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Kim DG, Cho S, Lee KY, Cheon SH, Yoon HJ, Lee JY, Kim D, Shin KS, Koh CH, Koo JS, Choi Y, Lee HH, Oh YK, Jeong YS, Chung SJ, Baek M, Jung KY, Lim HJ, Kim HS, Park SJ, Lee JY, Lee SJ, Lee BJ. Crystal structures of human NSDHL and development of its novel inhibitor with the potential to suppress EGFR activity. Cell Mol Life Sci 2021; 78:207-225. [PMID: 32140747 PMCID: PMC11068002 DOI: 10.1007/s00018-020-03490-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/29/2020] [Accepted: 02/17/2020] [Indexed: 02/03/2023]
Abstract
NAD(P)-dependent steroid dehydrogenase-like (NSDHL), an essential enzyme in human cholesterol synthesis and a regulator of epidermal growth factor receptor (EGFR) trafficking pathways, has attracted interest as a therapeutic target due to its crucial relevance to cholesterol-related diseases and carcinomas. However, the development of pharmacological agents for targeting NSDHL has been hindered by the absence of the atomic details of NSDHL. In this study, we reported two X-ray crystal structures of human NSDHL, which revealed a detailed description of the coenzyme-binding site and the unique conformational change upon the binding of a coenzyme. A structure-based virtual screening and biochemical evaluation were performed and identified a novel inhibitor for NSDHL harboring suppressive activity towards EGFR. In EGFR-driven human cancer cells, treatment with the potent NSDHL inhibitor enhanced the antitumor effect of an EGFR kinase inhibitor. Overall, these findings could serve as good platforms for the development of therapeutic agents against NSDHL-related diseases.
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Lee KY, Kim DG, Lee KY, Pathak C, Koo JS, Ahn HC, Lee BJ. Structural and functional study of SaAcP, an acylphosphatase from Staphylococcus aureus. Biochem Biophys Res Commun 2020; 532:173-178. [PMID: 32838967 DOI: 10.1016/j.bbrc.2020.07.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 07/16/2020] [Indexed: 11/18/2022]
Abstract
Acylphosphatase is the smallest enzyme that is widely distributed in many diverse organisms ranging from archaebacteria to higher-eukaryotes including the humans. The enzyme hydrolyzes the carboxyl-phosphate bonds of the acyl phosphates which are important intermediates in glycolysis, membrane pumps, tricarboxylic acid cycle, and urea biosynthesis. Despite its biological importance in critical cellular functions, very limited structural investigations have been conducted on bacterial acylphosphatases. Here, we first unveiled the crystal structure of SaAcP, an acylphosphatase from gram-positive S. aureus at the atomic level. Structural insights on the active site together with mutation study provided greater understanding of the catalytic mechanism of SaAcP as a bacterial acylphosphatase and as a putative apyrase. Furthermore, through NMR titration experiment of SaAcP in its solution state, the dynamics and the alterations of residues affected by the phosphate ion were validated. Our findings elucidate the structure-function relationship of acylphosphatases in gram-positive bacteria and will provide a valuable basis for researchers in the field related to bacterial acylphosphatases.
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Kim JW, Cho JY, Kim DG, Nam BH, Nho ES, Kim BS, Kim YO, Kong HJ. Establishment of Conditions for Long-Term Maintenance of Primary Embryonic Cell Cultures from Olive Flounder Paralichthys olivaceus. Dev Reprod 2020; 24:207-214. [PMID: 33110952 PMCID: PMC7576961 DOI: 10.12717/dr.2020.24.3.207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/08/2020] [Accepted: 09/20/2020] [Indexed: 11/24/2022]
Abstract
Primary cell culture is a sufficient method frequently used to study the cellular
properties and mechanisms of isolated cells in a controlled environment. In this
study, an embryonic cell line (FGBC8) derived from the blastula stages of
embryos of olive flounder Paralichthys olivaceus was developed.
Furthermore, conditions for optimal long-term maintenance of this primary
embryonic cell culture were investigated. Morphologically, FGBC8 cells were
composed primarily of epithelial-like cells. FGBC8 cells were subcultured for
>160 passages over ~830 days. The doubling time of FGBC8 cells was
73.8 h, and the modal diploid chromosome number was 48. FGBC8 cells transfected
with green fluorescence protein (GFP)-expression plasmid exhibited a strong
signal 48 h after transfection. Consequently, we demonstrated that fish serum is
a crucial supplement for the long-term survival and maintenance of comparable
morphology in these primary embryonic cells. Our results can be used as a guide
for primary embryonic cell cultures for other fish species and may be useful for
cell biotechnological applications.
