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Decoding transcriptional regulation via a human gene expression predictor

Journal of Genetics and Genomics 2023年第5期50卷 305-317页

作者： Yuzhou WANG Yu Zhang Ning Yu Bingyan Li Jiazhen Gong Yide Mei Jianqiang Bao Shisong Ma The First Affiliated Hospital of USTC Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui 230027China MOE Key Laboratory for Cellular Dynamics School of Life SciencesDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaInnovation Academy for Seed DesignChinese Academy of SciencesHefeiAnhui 230027China School of Data Science University of Science and Technology of ChinaHefeiAnhui 230027China

Transcription factors(TFs)regulate cellular activities by controlling gene expression,but a predictive model describing how TFs quantitatively modulate human transcriptomes is lacking.We construct a universal human gene expression predictor named EXPLICIT-Human and utilize it to decode transcriptional regulation.Using the expression of 1613 TFs,the predictor reconstitutes highly accurate transcriptomes for samples derived from a wide range of tissues and conditions.The broad applicability of the predictor indicates that it recapitulates the quantitative relationships between TFs and target genes ubiquitous across tissues.Significant interacting TF-target gene pairs are extracted from the predictor and enable downstream inference of TF regulators for diverse pathways involved in development,immunity,metabolism,and stress response.A detailed analysis of the hematopoiesis process reveals an atlas of key TFs regulating the development of different hematopoietic cell lineages,and a portion of these TFs are conserved between humans and mice.The results demonstrate that our method is capable of delineating the TFs responsible for fate determination.Compared to other existing tools,EXPLICIT-Human shows a better performance in recovering the correct TF regulators.

关键词： Gene expression predictor Gene regulatory network Graphical Gaussian model Gene module Human Mouse

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Corrosion behavior of a Mg-Zn-Ca-La alloy in 3.5 wt%NaCl solution

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Journal of Magnesium and Alloys 2022年第2期10卷 567-580页

作者： yuzhou Du Xin wang Dongjie Liu Wanting Sun Bailing Jiang School of Materials Science and Engineering Xi’an University of TechnologyXi’an 710048China Shaanxi Province Engineering Research Center for Magnesium Alloys Xi’an University of TechnologyXi’an 710048China School of Materials Science and Engineering Dongguan University of TechnologyDongguan 523808China

The present study investigates the corrosion behavior of a Mg–Zn–Ca–La alloy.Results indicate that the corrosion resistance is enhanced by rolling deformation and subsequent annealing treatment significantly.The microstructure,distribution of second phase and grain orientation are the main factors affecting corrosion properties.The second phase with semi-continuous network in the as-cast alloy gives rise to the penetration of corrosion into the matrix.However,the dispersed second phase after deformation results in uniform corrosion.The formation of dense corrosion layer at the initial stage of corrosion is favorable for the improvement of corrosion resistance.The sample withplane oriented towards surface exhibits good corrosion resistance,which is ascribed to the homogeneous microstructure and strong basal texture.

关键词： Mg–Zn–Ca–La Rolling Second phase Texture Corrosion properties

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In-situ construction of PDOL electrolyte with dual-reinforced stable interface for high-voltage lithium metal batteries

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Science China Chemistry 2024年第5期67卷 1664-1671页

作者： Yingkang Wu yuzhou Bai Wujie Dong Xue wang Wenqin Ma Fuqiang Huang State Key Lab of Metal Matrix Composites School of Materials Science and EngineeringShanghai Jiao Tong UniversityShanghai 200240China School of Physical Science and Technology Shanghai Tech UniversityShanghai 201210China Shanghai Institute of Ceramics Chinese Academy of SciencesShanghai 200050China

