• Journal of Korean Neurosurgical Society
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• 제65권1호
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• pp.4-12
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• 2022

Objective : We reported the differentially methylated genes in patients with subarachnoid hemorrhage (SAH) using bioinformatics analyses to explore the biological characteristics of the development of delayed cerebral ischemia (DCI). Methods : DNA methylation profiles obtained from 40 SAH patients from an epigenome-wide association study were analyzed. Functional enrichment analysis, protein-protein interaction (PPI) network, and module analyses were carried out. Results : A total of 13 patients (32.5%) experienced DCI during the follow-up. In total, we categorized the genes into the two groups of hypermethylation (n=910) and hypomethylation (n=870). The hypermethylated genes referred to biological processes of organic cyclic compound biosynthesis, nucleobase-containing compound biosynthesis, heterocycle biosynthesis, aromatic compound biosynthesis and cellular nitrogen compound biosynthesis. The hypomethylated genes referred to biological processes of carbohydrate metabolism, the regulation of cell size, and the detection of a stimulus, and molecular functions of amylase activity, and hydrolase activity. Based on PPI network and module analysis, three hypermethylation modules were mainly associated with antigen-processing, Golgi-to-ER retrograde transport, and G alpha (i) signaling events, and two hypomethylation modules were associated with post-translational protein phosphorylation and the regulation of natural killer cell chemotaxis. VHL, KIF3A, KIFAP3, RACGAP1, and OPRM1 were identified as hub genes for hypermethylation, and ALB and IL5 as hub genes for hypomethylation. Conclusion : This study provided novel insights into DCI pathogenesis following SAH. Differently methylated hub genes can be useful biomarkers for the accurate DCI diagnosis.

• Animal Bioscience
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• 제35권7호
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• pp.975-988
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• 2022

Objective: In this study, we aimed to identify long non-coding RNAs (lncRNAs) that play important roles in starvation stress, analyze their functions, and discover potential molecular targets to alleviate starvation stress to provide a theoretical reference for subsequent in-depth research. Methods: We generated a piglet starvation stress animal model. Nine Yorkshire weaned piglets were randomly divided into a long-term starvation stress group (starved for 72 h), short-term starvation stress group (starved for 48 h), and the control group. LncRNA libraries were constructed using high-throughput sequencing of piglet ileums. Results: We obtained 11,792 lncRNAs, among which, 2,500 lncRNAs were novel. In total, 509 differentially expressed (DE)lncRNAs were identified in this study. Target genes of DElncRNAs were predicted via cis and trans interactions, and functional and pathway analyses were performed. Gene ontology functions and Kyoto encyclopedia of genes and genomes analysis revealed that lncRNA-targeted genes mainly participated in metabolic pathways, cellular processes, immune system processes, digestive systems, and transport activities. To reveal the mechanism underlying starvation stress, the interaction network between lncRNAs and their targets was constructed based on 26 DElncRNAs and 72 DEmRNAs. We performed an interaction network analysis of 121 DElncRNA-DEmRNA pairs with a Pearson correlation coefficient greater than 0.99. Conclusion: We found that MSTRG.19894.13, MSTRG.16726.3, and MSTRG.12176.1 might play important roles in starvation stress. This study not only generated a library of enriched lncRNAs in piglets, but its outcomes also provide a strong foundation to screen key lncRNAs involved in starvation stress and a reference for subsequent in-depth research.

• Molecules and Cells
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• 제45권5호
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• pp.306-316
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• 2022