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Eun HJ, Lee KY, Kim DG, Im D, Lee BJ. Crystal structure of the YoeB Sa1-YefM Sa1 complex from Staphylococcus aureus. Biochem Biophys Res Commun 2020; 527:264-269. [PMID: 32446378 DOI: 10.1016/j.bbrc.2020.04.089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 04/16/2020] [Indexed: 12/31/2022]
Abstract
Toxin-antitoxin (TA) systems are ubiquitously found in bacteria and are related to cell maintenance and survival under environmental stresses such as heat shock, nutrient starvation, and antibiotic treatment. Here, we report for the first time the crystal structure of the Staphylococcus aureus TA complex YoeBSa1-YefMSa1 at a resolution of 1.7 Å. This structure reveals a heterotetramer with a 2:2 stoichiometry between YoeBSa1 and YefMSa1. The N-terminal regions of the YefMSa1 antitoxin form a homodimer characteristic of a hydrophobic core, and the C-terminal extended region of each YefMSa1 protomer makes contact with each YoeBSa1 monomer. The binding stoichiometry of YoeBSa1 and YefMSa1 is different from that of YoeB and YefM of E. coli (YoeBEc and YefMEc), which is the only structural homologue among YoeB-YefM families; however, the structures of individual YoeBSa1 and YefMSa1 subunits in the complex are highly similar to the corresponding structures in E. coli. In addition, docking simulation with a minimal RNA substrate provides structural insight into the guanosine specificity of YoeBSa1 for cleavage in the active site, which is distinct from the specificity of YoeBEc for adenosine rather than guanosine. Given the previous finding that YoeBSa1 exhibits fatal toxicity without inducing persister cells, the structure of the YoeBSa1-YefMSa1 complex will contribute to the design of a new category of anti-staphylococcal agents that disrupt the YoeBSa1-YefMSa1 complex and increase YoeBSa1 toxicity.
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Kim JW, Cho JY, Kim J, Kim DG, Nam BH, Kim YO, An CM, Kim BS, Park JY, Kong HJ. First report of cathepsin E in a teleost (Korean rose bitterling, Rhodeus uyekii): Molecular characterisation and tissue distribution. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 106:103607. [PMID: 31904433 DOI: 10.1016/j.dci.2020.103607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/31/2019] [Accepted: 01/01/2020] [Indexed: 06/10/2023]
Abstract
We isolated and characterised a cDNA encoding the aspartic protease cathepsin E (CTSE) in Korean rose bitterling, Rhodeus uyekii. The full-length Rhodeus uyekii CTSE (RuCTSE) cDNA (1396 bp) contains an open reading frame of 1218 bp, encoding 405 amino acids. Alignment of multiple CTSE protein sequences revealed that two of the aspartyl protease active site residues and a disulphide bond were well-conserved among the other CTSE sequences. Phylogenetic analysis revealed that RuCTSE is most closely related to freshwater fish cathepsin E. RuCTSE is widely expressed in the liver, spleen, ovary, testis, brain, eye, intestine, muscle, fin, stomach, and kidney. This first report of teleost CTSE will provide important information related to the identification of other cathepsin E genes in various fish species and will serve as a useful molecular tool to help clarify biological activities in other teleosts.
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Lee KY, Cheon SH, Kim DG, Lee SJ, Lee BJ. A structural study of TatD from Staphylococcus aureus elucidates a putative DNA-binding mode of a Mg 2+-dependent nuclease. IUCRJ 2020; 7:509-521. [PMID: 32431834 PMCID: PMC7201278 DOI: 10.1107/s2052252520003917] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/18/2020] [Indexed: 06/11/2023]
Abstract
TatD has been thoroughly investigated as a DNA-repair enzyme and an apoptotic nuclease, and still-unknown TatD-related DNases are considered to play crucial cellular roles. However, studies of TatD from Gram-positive bacteria have been hindered by an absence of atomic detail and the resulting inability to determine function from structure. In this study, an X-ray crystal structure of SAV0491, which is the TatD enzyme from the Gram-positive bacterium Staphylococcus aureus (SaTatD), is reported at a high resolution of 1.85 Å with a detailed atomic description. Although SaTatD has the common TIM-barrel fold shared by most TatD-related homologs, and PDB entry 2gzx shares 100% sequence identity with SAV0491, the crystal structure of SaTatD revealed a unique binding mode of two phosphates interacting with two Ni2+ ions. Through a functional study, it was verified that SaTatD has Mg2+-dependent nuclease activity as a DNase and an RNase. In addition, structural comparison with TatD homologs and the identification of key residues contributing to the binding mode of Ni2+ ions and phosphates allowed mutational studies to be performed that revealed the catalytic mechanism of SaTatD. Among the key residues composing the active site, the acidic residues Glu92 and Glu202 had a critical impact on catalysis by SaTatD. Furthermore, based on the binding mode of the two phosphates and structural insights, a putative DNA-binding mode of SaTatD was proposed using in silico docking. Overall, these findings may serve as a good basis for understanding the relationship between the structure and function of TatD proteins from Gram-positive bacteria and may provide critical insights into the DNA-binding mode of SaTatD.
