• Genomics & Informatics
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• 제21권3호
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• pp.36.1-36.19
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• 2023

The LIM domain-containing proteins are dominantly found in plants and play a significant role in various biological processes such as gene transcription as well as actin cytoskeletal organization. Nevertheless, genome-wide identification as well as functional analysis of the LIM gene family have not yet been reported in the economically important plant sorghum (Sorghum bicolor L.). Therefore, we conducted an in silico identification and characterization of LIM genes in S. bicolor genome using integrated bioinformatics approaches. Based on phylogenetic tree analysis and conserved domain, we identified five LIM genes in S. bicolor (SbLIM) genome corresponding to Arabidopsis LIM (AtLIM) genes. The conserved domain, motif as well as gene structure analyses of the SbLIM gene family showed the similarity within the SbLIM and AtLIM members. The gene ontology (GO) enrichment study revealed that the candidate LIM genes are directly involved in cytoskeletal organization and various other important biological as well as molecular pathways. Some important families of regulating transcription factors such as ERF, MYB, WRKY, NAC, bZIP, C2H2, Dof, and G2-like were detected by analyzing their interaction network with identified SbLIM genes. The cis-acting regulatory elements related to predicted SbLIM genes were identified as responsive to light, hormones, stress, and other functions. The present study will provide valuable useful information about LIM genes in sorghum which would pave the way for the future study of functional pathways of candidate SbLIM genes as well as their regulatory factors in wet-lab experiments.

• Animal Bioscience
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• 제36권11호
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• pp.1632-1646
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• 2023

Objective: The objective of the present study was to investigate the effect of dietary betaine (BT) supplementation on the hepatic transcriptome profiles in broiler chickens raised under heat stress (HS) conditions. Methods: A total of 180 (21-d-old) Ross 308 male broiler chicks were allotted to 1 of 3 treatment groups with 6 replicated cages in a completely randomized design. One group was kept under thermoneutral conditions at all times and was fed a basal diet (PC). Other 2 groups were exposed to a cyclic heat stress condition. One of the 2 groups under heat stress conditions was fed the basal diet as a negative control (NC), whereas the other group was fed the basal diet supplemented with 0.2% BT. All chickens were provided with diets and water ad libitum for 21 d. Following the experiment, the liver samples were collected for RNA sequencing analysis. Results: Broiler chickens in NC and BT group had decreased (p<0.05) growth performance. In the transcriptome analysis, the number of differentially expressed genes were identified in the liver by HS conditions and dietary BT supplementation. In the comparison between NC and PC treatments, genes related to energy and nucleic acid metabolism, amino acid metabolism, and immune system were altered by HS, which support the reason why heat-stressed poultry had decreased growth performance. In the comparison between NC and BT treatments, genes related to lipid metabolism, carbohydrate metabolism, and immune system were differently expressed under HS conditions. Conclusion: HS negatively impacts various physiological processes, including DNA replication, metabolism of amino acids, lipids, and carbohydrates, and cell cycle progression in broiler chickens. Dietary BT supplementation, however, offers potential counteractive effects by modulating liver function, facilitating gluconeogenesis, and enhancing immune systems. These findings provide a basis for understanding molecular responses by HS and the possible benefits of dietary BT supplementation in broiler chickens exposed to HS.

• BMB Reports
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• 제57권5호
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• pp.232-237
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• 2024

This study investigated how adipose tissue-derived mesenchymal stem cells (AT-MSCs) respond to chondrogenic induction using droplet-based single-cell RNA sequencing (scRNA-seq). We analyzed 37,219 high-quality transcripts from control cells and cells induced for 1 week (1W) and 2 weeks (2W). Four distinct cell clusters (0-3), undetectable by bulk analysis, exhibited varying proportions. Cluster 1 dominated in control and 1W cells, whereas clusters (3, 2, and 0) exclusively dominated in control, 1W, and 2W cells, respectively. Furthermore, heterogeneous chondrogenic markers expression within clusters emerged. Gene ontology (GO) enrichment analysis of differentially expressed genes unveiled cluster-specific variations in key biological processes (BP): (1) Cluster 1 exhibited up-regulation of GO-BP terms related to ribosome biogenesis and translational control, crucial for maintaining stem cell properties and homeostasis; (2) Additionally, cluster 1 showed up-regulation of GO-BP terms associated with mitochondrial oxidative metabolism; (3) Cluster 3 displayed up-regulation of GO-BP terms related to cell proliferation; (4) Clusters 0 and 2 demonstrated similar up-regulation of GO-BP terms linked to collagen fibril organization and supramolecular fiber organization. However, only cluster 0 showed a significant decrease in GO-BP terms related to ribosome production, implying a potential correlation between ribosome regulation and the differentiation stages of AT-MSCs. Overall, our findings highlight heterogeneous cell clusters with varying balances between proliferation and differentiation before, and after, chondrogenic stimulation. This provides enhanced insights into the single-cell dynamics of AT-MSCs during chondrogenic differentiation.

