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Polyhalogenated carbazoles induce hepatic metabolic disorders in mice via alteration in gut microbiota

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Journal of Environmental Sciences 2023年第5期127卷 603-614页

作者： Chenyang Ji Yunkai Luo jiawen yang Yaoyao Dai Jiahui Miao Siqing Yue Meirong Zhao Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province Interdisciplinary Research AcademyZhejiang Shuren UniversityHangzhou 310015China Department of Ultrasound in Medicine The Fourth Affiliated Hospital of Zhejiang University School of MedicalYiwu 322000China Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province College of EnvironmentZhejiang University of TechnologyHangzhou 310014China

Polyhalogenated carbazoles(PHCZs)have been widely accepted as emerging pollutants,whereas their ecological and health risks remain ***,female and male Sprague-Dawley(SD)mice were treated with four typical PHCZs to investigate their negative consequences,along with alternations in gutmicrobiota to indicate *** female mice,the relative liver weight ratio increased after four PHCZs exposure;2-bromocarbazole(2-BCZ)increased urine glucose level;3-bromocarbazole(3-BCZ)decreased the glucose and total cholesterol levels;3,6-dichlorocarbazole(3,6-DCCZ)decreased glucose *** only disturbed biochemical index in male mice was the promoted alkaline phosphatase(ALP)level by 3,*** also found that the differential blood biochemical indices were correlated with gut microbiota.3-BCZ and 3,6-DCCZ altered Bacteroidetes and Proteobacteria phyla in female and male mice,which were correlated with metabolic *** findings demonstrated the correlation between PHCZs induced potential hepatotoxicity andmetabolic disordersmay be due to their dioxin-like potentials and endocrine disrupting activities,and the gender differences might result from their estrogenic ***,data presented here can help to evaluate the ecological and health risks of PHCZs and reveal the underlying mechanisms.

关键词： Polyhalogenated carbazoles Liver Metabolic disorders Gut microbiota

Fundamental and practical approaches for single-cell ATAC-seq analysis

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aBIOTECH 2022年第3期3卷 212-223页

作者： Peiyu Shi Yage Nie jiawen yang Weixing Zhang Zhongjie Tang Jin Xu State Key Laboratory of Biocontrol School of Life SciencesSun Yat-Sen UniversityGuangzhou510275China Zhongshan School of Medicine Sun Yat-Sen UniversityGuangzhou510275China

Assays for transposase-accessible chromatin through high-throughput sequencing(ATAC-seq)are effective tools in the study of genome-wide chromatin accessibility *** the rapid development of single-cell technology,open chromatin regions that play essential roles in epigenetic regulation have been measured at the single-cell level using single-cell ATAC-seq *** application of scATAC-seq has become as popular as that of ***,owing to the nature of scATAC-seq data,which are sparse and noisy,processing the data requires different methodologies and empirical *** review presents a practical guide for processing scATAC-seq data,from quality evaluation to downstream analysis,for various *** addition to the epigenomic profiling from scATAC-seq,we also discuss recent studies in which the function of non-coding variants has been investigated based on cell type-specific cis-regulatory elements and how to use the by-product genetic information obtained from scATAC-seq to infer single-cell copy number variants and trace cell *** anticipate that this review will assist researchers in designing and implementing scATAC-seq assays to facilitate research in diverse fields.

关键词： Chromatin accessibility scATAC-seq Data analysis Bioinformatic tools

Roll angle of autocollimator measurement method based on hollow cube corner reflector

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Optoelectronics Letters 2022年第2期18卷 91-96页

作者： LIU Yu ZHEN Yan XIE Linyi WANG Wei yang jiawen LI Renpu Chongqing Engineering Research Center of Intelligent Sensing Technology and Microsystem Chongqing University of Post and TelecommunicationsChongqing 400065China School of Biology Chongqing University of Posts and TelecommunicationsChongqing 400065China

In this paper, a method of measuring roll angle with hollow cube corner reflector(HCCR) is proposed. Firstly, the space coordinate vector relationship between the mirror and the autocollimator is established by using the Euler rotation relationship, and the structure of the HCCR is designed. Secondly, through the actual measurement of the HCCR reflector’s angle sensitivity, the specific formula of roll angle measurement is obtained. The experimental results show that the method can be used to measure the roll angle, and the maximum root mean square(RMS) error is 15" in the range of 350", and the repeatability of the experiment is better than 2.7". On the basis of retaining the traditional autocollimator, the plane mirror is replaced with HCCR, which realizes the measurement of the roll angle of the autocollimator. This method does not change the internal structure of the autocollimator system, and there is no process error caused by special processing technology, so as to retain the autocollimator’s own long measurement distance, high measurement accuracy, high system stability, and large range of measurement performance, and it can also be used in industrial production.

