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Identification of DNA methylation and genetic alteration simultaneously from a single blood biopsy
Chen Xiaomin,Liu Jiahui,Li Jun,Xie Yinpeng,Yu Zichen,Shen Lu,Liu Qingfeng,Wu Wei,Zhao Qiang,Lin Haoxiang,Liu Gaotong,Luo Qiuping,Yang Ling,Huang Yi,Zhao Meiru,Yi Xin,Xia Xuefeng 한국유전학회 2023 Genes & Genomics Vol.45 No.5
Background High-throughput sequencing of blood cell-free DNA (cfDNA) techniques offer an opportunity to characterize and monitor cancer rapidly in a non-invasive and real-time manner. Nonetheless, there lacks a tool within therapeutic arsenal to identify multi-omics alterations simultaneously from a single biopsy. In current times, bisulfite-based sequencing detects 5mC and 5hmC at single-base resolution is the golden standard of DNA methylation, while the degradation of DNA and biased sequencing data are the problems of this method. Objective To identify the consistency analysis of methylation and genetic variation with single library, we presented a platform detecting multi-omics data simultaneously from a single blood biopsy using bisulfite-free method of genomic methylation sequencing (GM-seq) mediated by TET enzyme. Methods We detected methylomic and genetic changes simultaneously from a single blood biopsy in NA12878 and randomly chose ten blood biopsies from colorectal cancer or lung cancer patients to validate the ability of GM-seq. Results Similar cytosine methylation level between whole genome bisulfite sequencing (WGBS) and GM-seq were identified in NA12878. Moreover, longer insert size, CpGs coverage and GC distribution were outperformed than WGBS. In addition, the comparison of the single nucleotide polymorphism (SNP), insertion-deletion (Indel) and copy number variation (CNV) in NA12878 or ctDNA from liver cancer between GM-seq and whole genome sequencing (WGS) show a good consistency, indicating that this method is feasible for detecting genetic variation in blood. Conclusion In conclusion, our work demonstrated a method for identification of the methylated modification and genetic variations simultaneously from a single blood biopsy.
Qiu, Jijun,Weng, Binbin,Zhao, Lihua,Chang, Caleb,Shi, Zhisheng,Li, Xiaomin,Kim, Hyung-Kook,Hwang, Yoon-Hwae Hindawi Limited 2014 Journal of nanomaterials Vol.2014 No.-
<P>Flower-like bundles of ZnO nanosheets have been prepared by using preheating hydrothermal process without any surfactants. The flower-like bundles consist of many thin and uniform hexagonal-structured ZnO nanosheets, with a thickness of 50 nm. The selected area electronic diffraction (SAED) and high-resolution transmission electron microscope (HRTEM) images indicate that the ZnO nanosheets are single crystal in nature. The growth mechanism of the flower-like bundles of ZnO nanosheets is discussed based on the morphology evolution with growth times and reaction conditions. It is believed that the formation of flower-like bundles of ZnO nanosheets is related to the shielding effect of OH<SUP>−</SUP>ions and the self-assembly process, which is dominated by a preheating time. Room temperature photoluminescence spectra results show that the annealing atmosphere strongly affects the visible emission band, which is sensitive to intrinsic and surface defects, especially oxygen interstitials, in flower-like bundles of ZnO nanosheets.</P>
Formation of Rod-like via Mechanical Activation Followed by Thermal Processing
Chen Xiaohu,Chen Xiaomin,Zhao Huang,Wud Jihuai 한국분말야금학회 2006 한국분말야금학회 학술대회논문집 Vol.2006 No.1
A QM-ISP-4 Planetary Mill was employed to activate mechanically the mixtures of anatase and corundum at room temperature for different times. The milled powder mixtures were then sintered at for 1 h. The XRD results showed that the milled powder mixtures were completely transformed into after sintering, except the mixtures milled for 5 and 10 hours. The SEM observations showed the typical morphology of rod-like vary in the range: widths from 0.6 to , and lengths from 3.0 to . The rod-like formation was attributed to the positive effects caused by the mechanical activation.