Chronic stress contributes to the risk of developing depression; the habenula, a nucleus in epithalamus, is associated with many neuropsychiatric disorders. Using genome-wide gene expression analysis, we analyzed the transcriptome of the habenula in rats exposed to chronic restraint stress for 14 days. We identified 379 differentially expressed genes (DEGs) that were affected by chronic stress. These genes were enriched in neuroactive ligand-receptor interaction, the cAMP (cyclic adenosine monophosphate) signaling pathway, circadian entrainment, and synaptic signaling from the Kyoto Encyclopedia of Genes and Genomes pathway analysis and responded to corticosteroids, positive regulation of lipid transport, anterograde trans-synaptic signaling, and chemical synapse transmission from the Gene Ontology analysis. Based on protein-protein interaction network analysis of the DEGs, we identified neuroactive ligand-receptor interactions, circadian entrainment, and cholinergic synapse-related subclusters. Additionally, cell type and habenular regional expression of DEGs, evaluated using a recently published single-cell RNA sequencing study (GSE137478), strongly suggest that DEGs related to neuroactive ligand-receptor interaction and trans-synaptic signaling are highly enriched in medial habenular neurons. Taken together, our findings provide a valuable set of molecular targets that may play important roles in mediating the habenular response to stress and the onset of chronic stress-induced depressive behaviors.

• Journal of Ginseng Research
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• 제46권3호
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• pp.408-417
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• 2022

Background: Korean Red Ginseng extract (KRGE) has been used as a health supplement and herbal medicine. Astrocytes are one of the key cells in the central nervous system (CNS) and have bioenergetic potential as they stimulate mitochondrial biogenesis. They play a critical role in connecting the brain vasculature and nerves in the CNS. Methods: Brain samples from KRGE-administered mice were tested using immunohistochemistry. Treatment of human brain astrocytes with KRGE was subjected to assays such as proliferation, cytotoxicity, Mitotracker, ATP production, and O₂ consumption rate as well as western blotting to demonstrate the expression of proteins related to mitochondria functions. The expression of hypoxia-inducible factor-1α (HIF-1α) was diminished utilizing siRNA transfection. Results: Brain samples from KRGE-administered mice harbored an increased number of GFAP-expressing astrocytes. KRGE triggered the proliferation of astrocytes in vitro. Enhanced mitochondrial biogenesis induced by KRGE was detected using Mitotracker staining, ATP production, and O₂ consumption rate assays. The expression of proteins related to mitochondrial electron transport was increased in KRGE-treated astrocytes. These effects were blocked by HIF-1α knockdown. The factors secreted from KRGE-treated astrocytes were determined, revealing the expression of various cytokines and growth factors, especially those related to angiogenesis and neurogenesis. KRGE-treated astrocyte conditioned media enhanced the differentiation of adult neural stem cells into mature neurons, increasing the migration of endothelial cells, and these effects were reduced in the background of HIF-1α knockdown. Conclusion: Our findings suggest that KRGE exhibits prophylactic potential by stimulating astrocyte mitochondrial biogenesis through HIF-1α, resulting in improved neurovascular function.

• Molecules and Cells
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• 제45권8호
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• pp.575-587
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• 2022

Human ABCB6 is an ATP-binding cassette transporter that regulates heme biosynthesis by translocating various porphyrins from the cytoplasm into the mitochondria. Here we report the cryo-electron microscopy (cryo-EM) structures of human ABCB6 with its substrates, coproporphyrin III (CPIII) and hemin, at 3.5 and 3.7 Å resolution, respectively. Metal-free porphyrin CPIII binds to ABCB6 within the central cavity, where its propionic acids form hydrogen bonds with the highly conserved Y550. The resulting structure has an overall fold similar to the inward-facing apo structure, but the two nucleotide-binding domains (NBDs) are slightly closer to each other. In contrast, when ABCB6 binds a metal-centered porphyrin hemin in complex with two glutathione molecules (1 hemin: 2 glutathione), the two NBDs end up much closer together, aligning them to bind and hydrolyze ATP more efficiently. In our structures, a glycine-rich and highly flexible "bulge" loop on TM helix 7 undergoes significant conformational changes associated with substrate binding. Our findings suggest that ABCB6 utilizes at least two distinct mechanisms to fine-tune substrate specificity and transport efficiency.