• BMB Reports
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• 제57권5호
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• pp.244-249
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• 2024

Many types of cancer are associated with excessive angiogenesis. Anti-angiogenic treatment is an effective strategy for treating solid cancers. This study aimed to demonstrate the inhibitory effects of (E)-2-methoxy-4-(3-(4-methoxyphenyl) prop-1-en-1-yl) phenol (MMPP) in VEGFA-induced angiogenesis. The results indicated that MMPP effectively suppressed various angiogenic processes, such as cell migration, invasion, tube formation, and sprouting of new vessels in human umbilical vein endothelial cells (HUVECs) and mouse aortic ring. The inhibitory mechanism of MMPP on angiogenesis involves targeting VEGFR2. MMPP showed high binding affinity for the VEGFR2 ATP-binding domain. Additionally, MMPP improved VEGFR2 thermal stability and inhibited VEGFR2 kinase activity, suppressing the downstream VEGFR2/AKT/ERK pathway. MMPP attenuated the activation and nuclear translocation of NF-κB, and it downregulated NF-κB target genes such as VEGFA, VEGFR2, MMP2, and MMP9. Furthermore, conditioned medium from MMPP-treated breast cancer cells effectively inhibited angiogenesis in endothelial cells. These results suggested that MMPP had great promise as a novel VEGFR2 inhibitor with potent anti-angiogenic properties for cancer treatment via VEGFR2/AKT/ERK/NF-κB signaling pathway.

• 생명과학회지
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• 제34권2호
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• pp.138-144
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• 2024

Crocin은 여러 가지 요리에 향미와 색깔을 주는 치자 열매나 사프란에 함유되어 있는 적노란색의 수용성 색소이다. 사프란과 치자는 전통의학 분야에서 부종, 해열, 해독 작용이 있어 바이러스성 간염, 식도염, 관상동맥심장병, 신경쇠약, 불면증, 퇴행성 신경질환, 호흡기 질환, 비뇨기 질환 등을 치료하는데 사용되어 왔다. Crocin (C₄₄H₆₄O₂₄)은 카로테노이드의 복합체로, dicarboxylic acid crocetin과 disaccharide gentiobiose로 이루어진 diester이다. Crocin은 혈액학적인, 병리학적인 독성이나 유전독성이 없다. 현재까지 수많은 생체 내 및 생체 외 연구들을 통해 Crocin의 생물학적인 약리작용이 밝혀지고 있다. 본 총설에서는 염증성 장질환, 위염, 천식, 동맥경화, 류머티스 관절염, 다발성 경화증, 당뇨, 알츠하이머병, 파킨슨병, 우울증 등의 염증 관련 질환에서 Crocin의 보호 효과를 요약한다. Crocin은 다양한 작용 기전을 통해 항염, 항산화, 세포 자살 방지 기능을 함으로써 이들 질환을 개선하는 것으로 추론된다.

• Journal of Applied Biological Chemistry
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• 제66권
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• pp.311-319
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• 2023

Caveolin-1 (Cav-1) is the main structural component of the caveolae on the plasma membrane, which regulates various cellular processes, including cell growth, differentiation, and endocytosis. Although a recent study demonstrated that Cav-1 might be involved in diabetes-associated inflammation, its exact role in the intestine was unclear. In this study, we examined the intestinal expression of Cav-1 in diabetic conditions. We also investigated its effect on lipopolysaccharide (LPS)-induced inflammation by expressing this protein in human intestinal Caco-2 cells lacking Cav-1. We observed that increased Cav-1 levels and decreased expression of tight junction proteins affected intestinal permeability in high-fat diet-induced diabetic mice. When Caco-2 cells were treated with LPS, Cav-1 enhanced the NF-κB signaling. Moreover, LPS reduced the expression of tight junction proteins while it increased cell-cell permeability and reactive oxygen species generation in Caco-2 cells and this effect was amplified by cav-1 overexpression. LPS treatment promoted phosphorylation of tyrosine-14 (Y14) on Cav-1, and the LPS-induced NF-κB signaling was suppressed in cells expressing non-phosphorylatable Cav-1 (tyrosine-14 to phenylalanine mutant), which reduced intestinal barrier permeability. These results suggest that Cav-1 expression promotes LPS-induced inflammation in Caco-2 cells, and phosphorylation of Y14 on Cav-1 might contribute to the anti-inflammatory response in LPS-induced NF-κB signaling and cell permeability.

