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High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads

Genomics, Proteomics & Bioinformatics 2022年第1期20卷 4-13页

作者： Bo Wang Xiaofei Yang Yanyan Jia Yu Xu Peng Jia Ningxin Dang Songbo Wang Tun Xu Xixi Zhao Shenghan Gao Quanbin Dong kai ye MOE Key Laboratory for Intelligent Networks&Network Security Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China School of Computer Science and Technology Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China School of Life Science and Technology Xi’an Jiaotong UniversityXi’an 710049China School of Automation Science and Engineering Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China Genome Institute the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China

Arabidopsis thaliana is an important and long-established model species for plant molecular biology,genetics,epigenetics,and ***,the latest version of reference genome still contains a significant number of missing ***,we reported a high-quality and almost complete Col-0 genome assembly with two gaps(named Col-XJTU)by combining the Oxford Nanopore Technologies ultra-long reads,Pacific Biosciences high-fidelity long reads,and Hi-C *** total genome assembly size is 133,725,193 bp,introducing 14.6 Mb of novel sequences compared to the TAIR10.1 reference *** five chromosomes of the Col-XJTU assembly are highly accurate with consensus quality(QV)scores>60(ranging from 62 to 68),which are higher than those of the TAIR10.1 reference(ranging from 45 to 52).We completely resolved chromosome(Chr)3 and Chr5 in a telomere-to-telomere ***4 was completely resolved except the nucleolar organizing regions,which comprise long repetitive DNA *** Chrl centromere(CEN1),reportedly around 9 Mb in length,is particularly challenging to assemble due to the presence of tens of thousands of CEN180 satellite *** the cutting-edge sequencing data and novel computational approaches,we assembled a 3.8-Mb-long CEN1 and a 3.5-Mb-long *** also investigated the structure and epigenetics of *** clusters of CEN180 monomers were detected,and the centromere-specific histone H3-like protein(CENH3)exhibited a strong preference for CEN180 Cluster ***,we observed hypomethylation patterns in CENH3-enriched *** believe that this high-quality genome assembly,Col-XJTU,would serve as a valuable reference to better understand the global pattern of centromeric polymorphisms,as well as the genetic and epigenetic features in plants.

关键词： Centromere architecture CENH3 Bacterial artificial chromosome Telomere-to-telomere Model plant

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Single-cell transcriptomes provide insights into expansion of glial cells in Bombyx mori

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Insect Science 2024年第4期31卷 1041-1054页

作者： Xiaojing Liu Zhongjie Zhang Bo Hu kai Chen ye Yu Hui Xiang Anjiang Tan Jiangsu Key Laboratory of Sericultural Biology and Biotechnology School of BiotechnologyJiangsu University of Science and TechnologyZhenjiangJiangsu ProvinceChina Key Laboratory of Silkworm and Mulberry Genetic Improvement Ministry of Agriculture and Rural AffairsThe Sericultural Research InstituteChinese Academy of Agricultural SciencesZhenjiangJiangsu ProvinceChina Guangzhou Key Laboratory of Insect Development Regulation and Application Research Institute of Insect Science and Technology and School of Life SciencesSouth China Normal UniversityGuangzhouChina

The diversity of cell types in the brain and how these change during different developmental stages,remains largely *** life cycle of insects is short and goes through 4 distinct stages including embryonic,larval,pupal,and adult *** postembryonic life,the larval brain transforms into a mature adult version after *** silkworm,Bombyx mori,is a lepidopteran model ***,we characterized the brain cell repertoire of larval and adult *** by obtaining 50708 single-cell *** and 12 cell clusters from larval and adult brains were assigned based on marker genes,*** cell types include Kenyon cells,optic lobe cells,monoaminergic neurons,surface glia,and astrocyte *** further assessed the cell type compositions of larval and adult *** found that the transition from larva to adult resulted in great expansion of glial *** glial cell accounted for 49.8%of adult midbrain *** to flies and ants,the mushroom body kenyon cell is insufficient in ***,which accounts for 5.4%and 3.6%in larval and adult brains,*** of neuropeptide expression showed that the abundance and specificity of expression varied among individual ***,we found that ion transport peptide was specifically expressed in glial cells of larval and adult *** cell atlas dataset provides an important resource to explore cell diversity,neural circuits and genetic profiles.