Melatonin prevents lung injury by regulating apelin 13 to improve mitochondrial dysfunction
Lu Zhang,Fangli Liu,Xiaomin Su,Yue Li,Yining Wang,Ruonan Fang,Yingying Guo,Tongzhu Jin,Huitong Shan,Xiaoguang Zhao,Rui Yang,Hongli Shan,Haihai Liang 생화학분자생물학회 2019 Experimental and molecular medicine Vol.51 No.-
Pulmonary fibrosis is a progressive disease characterized by epithelial cell damage, fibroblast proliferation, excessive extracellular matrix (ECM) deposition, and lung tissue scarring. Melatonin, a hormone produced by the pineal gland, plays an important role in multiple physiological and pathological responses in organisms. However, the function of melatonin in the development of bleomycin-induced pulmonary injury is poorly understood. In the present study, we found that melatonin significantly decreased mortality and restored the function of the alveolar epithelium in bleomycin-treated mice. However, pulmonary function mainly depends on type II alveolar epithelial cells (AECIIs) and is linked to mitochondrial integrity. We also found that melatonin reduced the production of reactive oxygen species (ROS) and prevented apoptosis and senescence in AECIIs. Luzindole, a nonselective melatonin receptor antagonist, blocked the protective action of melatonin. Interestingly, we found that the expression of apelin 13 was significantly downregulated in vitro and in vivo and that this downregulation was reversed by melatonin. Furthermore, ML221, an apelin inhibitor, disrupted the beneficial effects of melatonin on alveolar epithelial cells. Taken together, these results suggest that melatonin alleviates lung injury through regulating apelin 13 to improve mitochondrial dysfunction in the process of bleomycin-induced pulmonary injury.
Sun, Hainan,Xu, Xiaomin,Hu, Zhiwei,Tjeng, Liu Hao,Zhao, Jie,Zhang, Qin,Lin, Hong-Ji,Chen, Chien-Te,Chan, Ting-Shan,Zhou, Wei,Shao, Zongping The Royal Society of Chemistry 2019 Journal of Materials Chemistry A Vol.7 No.16
<P>If different active sites in a catalyst have optimal binding to different reaction intermediates and short reaction paths among them, they may work cooperatively to enhance the oxygen evolution reaction (OER) activity. Based on this design principle, in this study, we start with a B-site ordered double perovskite Sr2FeMoO6−δ with poor OER activity as the host material to fulfill the requirement of a short pathway, and then, replace Mo with Ni and Fe with Co to optimize the synergistic interplay of the multi-active sites. Replacing Mo with Ni indeed dramatically enhances the OER activity and structural/operating stability. Further improvement in OER performance is realized by partial substitution of Fe with Co, leading to the development of a material with the nominal composition of Sr2Fe0.8Co0.2Mo0.65Ni0.35O6−δ, which outperforms the noble metal oxide IrO2 and is better than most of the electrocatalysts developed based on a single descriptor, such as Ba0.5Sr0.5Co0.8Fe0.2O3−δ (eg occupancy close to unity), PrBaCo2O5+δ (O 2p-band center relative to the Fermi level), and La0.5Sr0.5CoO3−δ (charge-transfer energy) in many aspects. As a universal method, combined structural and compositional tuning to create a cooperative effect among different active sites for intermediate adsorption and reaction in an ordered structure may provide a new way for the design of superior electrocatalysts for various applications.</P>
Jiongming Sui,Guan Li,Guanxu Chen,Chunmei Zhao,Xiangyuan Kong,Xiaomin Hou,Lixian Qiao,Jingshan Wang 한국식물생명공학회 2017 Plant biotechnology reports Vol.11 No.1
Small GTP-binding proteins, Rab7, are known to be responsive to abiotic stresses in plants, but the molecular mechanism is poorly understood. To investigate how AhRab7 increases resistance to salinity stress in peanut, this study compared a transgenic genotype (S5) that overexpressed the AhRab7 gene and that had high salinity resistance with a non-transgenic genotype (S7) that had low salinity resistance. Digital gene expression (DGE) sequencing was performed with leaves of S5 and S7 before and after salinity-stress treatment. In total, 2697 differentially expressed genes (DEGs) were identified between S5 and S7, and KEGG enrichment analyses showed that the DEGs are involved pathways including endocytosis, lysosome, hormone signaling, phosphatidylinositol signaling, calcium, and others. Among them, 164 were differentially regulated after salinity-stress treatment. Of 164 DEGs, 110 were responsive to salinity stress in S5 and/or S7. The 110 DEGs included genes that encode the following kinds of transcription factors and proteins known to be involved in resistance to salinity stress: WRKY, NAC, MYM-type zinc finger, late embryogenesis abundant proteins, lipid transfer protein, 1-cys peroxiredoxin, aquaporin, oleosin, and others. AhRab7 gene might mediate signaling pathways including phosphatidylinositol, calcium, abscisic acid, etc., and then regulate the expression of transcription factors and downstream genes for ROS scavenging in peanut. The results of this study will be useful for further investigations of the mechanism underlying the role of the AhRab7 gene in resistance to salinity stress in peanut.