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Oh R, Lee MJ, Kim YO, Nam BH, Kong HJ, Kim JW, Park JY, Seo JK, Kim DG. Myticusin-beta, antimicrobial peptide from the marine bivalve, Mytilus coruscus. FISH & SHELLFISH IMMUNOLOGY 2020; 99:342-352. [PMID: 32061872 DOI: 10.1016/j.fsi.2020.02.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/07/2020] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
We isolated and purified an antimicrobial peptide (AMP) from the mantle of the hard-shelled mussel, Mytilus coruscus. The peptide was purified through C18 reversed-phase high-performance liquid chromatography, and displayed antibacterial activity. Total molecular mass of 11,182 Da was determined using matrix-assisted laser desorption ionization time-of-flight mass spectrophotometry. The N-terminal 23-amino acid sequence of its purified peak was obtained through Edman degradation, revealing 82% identity with myticusin-1 of M. coruscus. Complete sequence of the target peptide was determined through cDNA cloning and rapid amplification of cDNA ends. The complete sequence comprised 574 bp with a 387-bp open reading frame (ORF) encoding 24 amino acids of a signal peptide and 104 amino acids of a mature peptide, which was named myticusin-beta. Furthermore, we discovered two novel isoforms of myticusin-beta. We constructed and expressed recombinant myticusin-beta, which displayed antimicrobial activity against gram-positive (Bacillus cereus, Bacillus subtilis, Clostridium perfringens, Staphylococcus aureus, Streptococcus iniae, Streptococcus mutans) and gram-negative bacteria (Escherichia coli, Pseudomonas aeruginosa, Vibrio alginolyticus, Klebsiella pneumoniae). Purified recombinant myticusin-beta also showed anti-parasitic activity at various concentrations. A short AMP analog was designed and synthesized based on the sequence of myticusin-beta, with markedly improved antimicrobial activity. Expression of myticusin-beta was detected in the mantle at the highest level, followed by hemocytes. The results obtained in this work suggest that myticusin-beta is an immune-related AMP of M. coruscus and an effective alternative to antibiotics.
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Yang K, Kang YY, Ahn HJ, Kim DG, Park NK, Choi SQ, Won JC, Kim YH. Porous boron nitride/polyimide composite films with high thermal diffusivity and low dielectric properties via high internal phase Pickering emulsion method. J IND ENG CHEM 2020. [DOI: 10.1016/j.jiec.2019.10.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Zhang H, Chavez MB, Kolli TN, Tan MH, Fong H, Chu EY, Li Y, Ren X, Watanabe K, Kim DG, Foster BL. Dentoalveolar Defects in the Hyp Mouse Model of X-linked Hypophosphatemia. J Dent Res 2020; 99:419-428. [PMID: 31977267 DOI: 10.1177/0022034520901719] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Mutations in PHEX cause X-linked hypophosphatemia (XLH), a form of hypophosphatemic rickets. Hyp (Phex mutant) mice recapitulate the XLH phenotype. Dental disorders are prevalent in individuals with XLH; however, underlying dentoalveolar defects remain incompletely understood. We analyzed Hyp mouse dentoalveolar defects at 42 and 90 d postnatal to comparatively define effects of XLH on dental formation and function. Phex mRNA was expressed by odontoblasts (dentin), osteocytes (bone), and cementocytes (cellular cementum) in wild-type (WT) mice. Enamel density was unaffected, though enamel volume was significantly reduced in Hyp mice. Dentin defects in Hyp molars were indicated histologically by wide predentin, thin dentin, and extensive interglobular dentin, confirming micro-computed tomography (micro-CT) findings of reduced dentin volume and density. Acellular cementum was thin and showed periodontal ligament detachment. Mechanical testing indicated dramatically altered periodontal mechanical properties in Hyp versus WT mice. Hyp mandibles demonstrated expanded alveolar bone with accumulation of osteoid, and micro-CT confirmed decreased bone volume fraction and alveolar bone density. Cellular cementum area was significantly increased in Hyp versus WT molars owing to accumulation of hypomineralized cementoid. Histology, scanning electron microscopy, and nanoindentation revealed hypomineralized "halos" surrounding Hyp cementocyte and osteocyte lacunae. Three-dimensional micro-CT analyses confirmed larger cementocyte/osteocyte lacunae and significantly reduced perilacunar mineral density. While long bone and alveolar bone osteocytes in Hyp mice overexpressed fibroblast growth factor 23 (Fgf23), its expression in molars was much lower, with cementocyte Fgf23 expression particularly low. Expression and distribution of other selected markers were disturbed in Hyp versus WT long bone, alveolar bone, and cementum, including osteocyte/cementocyte marker dentin matrix protein 1 (Dmp1). This study reports for the first time a quantitative analysis of the Hyp mouse dentoalveolar phenotype, including all mineralized tissues. Novel insights into cellular cementum provide evidence for a role for cementocytes in perilacunar mineralization and cementum biology.