关键词： brain neuropeptide silkworm single-cell transcriptome

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Mapping Genome Variants Sheds Light on Genetic and Phenotypic Differentiation in Chinese

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Genomics, Proteomics & Bioinformatics 2019年第3期17卷 226-228页

作者： Li Guo kai ye MOE Key Laboratory for Intelligent Networks and Network Security Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China The School of Life Science and Technology Xi’an Jiaotong UniversityXi’an 710049China The First Affiliated Hospital of Xi’an Jiaotong University Xi’an 710061China

Every human being looks different in one way or the ***’s the work of genetic variations,the ultimate driving force for evolution as well as the cause for many human *** human genetic variants reveals global genetic ... 详细信息

关键词： Mapping driving ultimate

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矮地茶的化学成分研究

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广西中医药大学学报 2024年第2期27卷 47-50页

作者：谢滟俞春林伏江龙叶开文李冰韦晓莹侯小涛广西中医药大学广西南宁530200

[目的]研究矮地茶的化学成分。[方法]运用聚酰胺色谱以及反向制备HPLC色谱分离技术对矮地茶的化学成分进行分离和纯化,再依据化合物的光谱数据和理化性质进行结构鉴定。[结果]从矮地茶30%乙醇提取部位分离得到5个化学成分,分别鉴定为没... 详细信息

[目的]研究矮地茶的化学成分。[方法]运用聚酰胺色谱以及反向制备HPLC色谱分离技术对矮地茶的化学成分进行分离和纯化,再依据化合物的光谱数据和理化性质进行结构鉴定。[结果]从矮地茶30%乙醇提取部位分离得到5个化学成分,分别鉴定为没食子酸(1)、dimethyl 2,5-furandicarboxylate(2)、4-O-galloybergenin(3)、杨梅苷(4)、槲皮苷(5)。[结论]化合物2和化合物3首次从矮地茶中分离得到。

关键词：矮地茶化学成分分离鉴定

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Metal ion metabolism and osteoporosis:possible implications for pharmaceutical biotechnology and tissue engineering

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Science China(Life Sciences) 2024年第8期67卷 1763-1765页

作者： Huaqiang Tao Qiufei Wang kai Chen Pengfei Zhu ye Gu Dechun Geng Department of Orthopedics The First Affiliated Hospital of Soochow UniversitySuzhou 215000China Department of Orthopedics Changshu Hospital Affiliated to Soochow UniversityFirst People’s Hospital of Changshu CityChangshu 215506China Department of Orthopedics Hai’an People’s HospitalHai’an 226600China

Osteoporosis(OP)is a systemic metabolic bone disease characterized by low bone mass,damage to bone microstructure and increased bone *** imbalance of functional coupling between osteoblasts and osteoclasts contributes to the pathological progression of the disease(Rachner et al.,2011).The pathogenesis of OP is precisely controlled by the complex regulatory network of the bone *** elements,although present in small amounts in the body,are essential for their influence on the physiological activities of *** ions act as effective catalysts and have applications in all stages of cell biochemical evolution(Qian et al.,2021).Bone tissue contains various metal elements,and metal ions play indispensable roles in bone metabolism at the molecular and cellular levels(Luo et al.,2023).However,it is important to note that these metal ions can also contribute to the progression of OP by influencing multiple cellular pathways either directly or indirectly.

关键词： metabolism biotechnology indispensable

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Developing the plate tectonics from oceanic subduction to continental collision

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Chinese Science Bulletin 2009年第15期54卷 2549-2555页

作者： ZHENG YongFei ye kai ZHANG LiFei CAS Key Laboratory of Crust-Mantle Materials and Environments School of Earth and Space Sciences University of Science and Technology of China Hefei 230026 China State Key Laboratory of Lithospheric Evolution Institute of Geology and Geophysics Chinese Academy of Sciences Beijing 100029 China MOE Key Laboratory of Orogenic Belt and Crustal Evolution School of Earth and Space Sciences Peking University Beijing 100871. China

The studies of continental deep subduction and ultrahigh-pressure metamorphism have not only promoted the development of solid earth science in China, but also provided an excellent opportunity to advance the plate tectonics theory. In view of the nature of subducted crust, two types of subduction and collision have been respectively recognized in nature. On one hand, the crustal subduction occurs due to underflow of either oceanic crust (Pacific type) or continental crust (Alpine type). On the other hand, the continental collision proceeds by arc-continent collision (Himalaya-Tibet type) or continent-continent collision (Dabie-Sulu type). The key issues in the future study of continental dynamics are the chemical changes and differential exhumation in continental deep subduction zones, and the temporal-spatial transition from oceanic subduction to continental subduction.

