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Mixed secondary chromatin structure revealed by modeling radiation-induced DNA fragment length distribution

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Science China(Life Sciences) 2020年第6期63卷 825-834页

作者： Wenzong Ma Chenyang Gu Lin Ma Caoqi Fan Chao Zhang yujie sun Cheng Li Gen Yang State Key Laboratory of Nuclear Physics and Technology School of PhysicsPeking UniversityBejing 100871China Radiation Biology Center Graduate School of BiostudiesKyoto UniversityKyoto 606-8501Japan Medical Artificial Intelligence and Automation Department of Radiation OncologyUniversity of Texas Southwestern Medical CenterDallasTX 75390USA Center for Bioinformatics School of Life Sciences and Center for Statistical SciencePeking UniversityBejing 100871China State Key Laboratory of Membrane Biology School of Life Sciencesand Biomedical Pioneering Innovation Center(BIOPIC)Peking UniversityBejing 100871China

Spatial chromatin structure plays fundamental roles in many vital biological processes including DNA replication, transcription,damage and repair. However, the current understanding of the secondary structure of chromatin formed by local nucleosomenucleosome interactions remains controversial, especially for the existence and conformation of 30 nm structure. Since chromatin structure influences the fragment length distribution(FLD) of ionizing radiation-induced DNA strand breaks, a 3D chromatin model fitting FLD patterns can help to distinguish different models of chromatin structure. Here, we developed a novel "30-C" model combining 30 nm chromatin structure models with Hi-C data, which measured the spatial contact frequency between different loci in the genome. We first reconstructed the 3D coordinates of the 25 kb bins from Hi-C heatmaps. Within the25 kb bins, lower level chromatin structures supported by recent studies were filled. Simulated FLD patterns based on the 30-C model were compared to published FLD patterns induced by heavy ion radiation to validate the models. Importantly, the 30-C model predicted that the most probable chromatin fiber structure for human interphase fibroblasts in vivo was 45% zig-zag 30 nm fibers and 55% 10 nm fibers.

关键词： Hi-C DNA strand break ionizing radiation chromatin structure

Nitrogen-doped carbon dots-modified Prussian blue with sandwichlike structure as a high-performance electrochromic material

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Nano Research 2024年第10期17卷 9174-9180页

作者： Yaqi Zhang Lide Li Siming Zhao Yilin Ding Nan Shen yujie sun Hao Wang Jingfa Li Rufan Zhang School of Chemistry and Materials Science School of Physics and Optoelectronic EngineeringNanjing University of Information Science and TechnologyNanjing 210044China Beijing Key Laboratory of Green Chemical Reaction Engineering and Technology Department of Chemical EngineeringTsinghua UniversityBeijing 100084China

Prussian blue(PB),as a promising inorganic electrochromic material(ECM),has been widely used in smart windows,displays,sensors,***,there are still many challenges for PB to achieve high electrochromic ***,we synthesized nitrogen-doped carbon dots-modified PB film(defined as PB@N-CDs)with a sandwich-like structure by a simple stepwise electrodeposition *** carbon dots show an obvious advantage in ultrafast electron transfer ability,which can reduce charge loss during the transfer process,improve the electrochemical activity on both sides of PB,and thus facilitate a rapid electrochromic ***,the surface of nitrogen-doped carbon dots contains multiple organic functional groups,which widen the movement path of K+ions under electrostatic ***,the PB@N-CDs film exhibits a short bleaching/coloring time(0.5/0.9 s)and a superior optical modulation range(78.6%).Particularly,the coloring efficiency has been significantly improved to 137.71 cm^(2)/C(at 700 nm).All of these results open up new avenues for developing highperformance PB-based ECMs and promoting their applications in corresponding electrochromic devices(ECDs)and smart windows.

关键词： electrochromic Prussian blue carbon dots nanostructure

The Impacts of Urbanization on the Distribution and Body Condition of the Rice-paddy Frog(Fejervarya multistriata) and Gold-striped Pond Frog(Pelophylax plancyi) in Shanghai,China

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Asian Herpetological Research 2016年第3期7卷 200-209页

作者： Ben LI Wei ZHANG Xiaoxiao SHU Enle PEI Xiao YUAN yujie sun Tianhou WANG Zhenghuan WANG School of Life Science shanghai Key Laboratory of Urbanization and Ecological Restoration East China Normal University Shanghai 200062 China Shanghai Landscaping and City Appearance Administrative Bureau Shanghai 200040 China

Previous studies have suggested that urbanization presents a major threat to anuran populations. However, very few studies have looked at the relationship between urbanization and anuran body condition. We investigated whether the distribution and body condition of the rice-paddy frog（Fejervarya multistriata） and gold-striped pond frog（Pelophylax plancyi） are influenced by increasing urbanization in Shanghai, China. Four study sites with six indicators of the major land-cover types were scored to indicate their position on an urbanization gradient. We found that both the density and body condition of F. multistriata declined significantly along this gradient. Although we observed a significant difference in body condition of P. plancyi among study sites with different degrees of urbanization, we did not find any corresponding significant differences in population density. Our results indicate that both the densities and body condition of these two anuran species show a negative relationship with increasing urbanization, but that the density of P. plancyi was only slightly affected in Shanghai.