In-situ polymerized electrolytes significantly enhance the interfacial compatibility of lithium metal batteries(LMBs). Typically,in-situ polymerized 1,3-dioxolane(PDOL) exhibits low interfacial resistance, yet still suffers from low ionic conductivity and a narrow electrochemical stability window(ESW). Here, an ultra-stable PDOL-based polymer electrolyte is developed by incorporating plasticizers of tetramethylene sulfone(TMS) and fluorinated ethylene carbonate(FEC) into the 3D cross-linked network, achieving a significant enhancement in the transport capacity and efficiency of Li-ion. The ionic conductivity reaches3.63×10^(-4)S cm^(-1)even at room temperature, and the transference number(tLi^(+)) is even higher at 0.85. Furthermore, the ESW of this electrolyte can be increased to 4.5 V with the addition of TMS, which forms a thin and robust antioxidant cathode-electrolyte interface(CEI) on the surface of high-voltage LiCoO_(2). FEC generates an inorganic-rich solid-electrolyte interface(SEI) on the Li anode, which effectively inhibits the growth of lithium dendrites. Benefiting from the aforementioned advantages, the highvoltage lithium metal battery demonstrates outstanding long-cycle stability, with 93.2% capacity retention after 200 cycles. This work offers a straightforward and accessible method for the practical implementation of high energy density in-situ polymerized solid-state LMBs.

关键词： solid polymer electrolyte in-situ polymerization PDOL high-voltage LMBs

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Effect of environmental factors on the complexation of iron and humic acid

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Journal of Environmental Sciences 2015年第1期27卷 188-196页

作者： Kai Fang Dongxing Yuan Lei Zhang Lifeng Feng Yaojin Chen Yuzhou WANG State Key Laboratory of Marine Environmental Science College of the Environment and Ecology Xiamen University

A method of size exclusion chromatography coupled with ultraviolet spectrophotometry and off-line graphite furnace atomic absorption spectrometry was developed to assess the complexation properties of iron（Fe） and humic acid（HA） in a water environment. The factors affecting the complexation of Fe and HA, such as ionic strength, pH, temperature and UV radiation, were investigated. The Fe–HA complex residence time was also studied. Experimental results showed that pH could influence the deprotonation of HA and hydrolysis of Fe, and thus affected the complexation of Fe and HA. The complexation was greatly disrupted by the presence of NaCl. Temperature had some influence on the complexation. The yield of Fe–HA complexes showed a small decrease at high levels of UV radiation, but the effect of UV radiation on Fe–HA complex formation at natural levels could be neglected. It took about 10 hr for the complexation to reach equilibrium, and the Fe–HA complex residence time was about 20 hr.Complexation of Fe and HA reached a maximum level under the conditions of pH 6, very low ionic strength, in the dark and at a water temperature of about 25°C, for 10 hr. It was suggested that the Fe–HA complex could form mainly in freshwater bodies and reach high levels in the warm season with mild sunlight radiation. With changing environmental parameters, such as at lower temperature in winter or higher pH and ionic strength in an estuary, the concentration of the Fe–HA complex would decrease.

关键词： Iron Humic acid Complexation Size exclusion chromatography Graphite furnace atomic absorption spectrometry

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Relationship between corneal biomechanical parameters and corneal sublayer thickness measured by Corvis ST and UHR-OCT in keratoconus and normal eyes

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Eye and Vision 2021年第1期8卷 6-17页

作者： Yong Li Zhiqiang Xu Qiaoli Liu Yuzhou WANG Kan Lin Jiahui Xia Shihao Chen Liang Hu School of Ophthalmology and Optometry Eye HospitalWenzhou Medical University270 Xueyuan roadWenzhou 325000ZhejiangChina National Clinical Research Center for Ocular Diseases WenzhouZhejiangChina

Background:To explore the relationship between corneal biomechanical parameters and corneal sublayer thickness using corneal visualization Scheimpflug technology(Corvis ST)and ultrahigh-resolution optical coherence tomography(UHR-OCT)in clinical and suspected keratoconus and normal eyes.Methods:Cross-sectional prospective study.A total of 94 eyes of 70 participants were recruited.Twenty five eyes of 19 keratoconus patients,52 eyes of 34 patients showing high risk of developing keratoconus according to the Belin/Ambrosio Enhanced Ectasia Display,and each eye of 17 normal subjects were enrolled.All participants underwent Corvis ST,Pentacam,and UHR-OCT examinations at the same time.Stiffness parameter A1(SP-A1),deformation amplitude ratio(DA ratio),and other biomechanical parameters were recorded using Corvis ST.The vertical and horizontal thickness profiles of central 3mm corneal epithelium,Bowman’s layer,and stroma as measured by the perpendicular distance between the neighboring interfaces were generated using UHR-OCT.The flat keratometry and steep keratometry were obtained using Pentacam.Analysis of correlation was applied to explore the association between variables.Results:Most of the biomechanical parameters and corneal sublayer thickness profiles showed statistical differences among three groups.A statistically significant linear relationship was noted between SP-A1 and DA ratio in all three groups.SP-A1 was found to be positively correlated with epithelial and Bowman’s layer thickness in the keratoconus(KC)group,and with stromal thickness in all three groups.In the normal and suspected keratoconus(SKC)groups,only stromal thickness was included in the stepwise linear regression to predict SP-A1,whereas in the KC group,steep keratometry and Bowman’s layer thickness were included.Conclusions:Significant and different correlations were noted between corneal stiffness and corneal sublayer thickness in different groups,indicating that corneal sublayers may play different roles in maintaining corneal biomechanical