• 한국발생생물학회지:발생과생식
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• 제27권4호
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• pp.205-211
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• 2023

INTS14/VWA9, a component of the integrator complex subunits, plays a pivotal role in regulating the fate of numerous nascent RNAs transcribed by RNA polymerase II, particularly in the biogenesis of small nuclear RNAs and enhancer RNAs. Despite its significance, a comprehensive mutation model for developmental research has been lacking. To address this gap, we aimed to investigate the expression patterns of INTS14 during zebrafish embryonic development. We generated ints14 mutant strains using the CRISPR/Cas9 system. We validated the gRNA activity by co-injecting Cas9 protein and a single guide RNA into fertilized zebrafish eggs, subsequently confirming the presence of a 6- or 9-bp deletion in the ints14 gene. In addition, we examined the two mutant alleles through PCR analysis, T7E1 assay, TA-cloning, and sequencing. For the first time, we used the CRISPR/Cas9 system to create a model in which some sequences of the ints14 gene were removed. This breakthrough opens new avenues for in-depth exploration of the role of ints14 in animal diseases. The mutant strains generated in this study can provide a valuable resource for further investigations into the specific consequences of ints14 gene deletion during zebrafish development. This research establishes a foundation for future studies exploring the molecular mechanisms underlying the functions of ints14, its interactions with other genes or proteins, and its broader implications for biological processes.

• 한국산학기술학회논문지
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• 제19권1호
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• pp.537-545
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• 2018

본 연구에서는 메밀의 발아초기에 발현되는 전사체의 다양한 정보 수집을 위해 양절메밀과 대관 3-3호의 RNA를 추출하여 전사체 분석을 수행하였다. 제주산 양절메밀과 대관3-3호의 종자 및 발아 후 12, 24, 36시간별로 total RNA를 추출하고, llumina Hiseq 2000 플랫폼을 사용하여 시퀀싱 하였다. SolexaQA package의 DynamicTrim과 LengthsORT 프로그램으로 이용하여 raw 데이터 분석을 실시한 후, 어셈블리(assembly)와 annotation을 수행하였다. RNA-seq raw 데이터로부터 약 84.2%, 81.5%에 해당하는 16.5Gb, 16.2Gb의 transcriptome 데이터를 확보하였다. 47Mb에 해당하는 43,494개의 대표적인 전사체(representative transcripts)를 확보하였고, 그 중에서 annotation DB와 서열 유사도를 갖는 서열은 23,165개로 확인되었다. 메밀의 representative transcripts 유전자의 유전자 온톨로지(gene ontology) 분석결과, biological process는 metabolic process (49.49%)에서, cellular components는 cell (46.12%)에서, molecular function은 catalyltic activity (80.43%)에서 유전자가 많이 분포되어 있는 것을 확인하였다. 종자의 발아에 관련된 gibberellin receptor GID1C의 경우에는 양절메밀, 대관 3-3호의 발현양이 모두 시간이 지남에 따라 증가되는 것을 확인할 수 있었으며, gibberellin 20-oxidase1의 경우에는 양절메밀에서는 발아 후 12 시간이내에 증가되었으나, 대관 3-3호에서는 36시간까지 유전자 발현양 증가하는 것을 확인할 수 있었다. 이러한 제주산 메밀의 발아초기 단계별 전사체 분석 데이터는 종간의 기능적, 형태학적 차이를 일으키는 메커니즘 규명에 도움을 줄 것으로 사료된다.

• 한국막학회:학술대회논문집
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• 한국막학회 1999년도 The 7th Summer Workshop of the Membrane Society of Korea
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• pp.39-42
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• 1999