• BMB Reports
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• 제55권10호
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• pp.488-493
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• 2022

The specific pair of heat shock protein 70 (Hsp70) and Hsp40 constitutes an essential molecular chaperone system involved in numerous cellular processes, including the proper folding/refolding and transport of proteins. Hsp40 family members are characterized by the presence of a conserved J-domain (JD) that functions as a co-chaperone of Hsp70. Tumorous imaginal disc 1 (Tid1) is a tumor suppressor protein belonging to the DNAJA3 subfamily of Hsp40 and functions as a co-chaperone of the mitochondrial Hsp70, mortalin. In this work, we performed nuclear magnetic resonance spectroscopy to determine the solution structure of JD and its interaction with the glycine/phenylalanine-rich region (GF-motif) of human Tid1. Notably, Tid1-JD, whose conformation was consistent with that of the DNAJB1 JD, appeared to stably interact with its subsequent GF-motif region. Collectively with our sequence analysis, the present results demonstrate that the functional and regulatory mode of Tid1 resembles that of the DNAJB1 subfamily members rather than DNAJA1 or DNAJA2 subfamily proteins. Therefore, it is suggested that an allosteric interaction between mortalin and Tid1 is involved in the mitochondrial Hsp70/Hsp40 chaperone system.

• 생명과학회지
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• 제18권9호
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• pp.1194-1201
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• 2008

본 연구는 유해성 Cochlodinium polykrikoides 적조생물을 대상으로 수온변화에 따른 세포 생화학적 및 생리 활성도를 측정했다. Genomic DNA 함량은 $12^{\circ}C$ 및 $15^{\circ}C$에서 거의 비슷한 0.6을 보였으나, $18^{\circ}C$부터 급격히 높아져서 $24^{\circ}C$ 최고 1.8를 나타내었다. RNA와 total protein도 $24^{\circ}C$에 가장 높은 1.7과 0.07 ${\mu}g$ $ml^{-1}$으로 나타났다. 광합성량도 수온에 따른 큰 변화를 보였다. 빛의 파장에 관계없이 $18^{\circ}C$ 이상에서 현저히 높은 값을 보였다. $24^{\circ}C$ $ETR_{max}$ Ch1-Ch4까지의 범위는 537.9에서 602.5 ${\mu}mol$ electrons $g^{-1}$ Chl ${\alpha}s^{-1}$ 나타났다. Nitrate reductase와 ATPase 효소 활성도는 $24^{\circ}C$에서 각각 0.11 ${\mu}mol$ $NO_{2}^{-}$ ${\mu}g^{-1}$ Chl ${\alpha}h^{-1}$ , 0.78 pmol 100 $mg^{-1}$ 나타났다. CHN 분석에서도 수온에 따라 C, H, N의 함량이 현저하게 상이했다. $27^{\circ}C$ 배양시 $24^{\circ}C$에 비하여 대부분의 세포생리물질이 낮게 보였다. 따라서 C. polykrikoides는 수온 변화에 대하여 세포대사물질의 함량이 많은 차이를 볼 수 있어서 초기 적조 발생 조건은 $18^{\circ}C$로 추측된다. 본 실험의 결과로 $24^{\circ}C$ 이상이 되면 C. polykrikoides 대번식은 세포 내 생리물질의 현저한 저하로 형성되기가 어려울 것으로 보인다.

• 한국산학기술학회논문지
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• 제16권4호
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• pp.2951-2957
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• 2015

유해 유독 적조생물의 대발생은 해양생물 건강성과 수산어족자원에 심각한 피해를 입힌다. 본 연구에서는 미세조류의 대발생을 억제하기 위해 개발된 Thiazolidione 유도체(TD49)와 현장에서 적조생물을 제어하기 위하여 살포되는 황토에 대한 살조능을 조사하였다. 아울러 적조생물 생사판별과 관련된 자가영양생물의 광합성에 영향을 미칠 수 있는 활성엽록소(activity Chl. a), 광합성효율($F_v/F_m$), 전자 전달율(electron transport rate, ETR)등을 평가하였다. 대상적조생물은 유해조류 3종과 비유해 조류 1종을 선택하였으며, 유해조류는 침편모조류 Heterosigma akashiwo, Chattonella marina와 더불어 와편모조류 Heterocapsa circularisquama를 비교하였고, 비유해조류는 은편모조류 Rhodomonas salina에 대하여 평가하였다. 유해조류 3종은 살조물질(TD49)에 의하여 빠른 시간에 세포가 파괴되어 우수한 살조 효과(>80%)를 보인 반면, 황토에 관해서는 살조효율이 30%이하로 낮게 나타났다. 또한 TD49에 대한 유해조류 3종의 살조효율은 H. circularisquama> C. marina> H. akashiwo 순으로 높게 나타났으며, 광합성 효율 및 전자전달율 또한 극히 낮게 나타나, 광합성에 치명적인 영향을 미치는 것으로 사료되었다. 반면, 유해조류 3종에 관해서 황토에 대한 광합성 효율과 전자전달율은 대조군과 유의한 차이를 보이지 않았다(p>0.01). 비유해종 R. salina 은 대조군에 비하여 TD49와 황토의 살조 효과, 광합성효율 및 전자전달율의 차이는 명확하게 나타나지 않았고, 오히려 TD49물질에서 성장에 긍정적인 영향을 미치는 것을 확인하였다. 결과적으로 본 연구에서 TD49물질은 유해적조 생물을 선택적으로 제어 할 수 있으며, 현장 적용시 우수한 살조 효과를 가질 수 있을 것으로 판단된 반면, 황토는 적조생물 제어에 적합하지 않을 것으로 사료되었다.