关键词： Biomechanics Corneal thickness Keratoconus Corvis ST UHR-OCT

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DSEMR: A database for special environment microorganisms resource and associating them with synthetic biological parts

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Synthetic and Systems Biotechnology 2023年第4期8卷 647-653页

作者： Yuzhou WANG Jinyi Qian Fang Yan Yuetong wang Tianqiong Shi Zhidong Zhang Chao Ye He Huang School of Food Science and Pharmaceutical Engineering Nanjing Normal UniversityNanjing210023China Institute of Microbiology Xinjiang Academy of Agricultural SciencesUrumqi830091China

Special environmental microorganisms are considered to be of great industrial application value because of their special genotypes,physiological functions and metabolites.The research and development of special environmental microorganisms will certainly bring about some innovations in biotechnology processes and change the face of bioengineering.The Special Environmental Microbial Database(DSEMR)is a comprehensive database that provides information on special environmental microbial resources and correlates them with synthetic biological parts.DSEMR aggregates information on specific environmental microbial genomes,physiological properties,culture media,biological parts,and metabolic pathways,and provides online tool analysis data,including 5268 strains from 620 genera,31 media,and 42,126 biological parts.In short,DSEMR will become an important resource for the study of microorganisms in special environments and actively promote the development of synthetic biology.

关键词： Special environment microorganism Physiological functions Synthetic biological parts

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pH and lipase-responsive nanocarrier-mediated dual drug delivery system to treat periodontitis in diabetic rats

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Bioactive Materials 2022年第12期7卷 254-266页

作者： Lu wang yuzhou Li Mingxing Ren Xu wang Lingjie Li Fengyi Liu Yiqing Lan Sheng Yang Jinlin Song College of Stomatology Chongqing Medical UniversityChongqingChina Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences ChongqingChina Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education ChongqingChina

Precise and controlled drug delivery to treat periodontitis in patients with diabetes remains a significant clinical challenge.Nanoparticle-based drug delivery systems offer a potential therapeutic strategy;however,the low loading efficiency,non-responsiveness,and single effect of conventional nanoparticles hinder their clinical application.In this study,we designed a novel self-assembled,dual responsive,and dual drug-loading nanocarrier system,which comprised two parts:the hydrophobic lipid core formed by 1,2-Distearoyl-sn-glycero-3-phosphoethanolamine-Poly(ethylene glycol)(DSPE-PEG)loaded with alpha-lipoic acid(ALA);and a hydrophilic shell comprising a poly(amidoamine)dendrimer(PAMAM)that electrostatically adsorbed minocycline hydrochloride(Mino).This unique design allows the controlled release of antioxidant/ALA under lipase stimulation from periodontal pathogens and antimicrobial/Mino under the low pH of the inflammatory microenvironment.In vivo and in vitro studies confirmed that this dual nanocarrier could inhibit the formation of subgingival microbial colonies while promoting osteogenic differentiation of cells under diabetic pathological conditions,and ameliorated periodontal bone resorption.This effective and versatile drug-delivery strategy has good potential applications to inhibit diabetes-associated periodontal bone loss.