关键词： tor angle mirror

Optic-electronics stereo system for spatial position measurement of railway track

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Optoelectronics Letters 2022年第7期18卷 434-439页

作者： Igor Konyakhin XIAO Han LI Renpu yang jiawen HUANG Guifu TAN Xin Faculty of Engineering Research Applied Optic ITMO UniversitySaint Petersburg 197101Russia Chongqing Key Laboratory of Autonomous Navigation and Microsystem Chongqing University of Post and TelecommunicationsChongqing 400065China

Railway departments in various countries are looking for a technology with convenient operation,low price,excellent measurement performance and stability for spatial position measurement of railway ***,we design an optic-electronics stereo system based on the principle of optical stereo *** experimental verification in the real railway environment shows that the performance of the system is that the longitudinal relative displacement measurement range is 200—10000 mm,the relative distance measurement range is 4500 mm and the measured root mean square(RMS)error value is less than 1.1 mm in the whole ***,it meets the relevant needs of the Russian Ministry of railways.

关键词： measurement. system price

Measuring the spatiotemporal variation and evolution of transport network of China＇s megaregions

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Journal of Geographical Sciences 2016年第10期26卷 1497-1516页

作者： SONG Ge yang jiawen School of Management University of Science and Technology of China Hefei 230026 China School of Urban Planning and Design Peking University Shenzhen Graduate School Shenzhen 518055 Guangdong China

Megaregion has become a prominent feature of modern China. Reflecting upon China＇s recent path of transport infrastructure construction, this research examines the spatiotemporal characteristics of transport network development and its accessibility impacts in China＇s ten megaregions from 1982 to 2010. Using historical transport network data and multiple national censuses （1982, 1990, 2000 and 2010）, we computed two levels of indicators of megaregional transport network： megaregion level and county level, and analyzed the intra-megaregion and inter-megaregion disparities of transport network of the ten megaregions of China. Transport networks at the megaregion level are measured by three indicators： 1） transport network density; 2） infrastructure endowment per capita; and 3） size of transport network＇s standard ellipse. Two accessibility indicators for measuring transportation network at the county level are calculated： weighted average travel time and potential accessibility. The research results show the following： 1） Road and rail network densities witnessed the greatest growth during the 2000-2010 period, and growth was more significant for railway network. 2） By 2010, average road endowments per capita in inland megaregions became higher than in coastal megaregions, while average rail endowments per capita in coastal megaregions became higher than in inland megaregions. 3） The sizes and directions of the standard deviational ellipses of road and rail network changed continuously during the study period. However the changes of road network ellipses were relatively small, while the changes of railway network ellipses were more significant. 4） Megaregions have all benefited significantly from transportation infrastructure improvement in the past few decades in terms of WATT and potential accessibility, but the three giant megaregions benefited most.

关键词： China megaregions transport network accessibility GIS transport network model

Construction of a transposase accessible chromatin landscape reveals chromatin state of repeat elements and potential causal variant for complex traits in pigs

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Journal of Animal Science and Biotechnology 2023年第2期14卷 529-545页

作者： Tao Jiang Ziqi Ling Zhimin Zhou Xiaoyun Chen Liqing Chen Sha Liu Yingchun Sun jiawen yang Bin yang Jianzhen Huang Lusheng Huang State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural UniversityNanchang 330045China

Background:A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex ***,the genome-wide chromatin accessibility has been only reported in limited tissue types in ***:Here we report a genome-wide landscape of chromatin accessibility of 20 tissues in two female pigs at ages of 6 months using ATAC-seq,and identified 557,273 merged peaks,which greatly expanded the pig regulatory ele-ment *** revealed tissue-specific regulatory elements which were associated with tissue-relevant biologi-cal *** identified both positive and negative significant correlations between the regulatory elements and gene transcripts,which showed distinct distributions in terms of their strength and distances from corresponding *** investigated the presence of transposable elements(TEs)in open chromatin regions across all tissues,these included identifications of porcine endogenous retroviruses(PERVs)exhibiting high accessibility in liver and homology of porcine specific virus sequences to universally accessible transposable ***,we prior-itized a potential causal variant for polyunsaturated fatty acid in the ***:Our data provides a novel multi-tissues accessible chromatin landscape that serve as an important resource for interpreting regulatory sequences in tissue-specific and conserved biological functions,as well as regula-tory variants of loci associated with complex traits in pigs.

关键词： Chromatin accessibility Pig Tissue specific Transcriptome Transposable elements

Mimotope peptide modified pompon mum-like magnetic microparticles for precise recognition,capture and biotransformation analysis of rituximab in biological fluids

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Acta Pharmaceutica Sinica B 2024年第3期14卷 1317-1328页

作者： jiawen yang Aixuan Zhou Minyi Li Qiaoxian He Jingwei Zhou Jacques Crommen Wentao Wang Zhengjin Jiang Qiqin Wang Institute of Pharmaceutical Analysis College of Pharmacy/State Key Laboratory of Bioactive Molecules and Druggability Assessment/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education(MOE)of ChinaJinan UniversityGuangzhou 510632China Laboratory for the Analysis of Medicines Department of Pharmaceutical SciencesCIRMUniversity of LiegeLiege B-4000Belgium SCIEX Shanghai 200050China