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Han ES, Na GH, Choi HJ, You YK, Kim DG. Effectiveness of Perioperative Immunologic Markers Monitoring for Predicting Early Acute Cellular Rejection After Living Donor Liver Transplantation. Transplant Proc 2019; 51:2648-2654. [PMID: 31477418 DOI: 10.1016/j.transproceed.2019.03.077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/20/2019] [Accepted: 03/04/2019] [Indexed: 11/25/2022]
Abstract
BACKGROUND The objective of this study was to determine whether perioperative immunologic markers monitoring could predict early acute cellular rejection (ACR) after living donor liver transplantation (LDLT). MATERIALS AND METHODS From September 2010 to June 2013, a total of 172 patients underwent LDLT at our transplant center. Of them, 26 patients were excluded because of infection. We retrospectively reviewed the remaining 146 patients. CD4 lymphocyte activity, T cell subsets test, and serum cytokine panel were checked on the day before transplantation and at 20 days after transplantation. These patients were divided into 3 groups: 1. normal liver function test (LFT) group; 2. increased LFT without rejection group; and 3. early ACR group. We excluded the increased LFT without rejection group in order to rule out multiple factors influencing immunologic factors. RESULTS CD4 lymphocyte activity (P = .004) was significantly increased while CD4+/CD25+/FOXP3+ cells (P < .001) and interleukin (IL)-17 (P = .002) levels were significantly decreased during the perioperative period. Pretransplant IL-6 (P = .014) and IL-17 (P = .029) levels in the early ACR group were significantly lower than those in the normal LFT group. The proportion of patients with increased IL-6 during perioperative period in the early ACR group was higher than that in the normal LFT group, although the difference was not statistically significant (P = .065). CONCLUSION Our results suggest that IL-6 and IL-17 levels are associated with early ACR in LDLT patients. However, whether monitoring perioperative immunologic markers could predict early ACR remains unclear. Further prospective studies are needed to reach a definite conclusion.
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Kim DG, Gomberg MA, Gushchin AE, Zaycev AV. [Non-gonococcal urethritis in men]. UROLOGIIA (MOSCOW, RUSSIA : 1999) 2019:122-128. [PMID: 31535818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This literature review is dedicated to urethritis which is one of the most common disorders of urogenital tract in men. The current views in its etiology as well as problems in diagnosis with the main being the frequent inability to isolate etiological factor of inflammation it the urethra are described. The analysis of literature suggests a possible role of bacteria, which are associated with bacterial vaginosis in women, in the development of the urethritis in men. However, the frequency of such urethritis and causative role of specific pathogens has not been studied yet. Meanwhile, the exact determination of the causes of inflammation has direct influence on the choice of appropriate etiologic treatment and can increase its efficiency.
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Lee JM, Noh GY, Kim BG, Yoo Y, Choi WJ, Kim DG, Yoon HG, Kim YS. Synthesis of Poly(phenylene polysulfide) Networks from Elemental Sulfur and p-Diiodobenzene for Stretchable, Healable, and Reprocessable Infrared Optical Applications. ACS Macro Lett 2019; 8:912-916. [PMID: 35619488 DOI: 10.1021/acsmacrolett.9b00306] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The synthesis and characterization of poly(phenylene polysulfide) networks (PSNs) with controlled average sulfur ranks, from elemental sulfur (ES) and p-diiodobenzene (DIB), are investigated. The PSN films, prepared via simple hot pressing, are found to possess large extensibility up to around 300% and complete recovery of shape and mechanical properties after deformation, which are attributed to the loosely cross-linked network structures mainly consisting of linear poly(phenylene polysulfide) chains. The covalent polysulfide linkages in the PSNs also exhibit dynamic behaviors under ultraviolet (UV) or thermal treatment, thus, enabling self-healing and reprocessing of the films when scratched and broken, respectively. Combined with the unique mechanical properties of the PSNs, their high refractive index and excellent infrared (IR) transparency contribute to the preparation of stretchable, healable, and reprocessable IR transmitting materials for potential deformable and stretchable optical applications.
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Kim YO, Park IS, Park S, Kim H, Nam BH, Kim DG, Won SM, Yoon JH. Aliishimia ponticola gen. nov., sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2019; 69:3109-3115. [PMID: 31334695 DOI: 10.1099/ijsem.0.003596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated MYP11T, was isolated from seawater around Jeju island, Republic of Korea and identified by polyphasic taxonomic study. A neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain MYP11T joined the cluster comprising the type strains of Shimiaabyssi, Shimiaaestuarii and Shimiaaquaeponti, showing 16S rRNA gene sequence similarities of 96.3-96.8 %. Strain MYP11T exhibited 16S rRNA gene sequence similarity values of 94.2-94.9 % to the type strains of other Shimia species. In the upgma dendrogram based on the average nucleotide identity values of genomic sequences, strain MYP11T formed an evolutionary lineage independent of those of Shimia species and other taxa. Strain MYP11T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c and cyclo C19 : 0 ω8c as the major fatty acids. The major polar lipids of strain MYP11T were phosphatidylcholine, phosphatidylglycerol, two unidentified lipids and one unidentified aminolipid. The DNA G+C content of strain MYP11T was 63.1 or 61.5 mol%. The differences in the fatty acid and polar lipid profiles and DNA G+C contents made it reasonable to distinguish strain MYP11T from the type strains of S. abyssi, S. aestuarii and S. aquaeponti and those of other Shimia species. On the basis of the polyphasic data presented here, strain MYP11T is considered to constitute a new genus and species within the class Alphaproteobacteria, for which the name Aliishimia ponticola gen. nov., sp. nov. is proposed. The type strain is MYP11T (=KCTC 62899T=NBRC 113544T).
