebral cortexs, and the outer and the inner monolayer separately, were evaluated with 1,6-diphenyl-1,3,5-hexatriene (DPH) and 1,3-di(1-pyrenyl)propane (Py-3-Py) as fluorescent reporters and trinitrophenyl groups as quenching agents. The methanol increased bulk rotational and lateral mobilities of SPMVs lipid bilayers. The methanol increased the rotational and lateral mobilities of the outer monolayers more than of the inner monolayers. n-(9-Anthroyloxy)stearic acid (n-AS) were used to evaluate the effect of the methanol on the rotational mobility at the 16, 12, 9, 6, and 2 position of aliphatic chains present in phospholipids of the SPMVs outer monolayers. The methanol decreased the anisotropy of the 16-(9-anthroyloxy)palmitic acid (16-AP), 12-(9-anthroyloxy)stearic acid (12-AS), 9-(9-anthroyloxy)stearic acid (9-AS), and 6-(9-anthroyloxy)stearic acid (6-AS) in the SPMVs outer monolayer but it increased the anisotropy of 2-(9-anthroyloxy)stearic acid (2-AS) in the monolayers. The magnitude of the increased rotational mobility by the methanol was in the order at the position of 16, 12, 9, and 6 of aliphatic chains in phospholipids of the outer monolayers. Furthermore, the methanol increased annular lipid fluidity and also caused membrane proteins to cluster. The important finding is that was far greater increase by methanol in annular lipid fluidity than increase in lateral and rotational mobilities by the methanol. Methanol alters the stereo or dynamics of the proteins in the lipid bilayers by combining with lipids, especially with the annular lipids. In conclusion, the present data suggest that methanol, in additions to its direct interaction with proteins, concurrently interacts with membrane lipids, fluidizing the membrane, and thus inducing conformational changes of proteins known to be intimately associated with membranes lipids.