Due to low immobilized ligand density,limited binding capacity,and severe interference from serum proteins,developing ideal peptide-based biomaterials for precise recognition and in vivo analysis of biopharmaceuticals remains a huge *** this study,mimotope peptide modified pompon mum-like biomimetic magnetic microparticles(MMPs,3.8μm)that mimic the specific functionalities of CD20 on malignant B cells were developed for the first *** from the numerous ligand binding sites(Ni^(2+))on the pompon mum-like MMPs,these novel materials achieved≥10 times higher peptide ligand densities(>2300 mg/g)and antibody binding capacities(1380 mg/g)compared to previous reported *** the high specificity of the mimotope peptide,rituximab can be precisely recognized and enriched from cell culture media or serum *** also established an LC-MS/MS method using the MMPs for tracking rituximab biotransformation in patient ***,deamidation of Asn55 and Asn33,as well as oxidation of Met81 and Met34 were observed at the key complementarity determining regions of rituximab,which could potentially influence antibody function and require careful ***,these versatile biomimetic MMPs demonstrate superior recognition and enrichment capabilities for target antibodies,offering interesting possibilities for biotransformation analysis of biopharmaceuticals in patient serum.

关键词： Therapeutic monoclonal antibody Mimotope peptide Precise recognition Peptide-based biomaterials Biotransformation Patient serum

Rational construction of high-active CO_(3)O_(4) electrocatalysts for oxygen evolution reaction

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Nano Research 2023年第1期16卷 624-633页

作者： Tianyun Zhang Shichao Zhao Chuanming Zhu Jing Shi Chao Su jiawen yang Meng Wang Jun Li Junhui Li Pingle Liu Conghui Wang College of Chemical Engineering Xiangtan UniversityXiangtan 411105China State Key Laboratory of Coal Conversion Institute of Coal ChemistryChinese Academy of SciencesTaiyuan 030001China Analytical Instrumentation center Institute of Coal ChemistryChinese Academy of SciencesTaiyuan 030001China

Rational construction of high-efficiency electrocatalysts for oxygen evolution reaction(OER)is critical for renewable-energy technologies,but it is highly challenging to rationally regulate their surface structures to improve the OER ***,we proposed a“model-etching”strategy to investigate chemical etching of CO_(3)O_(4).The cubic CO_(3)O_(4)nanocrystals enclosed by well-defined facets are synthesized as model crystals,whose uniform surface structures allow us to study the etching mechanism at atomic *** kinetics study together with DFT calculations discloses that{111}facets,the highly active facets for OER,serve as etch-stop facets in the etching reaction and H_(2)SO_(4)molecules play a special role in creating surface Co2^(+),the active center of *** results direct us to rationally optimize the surface structures of CO_(3)O_(4) to develop highly active OER *** favorable performance of overpotential(η)and the Tafel slope decrease even to 268 mV@10 mA·cm−2 and 74 mV·dec−1,*** general,our study shows that chemical etching of model crystals could help us rationally construct high-efficiency electrocatalysts.

关键词： cobalt oxide chemical etching high active facets oxygen evolution reaction surface structure

Mapping and analysis of a spatiotemporal H3K27ac and gene expression spectrum in pigs

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Science China(Life Sciences) 2022年第8期65卷 1517-1534页

作者： Yaling Zhu Zhimin Zhou Tao Huang Zhen Zhang Wanbo Li Ziqi Ling Tao Jiang jiawen yang Siyu yang Yanyuan Xiao Carole Charlier Michel Georges Bin yang Lusheng Huang State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural UniversityNanchang 330045China Laboratory Animal Research Center School of Basic Medical SciencesAnhui Medical UniversityHefei 230032China Unit of Animal Genomics GIGA-Institute and Faculty of Veterinary MedicineUniversity of Liege4000 LiegeBelgium

The limited knowledge of genomic noncoding and regulatory regions has restricted our ability to decipher the genetic mechanisms underlying complex traits in pigs. In this study, we characterized the spatiotemporal landscape of putative enhancers and promoters and their target genes by combining H3K27ac-targeted Ch IP-Seq and RNA-Seq in fetal(prenatal days 74–75) and adult(postnatal days 132–150) tissues(brain, liver, heart, muscle and small intestine) sampled from Asian aboriginal Bama Xiang and European highly selected Large White pigs of both sexes. We identified 101,290 H3K27ac peaks, marking 18,521promoters and 82,769 enhancers, including peaks that were active across all tissues and developmental stages(which could indicate safe harbor locus for exogenous gene insertion) and tissue-and developmental stage-specific peaks(which regulate gene pathways matching tissue-and developmental stage-specific physiological functions). We found that H3K27ac and DNA methylation in the promoter region of the XIST gene may be involved in X chromosome inactivation and demonstrated the utility of the present resource for revealing the regulatory patterns of known causal genes and prioritizing candidate causal variants for complex traits in pigs. In addition, we identified an average of 1,124 super-enhancers per sample and found that they were more likely to show tissue-specific activity than ordinary peaks. We have developed a web browser to improve the accessibility of the results(http://***/pencode/?genome=sus Scr11).

关键词： H3K27ac ChIP-Seq RNA-Seq pig XIST complex traits