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Kim YO, Park S, Park IS, Nam BH, Kim DG, Yoon JH. Empedobacter tilapiae sp. nov., isolated from an intestine of Nile tilapia ( Oreochromis niloticus). Int J Syst Evol Microbiol 2019; 69:2781-2786. [PMID: 31246165 DOI: 10.1099/ijsem.0.003558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
A Gram-stain-negative, aerobic, non-motile and ovoid or rod-shaped bacterial strain, MRS2T, was isolated from an intestine of Nile tilapia (Oreochromisniloticus) collected from the Republic of Korea. Strain MRS2T grew optimally at 30 °C and in the presence of 0-2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain MRS2T clustered with the type strains of Empedobacter species. It exhibited the highest 16S rRNA gene sequence similarity (98.5 %) to the type strain of Empedobacter falsenii and sequence similarities of 97.4-97.6 % to the type strains of two other Empedobacter species. Strain MRS2T contained MK-6 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH and iso-C15 : 0 as the major fatty acids. The major polar lipids of strain MRS2T were phosphatidylethanolamine, one unidentified lipid and one unidentified aminolipid. The DNA G+C contents of strain MRS2T were 32.2 mol% or 30.65 mol%. Strain MRS2T exhibited DNA-DNA relatedness values of 12-20 % to the type strains of Empedobacter falsenii, Empedobacter brevis and Empedobacter stercoris. The average nucleotide identity values between strain MRS2T and five strains of E. falsenii and E. brevis were 84.8-91.0 %. The phylogenetic, genetic and differential phenotypic properties indicated that strain MRS2T is separated from Empedobacter species. On the basis of the data presented here, strain MRS2T is considered to represent a novel species of the genus Empedobacter, for which the name Empedobactertilapiae sp. nov. is proposed. The type strain is MRS2T (=KCTC 62904T=NBRC 113550T).
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Jo YH, Choi WM, Kim DG, Zargaran A, Sohn SS, Kim HS, Lee BJ, Kim NJ, Lee S. FCC to BCC transformation-induced plasticity based on thermodynamic phase stability in novel V 10Cr 10Fe 45Co xNi 35-x medium-entropy alloys. Sci Rep 2019; 9:2948. [PMID: 30814569 PMCID: PMC6393512 DOI: 10.1038/s41598-019-39570-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 01/21/2019] [Indexed: 11/09/2022] Open
Abstract
We introduce a novel transformation-induced plasticity mechanism, i.e., a martensitic transformation from fcc phase to bcc phase, in medium-entropy alloys (MEAs). A VCrFeCoNi MEA system is designed by thermodynamic calculations in consideration of phase stability between bcc and fcc phases. The resultantly formed bcc martensite favorably contributes to the transformation-induced plasticity, thereby leading to a significant enhancement in both strength and ductility as well as strain hardening. We reveal the microstructural evolutions according to the Co-Ni balance and their contributions to a mechanical response. The Co-Ni balance plays a leading role in phase stability and consequently tunes the cryogenic-temperature strength-ductility balance. The main difference from recently-reported metastable high-entropy dual-phase alloys is the formation of bcc martensite as a daughter phase, which shows significant effects on strain hardening. The hcp phase in the present MEA mostly acts as a nucleation site for the bcc martensite. Our findings demonstrate that the fcc to bcc transformation can be an attractive route to a new MEA design strategy for improving cryogenic strength-ductility.