Perfluoropolymers represent the ultimate resistance to hostile chemical environments and high service temperature, attributed to the presence of fluorine in the polymer backbone, i.e. to the high bond energy of C-F and C-C bonds of fluorocarbons. Copolymers of Tetrafluoroethylene (TEE) and 2, 2, 4Trifluoro-5Trifluorometoxy- 1, 3Dioxole (TTD), commercially known as HYFLON AD, are amorphous perfluoropolymers with glass transition temperature (Tg)higher than room temperature, showing a thermal decomposition temperature exceeding 40$0^{\circ}C$. These polymer systems are highly soluble in fluorinated solvents, with low solution viscosities. This property allows the preparation of self-supported and composite membranes with desired membrane thickness. Symmetric and asymmetric perfluoropolymer membranes, made with HYFLON AD, have been prepared and evaluated. Porous and not porous symmetric membranes have been obtained by solvent evaporation with various processing conditions. Asymmetric membranes have been prepared by th wet phase inversion method. Measure of contact angle to distilled water have been carried out. Figure 1 compares experimental results with those of other commercial membranes. Contact angles of about 120$^{\circ}$for our amorphous perfluoropolymer membranes demonstrate that they posses a high hydrophobic character. Measure of contact angles to hexandecane have been also carried out to evaluate the organophobic character. Rsults are reported in Figure 2. The observed strong organophobicity leads to excellent fouling resistance and inertness. Porous membranes with pore size between 30 and 80 nanometers have shown no permeation to water at pressures as high as 10 bars. However high permeation to gases, such as O2, N2 and CO2, and no selectivities were observed. Considering the porous structure of the membrane, this behavior was expected. In consideration of the above properties, possible useful uses in th field of gas- liquid separations are envisaged for these membranes. A particularly promising application is in the field of membrane contactors, equipments in which membranes are used to improve mass transfer coefficients in respect to traditional extraction and absorption processes. Gas permeation properties have been evaluated for asymmetric membranes and composite symmetric ones. Experimental permselectivity values, obtained at different pressure differences, to various single gases are reported in Tab. 1, 2 and 3. Experimental data have been compared with literature data obtained with membranes made with different amorphous perfluoropolymer systems, such as copolymers of Perfluoro2, 2dimethyl dioxole (PDD) and Tetrafluorethylene, commercialized by the Du Pont Company with the trade name of Teflon AF. An interesting linear relationship between permeability and the glass transition temperature of the polymer constituting the membrane has been observed. Results are descussed in terms of polymer chain structure, which affects the presence of voids at molecular scale and their size distribution. Molecular Dyanmics studies are in progress in order to support the understanding of these results. A modified Theodoru- Suter method provided by the Amorphous Cell module of InsightII/Discover was used to determine the chain packing. A completely amorphous polymer box of about 3.5 nm was considered. Last but not least the use of amorphous perfluoropolymer membranes appears to be ideal when separation processes have to be performed in hostile environments, i.e. high temperatures and aggressive non-aqueous media, such as chemicals and solvents. In these cases Hyflon AD membranes can exploit the outstanding resistance of perfluoropolymers.

• 한국지하수토양환경학회지:지하수토양환경
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• 제12권5호
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• pp.105-114
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• 2007

Advanced oxidation processes(AOPs)는 강력한 산화제인 hydroxyl radical(${\cdot}OH$)를 생성하여 오염물질을 산화시키는 기법이다. 본 연구에서는 DNAPL인 trichloroethylene(TCE)과 tetrachloroethylene(PCE)의 수리학적 특성을 고려하여 우수한 고도산화처리기법($UV/Fe^{3+}$-chelating agent/$H_2O_2$기법, $UV/H_2O_2$기법)의 적용성 평가를 실시하였다. TCE, PCE 처리에 있어 가장 높은 분해효율을 보인 기법은 $UV/H_2O_2$기법으로 pH 6의 중성조건에서 TCE의 경우 150분 만에 99.92%의 TCE 분해를 나타내었고($[H_2O_2]$ = 147 mM, UV dose = 17.4 kwh/L), PCE의 경우 반응 2시간에 99.99%가 분해되었다($[H_2O_2]$ = 29.4 mM, UV dose = 52.2 kwh/L). 또한, $UV/Fe^{3+}$-chelating agent/$H_2O_2$기법을 적용하였을 경우, TCE는 90분 만에 99.9% (UV dose = 34.8 kwh/L, $[Fe^{3+}]$ = 0.1 mM, [Oxalate] = 0.6 mM, $[H_2O_2]$ = 147 mM) PCE는 반응시간 6시간 만에 99.81% (UV dose = 17.4 kwh/L, $[Fe^{3+}]$ = 0.1 mM, [Oxalate] = 0.6 mM, $[H_2O_2]$ = 29.4 mM)의 빠른 분해경향을 보였다. 이러한 결과는 기존의 고도산화처리기법 중 modified Fenton 반응에 UV를 적용함으로서 반응 중 $H_2O_2$의 재생산을 증가시킬 수 있음을 보여주고 있다. 또한, Fe(III) 이온의 Fe(II) 이온으로의 환원을 용이하게 하여 기존 Fenton 반응에 비해 처리시간의 단축 및 분해효율의 향상을 기대할 수 있을 것이다. 그리고, oxalate나 acetate같은 저분자 유기산 착제의 적용으로 pH의 안정성과 분해효율의 향상이 가능하고, 철이온 및 oxalate나 acetate와 같은 물질이 자연상에 존재함에 따라 보다 경제적이고 친환경적인 실용적 처리기법 도출이 가능할 것이다.