关键词： urbanization paddy indicators declined populations capture Figure habitat vegetation threat

p53 exerts anticancer effects by regulating enhancer formation and activity

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Journal of Biomedical Research 2024年第4期38卷 334-347页

作者： Shuhan Chen Xuchun Wang Nan Yang Yuechi Song He Cheng yujie sun Key Laboratory of Human Functional Genomics of Jiangsu Province School of Basic Medical SciencesNanjing Medical UniversityNanjingJiangsu 211166China Department of Cell Biology School of Basic Medical SciencesNanjing Medical UniversityNanjingJiangsu 211166China Jiangsu Key Lab of Cancer Biomarkers Prevention and TreatmentCollaborative Innovation Center for Personalized Cancer MedicineNanjing Medical UniversityNanjingJiangsu 211166China

The abnormality of the p53 tumor suppressor is crucial in lung cancer development,because p53 regulates target gene promoters to combat *** studies have shown extensive p53 binding to enhancer ***,whether p53 exerts a tumor suppressor role by shaping the enhancer landscape remains poorly *** the current study,we employed several functional genomics approaches to assess the enhancer activity at p53 binding sites throughout the genome based on our established TP53 knockout(KO)human bronchial epithelial cells(BEAS-2B).A total of 943 active regular enhancers and 370 super-enhancers(SEs)disappeared upon the deletion of p53,indicating that p53 modulates the activity of hundreds of enhancer *** found that one p53-dependent SE,located on chromosome 9 and designated as KLF4-SE,regulated the expression of the Krüppel-like factor 4(KLF4)***,the deletion of p53 significantly decreased the KLF4-SE enhancer activity and the KLF4 expression,but increased colony formation ability in the nitrosamines 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone-induced cell transformation ***,in TP53 KO cells,the overexpression of KLF4 partially reversed the increased clonogenic capacity caused by p53 ***,KLF4 expression also decreased in lung cancer tissues and cell *** appeared that overexpression of KLF4 significantly suppressed the proliferation and migration of lung cancer ***,our results suggest that the regulation of enhancer formation and activity by p53 is an integral component of the p53 tumor suppressor ***,our findings offer some novel insights into the regulation mechanism of p53 in lung oncogenesis and introduce a new strategy for screening therapeutic targets.

关键词： p53 enhancer tumor malignant transformation

Extraction of tight binding parameters from in-situ ARPES on the continuously doped surface of cuprates

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Science China(Physics,Mechanics & Astronomy) 2018年第12期61卷 25-29页

作者： YiGui Zhong YiMeng Chen JianYu Guan Jin Zhao ZhiCheng Rao CenYao Tang HaiJiang Liu yujie sun Hong Ding Beijing National Laboratory for Condensed Matter Physics and Institute of Physics Chinese Academy of SciencesBeijing 100190China School of Physics University of Chinese Academy of SciencesBeijing 100190China Collaborative Innovation Center of Quantum Matter Beijing 100190China

Recently we developed a technique of ozone/vacuum annealing to continuously change the doping level of the surface of Bi_2Sr_2CaCu_2O_(8+)and measured a nearly whole superconducting dome on one surface by in-situ angle-resolved photoemission spectroscopy [arXiv: 1805.06450]. Here we study the evolution of the electronic structures of Bi_2Sr_2CaCu_2O_(8+)xusing this technique together with tight binding fits. The tight binding parameters are extracted to study their evolution with doping.

关键词： cuprates electronic structures doping evolution tight binding ARPES

Homologous gradient heterostructure-based artificial synapses for neuromorphic computation

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InfoMat 2023年第1期5卷 95-105页

作者： Changjiu Teng Qiangmin Yu yujie sun Baofu Ding Wenjun Chen Zehao Zhang Bilu Liu Hui-Ming Cheng Shenzhen Geim Graphene Center Tsinghua-Berkeley Shenzhen Institute and Institute of Materials ResearchShenzhen International Graduate SchoolTsinghua UniversityShenzhenPeople's Republic of China Faculty of Materials Science and Engineering/Institute of Technology for Carbon Neutrality Shenzhen Institute of Advanced TechnologyChinese Academy of ScienceShenzhenPeople's Republic of China School of Electronic and Information Engineering Foshan UniversityFoshanPeople's Republic of China Shenyang National Laboratory for Materials Science Institute of Metal ResearchChinese Academy of SciencesShenyangPeople's Republic of China

Gradient heterostructure is one of fundamental interfaces and provides an effective platform to achieve gradually changed properties in mechanics,optics,and *** different types of heterostructures,the gradient one may provide multiple resistive states and immobilized conductive fila-ments,offering great prospect for fabricating memristors with both high neuromorphic computation capability and ***,we invent a memristor based on a homologous gradient heterostructure(HGHS),compris-ing a conductive transition metal dichalcogenide and an insulating homolo-gous metal *** made of Ta–TaS_(x)O_(y)–TaS 2 HGHS exhibits continuous potentiation/depression behavior and repeatable forward/backward scanning in the read-voltage range,which are dominated by multi-ple resistive states and immobilized conductive filaments in HGHS,***,the continuous potentiation/depression behavior makes the memristor serve as a synapse,featuring broad-frequency response(10^(-1)–10^(5) Hz,covering 106 frequency range)and multiple-mode learning(enhanced,depressed,and random-level modes)based on its natural and moti-vated forgetting *** HGHS-based memristor also shows good unifor-mity for 5?7 device *** work paves a way to achieve high-performance integrated memristors for future artificial neuromorphic computation.