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Nam BH, Park EH, Shin EH, Kim YO, Kim DG, Kong HJ, Park JY, Seo JK. Development of novel antimicrobial peptides derived from anti-lipopolysaccharide factor of the swimming crab, Portunus trituberculatus. FISH & SHELLFISH IMMUNOLOGY 2019; 84:664-672. [PMID: 30336284 DOI: 10.1016/j.fsi.2018.10.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 06/08/2023]
Abstract
Anti-lipopolysaccharide factors (ALFs) are a representative host defense protein in crustaceans. In this study, we successfully developed two novel antimicrobial peptides (AMPs), named crab-ALF2A and crab-ALF6A, which contain changes to the amino acid sequences of the lipopolysaccharide binding domain and signal peptide, respectively, of the ALF of the swimming crab Portunus trituberculatus. The crab-ALF2A peptide showed potent antimicrobial activity against the Gram-positive bacteria Bacillus cereus, Staphylococcus aureus, and Streptococcus iniae (minimal effective concentration [MEC] 1.51-1.93 μg/mL) and the Gram-negative bacteria Pseudomonas aeruginosa and Escherichia coli (MEC 1.87-1.98 μg/mL), with maximal bactericidal activity at a peptide concentration of 5 μg/mL. The crab-ALF6A peptide also showed potent antimicrobial activity against B. cereus, S. aureus, and S. iniae (MEC 1.49-2.3 μg/mL) and P. aeruginosa and E. coli (MEC 1.72-1.19 μg/mL) at a peptide concentration of 5 μg/mL. Notably, the crab-ALF2A and crab-ALF6A peptides exhibited strong activity against Candida albicans (MECs of 2.11 and 1.95 μg/mL, respectively). These activities were stable following heat treatment. Moreover, the effect of crab-ALF2A and crab-ALF6A peptide treatment on microbe cell morphology was confirmed by scanning electron microscopy. Membrane disruption and damage, and the leakage of cytoplasmic content were clearly observed. A downsizing peptide approach illustrated that the hexapeptide ALF6A8 (RVLLRL) was the shortest peptide showing significant antimicrobial activity. Our approach allows for the generation of novel antimicrobial peptides in a cost effective manner as potential next-generation antibiotics.
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Cha EJ, Lee DS, Kim H, Kim YH, Kim BG, Yoo Y, Kim YS, Kim DG. Tailoring biomimetic polymer networks towards an unprecedented combination of versatile mechanical characteristics. RSC Adv 2019; 9:15780-15784. [PMID: 35521414 PMCID: PMC9064385 DOI: 10.1039/c9ra02760b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 05/13/2019] [Indexed: 12/02/2022] Open
Abstract
Biomimetic polymeric materials, adopting the basic molecular design principles of biological materials, have been extensively studied in recent years but it is still challenging to combine assorted mechanical characteristics in a single material. Here, we present a simple and effective strategy to prepare mechanically robust yet resilient biomimetic polymer networks by utilizing dual noncovalent and covalent cross-linkings. Tailoring the dual cross-links consisting of thiourea noncovalent interactions and epoxy–amine covalent linkages in the biomimetic polymer networks enables a rare combination of excellent elastic modulus (1.1 GPa), yield stress (39 MPa), extensibility (320%), as well as complete strain and performance recovery after deformation at room temperature. The biomimetic polymer networks also exhibit highly adaptive mechanical properties in response to multiple-stimuli including strain rate, temperature, light, and solvent. A simple and effective strategy to prepare biomimetic polymer networks with stiff, strong, tough, resilient, and adaptive mechanical properties, through controlling thiourea noncovalent and epoxy–amine covalent cross-linkings, is presented.![]()
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Kim NK, Cha EJ, Jung M, Kim J, Jeong GJ, Kim YS, Choi WJ, Kim BS, Kim DG, Lee JC. 3D hierarchical scaffolds enabled by a post-patternable, reconfigurable, and biocompatible 2D vitrimer film for tissue engineering applications. J Mater Chem B 2019. [DOI: 10.1039/c9tb00221a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A mechanically tissue-like, biocompatible vitrimer yields 3D hierarchical tissue engineering scaffolds via hot embossing patterning and additional reconfiguration processes.
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Oh R, Lee MJ, Kim YO, Nam BH, Kong HJ, Kim JW, Park JY, Seo JK, Kim DG. Purification and characterization of an antimicrobial peptide mytichitin-chitin binding domain from the hard-shelled mussel, Mytilus coruscus. FISH & SHELLFISH IMMUNOLOGY 2018; 83:425-435. [PMID: 30195913 DOI: 10.1016/j.fsi.2018.09.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/23/2018] [Accepted: 09/05/2018] [Indexed: 06/08/2023]
Abstract
An antimicrobial peptide with 55 amino acid residues was purified by C18 reversed-phase high-performance liquid chromatography (HPLC) from foot extract of the hard-shelled mussel, Mytilus coruscus. This peptide showed strong antimicrobial activity against Gram-positive and Gram-negative bacteria, as well as fungi. The purified peptide was determined to have a molecular mass of 6202 Da by matrix-assisted laser desorption/ionization time-of-flight mass spectrophotometry (MALDI-TOF/MS). The identified 20-amino acid sequence of the purified peak by Edman degradation shared 100% identity with the N-terminal regions of mytichitin-1, mytichitin-2, mytichitin-3, mytichitin-4, mytichitin-5, and chitinase-like protein-1, and so was named mytichitin-CBD. The cDNA of mytichitin-CBD was cloned and sequenced by rapid amplification of cDNA ends (RACE). The mRNA transcripts were mainly detected in foot tissue, and they were up-regulated and peaked at 4 h after bacterial infection. We constructed and expressed recombinant mytichitin-CBD protein which displayed antimicrobial activity against Gram-negative bacteria Gram-positive bacteria and the fungus as well as anti-parasitic activity against scuticociliates. The results of this study demonstrate that the peptide isolated from M. coruscus is related to the innate immune system of this marine invertebrate and is a possible alternative to antibiotics.