关键词：板块构造理论板块俯冲发展中国家大陆碰撞大洋地壳大陆深俯冲带超高压变质作用固体地球科学

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Organic materials with hydrostatic pressure induced mechanochromic properties

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Chinese Chemical Letters 2016年第8期27卷 1367-1375,1470页

作者： Lu Wang kai-Qi ye Hong-Yu Zhang State Key Laboratory of Supramolecular Structure and Materials College of ChemistryJilin University

Mechanochromic organic materials are a typical class of stimuli materials that has response to external physical stimuli such as shearing,grinding,and compressing *** compounds with mechanochromic characters in solid forms have attracted significant attention in the past decades due to their potential applications in sensors and memory *** anvil cell is an emerging technology that can provide isotropic pressure in a tiny *** a new stimuli method can be applied in investigating optical variation of mechanochromic *** this review,we focus on mechanoluminescence systems that are responsive to isotropic compression under high pressure and summarize the recent advances on organic materials studied by the diamond anvil cell.

关键词： Organic solids Mechanochromic Diamond anvil cell Stimuli response Hydrostatic pressure

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PACS gene family-related neurological diseases: limited genotypes and diverse phenotypes

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World Journal of Pediatrics 2024年第1期20卷 82-91页

作者： Han Zhang kai Gao Shuang Wang Yue-Hua Zhang Zhi-Xian Yang ye Wu Yu-Wu Jiang Department of Pediatrics Peking University First Hospital.No.1 Xi'an Men StreetWest DistrictBeijing 100034China Bejing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases BeijingChina Children Epilepsy Center Peking University First HospitalBeijingChina Key Laboratory for Neuroscience Ministry of Education/National Health and Family Planning CommissionPeking UniversityBeijingChina Center of Epilepsy Beijing Institute for Brain DisordersBeijingChina

Background The PACS gene family has been demonstrated to be related to intracellular vesicular *** phenotypic manifestations caused by the pathogenic variants of PACS include epilepsy,intellectual disability/developmental delay,and malformations,such as facial *** We identified seven new cases with pathogenic or likely pathogenic PACS variants using next-generation *** information obtained from these patients was analyzed along with that obtained from previously reported *** With the inclusion of the newly diagnosed cases in this study,103 cases with PACS gene family-related neurological diseases were reported,of which 43 were PACS2-related cases and the remaining were PACSI-related *** patients had seizures,which have been reported to be effectively controlled by several types of anti-seizure medications(ASMs).The most efficacious and frequently prescribed ASMs included sodium valproate(43.3%,13/30),oxcarbazepine/carbamazepine(26.7%,8/30),and levetiracetam(20%,6/30).Almost all patients had intellectual disability/developmental *** most common pathogenic missense variants were PACSI ***203Trp and PACS2 *** addition,we report a patient carrying a likely pathogenic copy number variation(CNV)(de novo heterozygous deletion of chr14:105821380-106107443,286 kilobase,destroyed part of the furin-binding region domain and the protein structure after it)with more severe and refractory late-onset *** The clinical phenotypes of the different PACS heterozygous missense variants were *** pathogenic variant sites of PACSI and PACS2 were quite limited but located in different regions.A CNV destroying part of the PACS2 gene might also be *** findings may provide an important clue for further functional studies on the pathogenic mechanism of neurological disorders related to the PACS gene family.