关键词： Diabetes mellitus Periodontitis Bone loss PAMAM Drug delivery

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The disease resistance potential of Trichoderma asperellum T-Pa2 isolated from Phellodendron amurense rhizosphere soil

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Journal of Forestry Research 2022年第1期33卷 321-331页

作者： Zeyang Yu Zhihua Liu yuzhou Zhang Zhiying wang School of Forestry Northeast Forestry University26 Hexing RoadHarbin 150040People’s Republic of China General Station of Forest and Grassland Pest Management National Forestry and Grassland AdministrationShenyang 110034People’s Republic of China College of Forestry Shenyang Agricultural UniversityShenyang 110866People’s Republic of China

To promote the application of Trichoderma,many countries have collected Trichoderma resources.In the present study,nine isolates were isolated from a rhizosphere soil of Phellodendron amurense and were identified as three species:Trichoderma brevicompactum(one isolate),T.asperellum(two isolates),T.atroviride(six isolates).Dual culture experiments showed that T.asperellum T-Pa2 grew fast and produced the best inhibition rates against six tested pathogens(80.25–91.65%)via competition and mycoparasitism.Populus davidiana×P.alba var.pyramidalis Louche(PdPap poplar)was treated with T-Pa2,which increased the catalase activity,nitrate reductase activity,and content of osmosis molecules significantly(P<0.05).Meanwhile,induction by T-Pa2 increased the resistance of PdPap poplar against Alternaria alternata via modulating the expression of salicylic acid,jasmonic acid,and auxin transduction pathway genes.The results will form the basis for the collection and application of biocontrol agents in forestry.

关键词： Biological control Trichoderma identification Antifungal property Enzyme activity

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Simulation of Coupling Process of Flexible Needle Insertion into Soft Tissue Based on ABAQUS

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Computers, Materials & Continua 2020年第8期64卷 1153-1169页

作者： Linze wang Dedong Gao Jiajie Fu yuzhou Luo Shijian Zhao School of Mechanical Engineering Qinghai UniversityXining810016China Yamaguchi University Graduate School of Sciences and Technology for InnovationYamaguchi7558611Japan

In order to get to the desired target inside the body,it is essential to investigate the needle-tissue coupling process and calculate the tissue deformation.A cantilever beam model is presented to predicting the deflection and bending angle of flexible needle by analyzing the distribution of the force on needle shaft during the procedure of needle insertion into soft tissue.Furthermore,a finite element(FE)coupling model is proposed to simulate the needle-tissue interactive process.The plane and spatial models are created to relate the needle and tissue nodes.Combined with the cantilever beam model and the finite element needle-tissue coupling model,the simulation of needle-tissue interaction was carried out by the ABAQUS software.The comparing experiments are designed to understand the needle-tissue interactions,by which the same points in the experiments and simulation are compared and analyzed.The results show that the displacements in x and z directions in the simulation can accord with the experiments,and the deformation inside the tissue mainly occurs in the axial direction.The study is beneficial to the robot-assisted and virtual needle insertion procedure,and to help the physicians to predict the inside tissue deformation during the treatments.

关键词： Cantilever beam model needle-tissue coupling finite element tissue deformation

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Fluorescence imaging analysis of the glioma microenvironment

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Journal of Innovative Optical Health Sciences 2023年第1期16卷 55-66页

作者： Xuwen Peng yuzhou Chen Yuke wang Shuhong Qi Britton Chance Center for Biomedical Photonics Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology Wuhan Hubei 430074P.R.China MoE Key Laboratory for Biomedical Photonics School of Engineering Sciences Huazhong University of Science and Technology Wuhan Hubei 430074P.R.China

Glioma is the most malignant brain cancer.The neurons,macrophages,T cells and other immune ellls constitute the glioma immunosuppressive microenvironment.The accurate spatial distri-bution of these cells in the glioma microenvironment and its relationship with glioma metastasis is unknown.We constructed a mouse gliomna cell line stably expressing the large Stokes shifted yellow fluorescent protein and applied it to the multicolor immunofluorescence imaging.The inaging data revealed that the neurons were sparsely distributed in the glioma core and the mumber of neurons decreased by 90%compared with normal brain site.The spatial distribution of monocyte-macrophages and microglia is heterogeneous.The monocyte macrophages and T cells were heavily recrnuited into the glioma core and metastasis.There was no significant difference in the distribution of microglia amnong glioma core,margin,and normal brain site.Our results provided new perspectives for targeting immune regulation cells and developing new immuno-therapy strategies for glioma.

关键词： Glioma microenvironment spatial distribution heterogeneity multicolor immuno-fluorescence large Stokes-shifted fluorescent protein.

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