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Kwon OH, Ha T, Kim DG, Kim BG, Kim YS, Shin TJ, Koh WG, Lim HS, Yoo Y. Anisotropy-Driven High Thermal Conductivity in Stretchable Poly(vinyl alcohol)/Hexagonal Boron Nitride Nanohybrid Films. ACS APPLIED MATERIALS & INTERFACES 2018; 10:34625-34633. [PMID: 30216038 DOI: 10.1021/acsami.8b12075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Controlling the anisotropy of two-dimensional materials with orientation-dependent heat transfer characteristics is a possible solution to resolve severe thermal issues in future electronic devices. We demonstrate a dramatic enhancement in the in-plane thermal conductivity of stretchable poly(vinyl alcohol) (PVA) nanohybrid films containing small amounts (below 10 wt %) of hexagonal boron nitride ( h-BN) nanoplatelets. The h-BN nanoplatelets were homogeneously dispersed in the PVA polymer solution by ultrasonication without additional surface modification. The mixture was used to prepare thermally conductive nanocomposite films. The in-plane thermal conductivity of the resulting PVA/ h-BN nanocomposite films increased to 6.4 W/mK when the strain was increased from 0 to 100% in the horizontal direction. More specifically, the thermal conductivity of a PVA/ h-BN composite film with 10 wt % filler loading can be improved by up to 32 times as compared to pristine PVA. This outstanding thermal conductivity value is significantly larger than that of materials currently used in in-plane thermal management systems. This result is attributed to the anisotropic alignment of h-BN particles in the PVA chain matrix during stretching, enhancing phonon conductive paths and hence improving the thermal conductivity and thermal properties of PVA/ h-BN nanocomposite films. These polymer nanocomposites have low cost as the amount of expensive conductive fillers is reduced and can be potentially used as high-performance materials for thermal management systems such as heat sink and thermal interface materials, for future electronic and electrical devices.
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Hong SY, Kim DG, Kim YO, Park JY, Seo JK, Nam BH, Hong YK. Purification and cDNA cloning of the antimicrobial peptide apMolluscidin from the pen shell, Atrina pectinata. FISH & SHELLFISH IMMUNOLOGY 2018; 81:408-415. [PMID: 30055252 DOI: 10.1016/j.fsi.2018.07.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/18/2018] [Accepted: 07/21/2018] [Indexed: 06/08/2023]
Abstract
A 5.6 kDa antimicrobial peptide (AMP) was purified from acidified gill extract of the pen shell, Atrina pectinata, by cation exchange and C18 reversed-phase high performance liquid chromatography. Comparison of the amino acid sequences and molecular weight of this peptide with those of other known AMPs revealed that it had high sequence homology with that of cgMolluscidin or hdMolluscidin; it was designated apMolluscidin. apMolluscidin comprises 59 amino acid residues containing several dibasic residue repeats and sequence repeats such as Lys-Lys and Lys-Gly. apMolluscidin exhibited potent antimicrobial activity against both Gram-positive bacteria including Bacillus subtilis (minimal effective concentration [MEC], 2.1 μg/mL), and Gram-negative bacteria including E. coli D31 (MEC, 0.5 μg/mL), without hemolytic activity. However, it did not show any activity against fungi such as Candida albicans. Secondary structure prediction suggested that it might form two helical regions and have an amphipathic structure. Full-length apMolluscidin cDNA contained 812 base pairs (bp), including a 5'-untranslated region (UTR) of 82 bp, a 3'-UTR of 547 bp, and a coding sequence of 183 bp encoding 60 amino acids (containing Met). Furthermore, qPCR analyses revealed that the mature peptide translated from apMolluscidin mRNA is expressed in a tissue-specific manner in locations such as the gill and siphon. These results indicate that apMolluscidin might be related to the innate immune defense system of abalone and may not act directly on the bacterial membrane. This is the first report of an AMP from the pen shell with a fully identified amino acid sequence.