关键词： Developmental delay Epilepsy Intellectual disability PACSI PACS2

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Insights into in-situ imbibition behavior of fracturing fluid in propped shale fractures based on nuclear magnetic resonance:A case study from Longmaxi Formation shale,Sichuan Basin,China

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Petroleum Science 2024年第1期21卷 410-429页

作者： Jing-Jing Guo kai-Xiang Di Lie-Hui Zhang Yu-Long Zhao Hui-Ying Tang Rui-Han Zhang ye Tian National Key Laboratory of Oil and Gas Reservoir Geology and Exploitation Southwest Petroleum UniversityChengdu610500SichuanChina

Shale gas is an important component of unconventional oil and gas *** the imbibition behavior is helpful to optimize flowback parameters and enhance gas *** imbibition studies have focused on shale matrix,and the pressure conditions discussed were mostly *** initial imbibition behavior begins from propped fractures to matrix,but there are few studies working on explaining the imbibition behavior in propped fractures or the phenomenon of many shale wells exhibit higher productivity after a“soaking”***,propped fracture samples were designed for imbibition and migration *** order to accurately study the mechanism and main influencing factors of fracturing fluid imbibition and migration in propped and unpropped shale fractures under high temperature and high pressure,a series of experiments based on nuclear magnetic resonance(NMR)were carried *** showed that NMR T_(2) spectra of all samples exhibited a bimodal *** final imbibition volume of fracturing fluid was positively related to pressure and fracture *** imbibition effect of fracturing fluid was more evident in matrix pores under high *** the migration during soaking stage,the fracturing fluid gradually migrated from large pores to small pores and gradually displaced the shale gas from the matrix,thus allowing the water blocking in propped fractures to self-unlock to some *** permeability decreased in the imbibition stage,while it recovered in the migration stage to some extent.

关键词： Forced imbibition Migration Soaking NMR T_(2)spectra Propped fracture Permeability recovery

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Achieving exceptionally high strength and rapid degradation rate of Mg-Er-Ni alloy by strengthening with lamellar γ' and bulk LPSO phases

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Journal of Materials Science & Technology 2024年第1期168卷 88-102页

作者： Chaoneng Dai Jingfeng Wang Yuanlang Pan kai Ma Yinhong Peng ye Wang Danqian Wang Chunhua Ran Jinxing Wang Yanlong Ma College of Chemistry and Chemical Engineering Chongqing UniversityChongqing 401331China College of Materials Science and Engineering Chongqing UniversityChongqing 400044China National Engineering Research Center for Magnesium Alloys Chongqing 400044China College of Materials Science and Engineering Chongqing University of TechnologyChongqing 400054China

As-extruded Mg-Er-Ni alloys with different volume fractions of long-period stacking ordered(LPSO)phase and density of lamellar γ' phase were prepared,and the microstructure,mechanical,and degradation properties were *** the bulk LPSO phase and the lamellar γ' phase,and controlling the dynamic recrystallization processes during deformation by adjusting the volume fraction of LPSO and the density of the γ' phase,a synergistic increase in strength and degradation rate can be *** the one hand,the increase in corrosion rate was related to the increased volume fraction of the bulk LPSO phase and the densities of the lamellar γ' phase,which provide more galvanic ***,high densities of the lamellar γ' phase can provide more corrosion interface by inhibiting the recrystallization process to refine dynamic recrystallized(DRXed)grains during the hot *** the other hand,the ultimate tensile strength(UTS)and tensile yield strength(TYS)of the Mg-Er-Ni alloy increased from 345 and 265 MPa to 514 MPa and 358 MPa,respectively,which was mainly attributed to grain boundary and texture strengthening,bulk LPSO phase and lamellar γ' phase ***,Mg^(-1)4Er-4Ni alloy,which contains the highest volume fraction bulk LPSO phase and the densities of lamellar γ' phase,re-alized a synergistic enhancement of strength and degradation *** UTS,TYS,and degradation rate of Mg^(-1)4Er-4Ni were 514 MPa,358 MPa,and 142.5 mg cm^(-2)h^(-1)(3 wt%KCl solution at 93◦C),*** research provides new insight into developing Mg alloys with high strength and degradation rates for fracturing tool materials in the application of oil and gas exploitation in harsh environments.

关键词： Mg-Er-Ni alloy Lamellarγ'and bulk LPSO phases Rapid degradation rate High strength Mechanical and corrosion mechanism

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