• 한국작물학회지
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• 제67권1호
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• pp.41-52
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• 2022

1. 본 연구에서는 우리밀 품종인 금강밀과 염 저항성을 가지는 돌연변이 라인 2020-s1340을 재료로 200 mM 염 스트레스 처리에 따른 전사체 발현을 확인하였다. QuantSeq을 통해 23,634,438개의 reads가 생산되었고 7,331,269개의 reads가 mapping됐다. 2. 염 스트레스 상황에서 총 282개의 DEG가 확인이 되었고 이러한 DEGs는 UDP-glucosyltransferase, receptor kinase-like protein, Lectin receptor-like kinases, cytochrome P450등의 단백질들을 코딩하는 유전자들이다. 이러한 DEGs는 염 저항성과 관련된 후보 유전자들이 될 수 있다. 염 저항성과 관련하여 역할이 밝혀지지 않은 유전자들은 추후 연구를 통해 확인이 필요하다. 3. GO연구에서는 DEGs를 세가지 범주로 분류하였으며 대부분 식물체 내 세포 기초 경로와 관련된 GO term들이 주로 되었으며 각각 범주에 있어서 biological process, molecular process에서는 single-organism process (GO: 0044699), single-organism metabolic process (GO:0044710), oxidation-reduction process (GO:0055114), copper ion transport (GO:0006825), copper ion transmembrane transport (GO:0035434), alternative oxidase activity (GO:0009916) GO term들이 유의성이 높게 나타났다. 4. 이러한 QuantSeq의 분석결과는 밀에 관한 염에 의해 발현되는 전사 발현에 대한 이해를 향상시킬 수 있다. 또한 염 스트레스 반응의 복잡한 분자 메커니즘에 대한 좋은 통찰력을 제공하고 염분 스트레스에 대한 작물 내성의 유전적 개선을 위한 실질적인 토대를 마련할 수 있을 것이다.

• 생명과학회지
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• 제20권4호
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• pp.528-534
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• 2010

본 연구에서는 흑마늘 열수 추출물(ABG)의 암세포 전이억제 효능을 검정하였다. AGS AGS 인체위암세포의 이동성과 침윤성을 억제하였으며, 이는 TER의 증가와 연관성이 있었다. 또한 ABG에 의한 AGS 위암세포의 침윤성 억제는 TIMPs 발현 증가에 의한 MMPs의 발현 및 활성 저하에 의한 것임을 알 수 있었다. 아울러 AGS 위암세포에서 과발현을 나타내는 TJ 단백질인 claudins의 발현 저하 등이 ABG의 항전이 효과에 연관되어 있음을 알 수 있었다. 이상의 결과는 흑마늘 열수 추출물이 단순한 암세포의 증식억제를 통한 암예방 및 항암활성 뿐만 아니라 암세포의 전이 또한 효과적으로 억제할 수 있음을 보여주며, 이와 연관된 보다 구체적인 분자세포생물학적 접근 및 in vivo 연구의 필요성이 요구됨을 의미한다.