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Yoo S, Kim DG, Ha T, Chan Won J, Jang KS, Kim YH. Solution-Processable, Thin, and High-κ Dielectric Polyurea Gate Insulator with Strong Hydrogen Bonding for Low-Voltage Organic Thin-Film Transistors. ACS APPLIED MATERIALS & INTERFACES 2018; 10:32462-32470. [PMID: 30175586 DOI: 10.1021/acsami.8b11083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We developed a solution-processable, thin, and high-dielectric polyurea-based organic gate insulator for low-voltage operation and high performance of organic thin-film transistors (OTFTs). A 60 nm-thick polyurea thin film exhibited a high dielectric constant of 5.82 and excellent electrical insulating properties owing to strong hydrogen bonding. The hydrogen bonding of the synthesized polyurea was confirmed using infrared spectroscopy and was quantitatively evaluated by measuring the interactive force using atomic force microscopy. Moreover, the effect of hydrogen bonding of polyurea on the insulating properties was systematically investigated through the combination of various monomers and control of the thickness of the polyurea film. The dinaphtho[2,3- b:2',3'- f]thieno[3,2- b]thiophene-based OTFTs with the polyurea gate insulator showed excellent thin-film transistor (TFT) performance with a field-effect mobility of 1.390 cm2/V·s and an on/off ratio of ∼105 at a low operation voltage below 2 V. In addition, it is possible to fabricate flexible polymer organic semiconductor (OSC)-based TFT devices using a solution process, owing to excellent solvent stability in various organic solvents. We believe that the solution-processable polyurea gate insulator with a high dielectric constant and good insulation properties is a promising candidate for low-voltage-operated OTFTs using various OSCs.
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Kim JW, Oh BG, Kim J, Kim DG, Nam BH, Kim YO, Park JY, Cheong J, Kong HJ. Development and Characterization of a New Cell Line from Olive Flounder Paralichthys olivaceus. Dev Reprod 2018; 22:225-234. [PMID: 30324159 PMCID: PMC6182235 DOI: 10.12717/dr.2018.22.3.225] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/07/2018] [Accepted: 08/31/2018] [Indexed: 11/17/2022]
Abstract
A new embryonic cell line (OFEC-17FEN) derived from olive flounder Paralichthys olivaceus was developed. OFEC-17FEN cells were subcultured for <30 passages over ~200 days. OFEC-17FEN cells had a doubling time of 114.34 h and modal diploid chromosome number was 48. The pluripotency genes POU5f1 and NANOG were expressed in OFEC-17FEN cells. However, the lack of several pluripotency-related genes expression indicates that OFEC-17FEN cells are not stem cells. OFEC-17FEN cells transfected with plasmid pEGFP-c1 exhibited a strong green fluorescent signal at 48 h after transfection. Accordingly, OFEC-17FEN cells may be useful for both basic research and biotechnological application.
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Kim J, Kim JW, Kim DG, Nam BH, Kim YO, Park JY, Kong HJ. Molecular characterization of Rhodeus uyekii tripartite motif protein 1 (TRIM1) involved in IFN-γ/LPS-induced NF-κB signaling. FISH & SHELLFISH IMMUNOLOGY 2018; 79:42-51. [PMID: 29747011 DOI: 10.1016/j.fsi.2018.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/30/2018] [Accepted: 05/06/2018] [Indexed: 06/08/2023]
Abstract
The tripartite motif-containing (TRIM) proteins are involved in a wide range of cellular processes, and the role of TRIM1 in immunity has been explored. However, fundamental studies on fish TRIM1 are lacking. In this study, we cloned and characterized TRIM1 cDNA from the Korean rose bitterling, Rhodeus uyekii (RuTRIM1). Two RuTRIM1 isoforms (RuTRIM1-X1 and RuTRIM1-X2) were identified. The coding sequence (CDS) of RuTRIM1-X1 comprised 2157 bp encoding a 718-aa protein, and the CDS of RuTRIM1-X2 comprised 1929 bp encoding a 642-aa protein. Both RuTRIM1 isoforms contained a RING finger domain, B-box 1, B-box 2, coiled-coil domain, COS box, FN3 motif, and PRY/SPRY domain. The deduced RuTRIM1-X1 and RuTRIM1-X2 proteins had high amino acid identity (76.27-98.89%) with orthologs from various other species, and a phylogenetic tree was constructed. RuTRIM1-X1 and RuTRIM1-X2 mRNA were expressed in all tissues examined, with the highest expression levels detected in the hepatopancreas. During early development, RuTRIM1-X1 and RuTRIM1-X2 mRNA levels changed differently from the gastrula period to the first feeding stage. An in vivo ubiquitination assay showed that RuTRIM1 exhibited RING-dependent E3 ubiquitin ligase activity, mainly by comparing RuTRIM1-X2 to RuTRIM1-X1. The subcellular localization of the two RuTRIM1 protein isoforms was characterized, revealing that they formed aggregates in cytoplasmic bodies in Raw264.7 cells. Interferon-γ/lipopolysaccharide-induced nuclear factor-κB signaling was negatively regulated by RuTRIM1-X1 and RuTRIM1-X2, and the negative effect was reversed in RING deletion mutants. To our knowledge, this is the first study to characterize fish TRIM1, which may play a role in the inflammatory response.
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Kim YO, Park IS, Park S, Nam BH, Kim DG, Choi SG, Bae JW, Yoon JH. Corrigendum: Bizionia berychis sp. nov., isolated from intestinal tract of a splendid alfonsino (Beryx splendens). Int J Syst Evol Microbiol 2018; 68:2114. [PMID: 29855403 DOI: 10.1099/ijsem.0.002790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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