关键词： artificial synapses broad-frequency range gradient heterostructures homologous memristors neuromorphic computation

Engineering trienzyme cascade-triggered fluorescent immunosensor platform by sequentially integrating alkaline phosphatase, tyrosinase and horseradish peroxidase

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Chinese Chemical Letters 2023年第4期34卷 444-448页

作者： yujie sun Lei Wen Huili Ma Wenlin Ma Zhenqian Fu Yinhui Li Chengwu Zhang Lin Li Jinhua Liu Institute of Advanced Materials(IAM) Key Laboratory of Flexible Electronics(KLOFE)Nanjing Tech UniversityNanjing 211816China Key Laboratory for Green Organic Synthesis and Application of Hunan Province Key Laboratory of Environmentally Friendly ChemistryApplication of Ministry of EducationCollege of ChemistryXiangtan UniversityXiangtan 411105China School of Basic Medical Sciences Shanxi Medical UniversityTaiyuan 310003China

Mulit-enzyme cascades are a major type of chemical transformations and play a crucial role in biological signal transduction and metabolism. Herein, a trienzyme cascade-triggered fluorescent immunosensor platform was constructed by sequentially integrating alkaline phosphatase(ALP), tyrosinase(TYR)and horseradish peroxidase(HRP). The proposed platform was based on HRP-induced a rapid in situ fluorogenic reaction between dopamine(DA) and 1,5-dihydroxynaphthalene(DHA) to produce a strong yellow azamonardine fluorescent compound(AFC). The obtained AFC was clearly characterized by highresolution mass spectrum,1H NMR,^(13)C NMR and theoretical calculations. The integration of the twoenzyme system(TYR and HRP) or three-enzyme system(ALP, TYR and HRP) led to a maximum of 400.0-fold and 250.0-fold fluorescence enhancements, respectively. Using cardiac troponin I(c Tn I) as the model antigen, a trienzyme cascade-triggered fluorescent immunosensor platform was developed for quantitative detecting c Tn I in a wide linear range from 2 ng/m L to 150 ng/m L with a detection limit of 0.67ng/m L. In addition, the proposed platform was successfully applied in detection of c Tn I in serum of clinical patients. Overall, the developed fluorescent immunosensor performs powerful implications for researching enzyme cascade systems in the field of biomedicine.

关键词： Enzyme cascade Alkaline phosphatase Tyrosinase Horseradish peroxidase Cardiac troponin I

Consecutive topological transitions of helical Fermi arcs at saddle points in CoSi

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Science China(Physics,Mechanics & Astronomy) 2022年第5期65卷 97-103页

作者： Zhicheng Rao Shangjie Tian Shunye Gao Quanxin Hu Wenhui Fan Jierui Huang Cenyao Tang Yaobo Huang Hechang Lei yujie sun Tian Qian Hong Ding Beijing National Laboratory for Condensed Matter Physics and Institute of Physics Chinese Academy of SciencesBeijing 100190China University of Chinese Academy of Sciences Beijing 100049China Department of Physics and Beijing Key Laboratory of Opto-electronic Functional Materials&Micro-nano Devices Renmin University of ChinaBeijing 100872China Shanghai Synchrotron Radiation Facility Shanghai Advanced Research InstituteChinese Academy of SciencesShanghai 201210China Songshan Lake Materials Laboratory Dongguan 523808China CAS Center for Excellence in Topological Quantum Computation University of Chinese Academy of SciencesBeijing 100190China Department of Physics South University of Science and TechnologyShenzhen 518055China

The CoSi family hosts unconventional topological nodes with nonzero Chern *** nontrivial topology is manifested by conspicuous surface Fermi arcs connecting surface projections of the ***,using angle-resolved photoemission spectroscopy,we have systematically investigated the(001)surface states of pristine and Ni-doped Co *** surface states form saddle-like band structures at/near the time-reversal invariant point near the Fermi *** Fermi arcs undergo consecutive Lifshitz transitions at the saddle points X,leading to changes of the Fermi arc *** the density of states has a van Hove singularity at the saddle points,exotic many-body physical phenomena may emerge accompanied by the topological transitions of surface Fermi arcs.

关键词： topological transition Fermi arcs saddle point

Casualties Analysis in Fire Accident of Passenger Transport Station Based on FTA

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Casualties Analysis in Fire Accident of Passenger Transport ...