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Genes and proteins expressed at different life cycle stages in the model protist Euplotes vannus revealed by both transcriptomic and proteomic approaches

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Science China Life Sciences 2025年第1期 232-248页

作者： Yaohan Jiang Xiao Chen Chundi Wang Liping Lyu Saleh A.Al-Farraj Naomi A.Stover Feng Gao key laboratory of Evolution & Marine Biodiversity (Ministry of education) and Institute of Evolution & Marine Biodiversity Ocean University of China Marine College Shandong University Zoology Department College of ScienceKing Saud University Department of biology Bradley University laboratory for Marine biology and biotechnology Qingdao Marine Science and Technology Center

Sexual reproduction first appeared in unicellular protists and has continued to be an essential biological process in almost all *** protists, which contain both germline and somatic genomes within a single cell, have evolved a special form of sexual reproduction called conjugation that involves mitosis, meiosis, fertilization, nuclear differentiation, genome rearrangement, and the development of unique cellular structures. The molecular basis and mechanisms of conjugation vary dramatically among ciliates, and many details of the process and its regulation are still largely unknown. In order to better comprehend these processes and mechanisms from an evolutionary perspective, this study provides the first comprehensive overview of the transcriptome and proteome profiles during the entire life cycle of the newly-established marine model ciliate Euplotes vannus. Transcriptome analyses from 14 life cycle stages(three vegetative stages and 11 sexual stages) revealed over 26,000 genes that are specifically expressed at different stages, many of which are related to DNA replication,transcription, translation, mitosis, meiosis, nuclear differentiation, and/or genome rearrangement. Quantitative proteomic analyses identified 338 proteins with homologs associated with conjugation and/or somatic nuclear development in other ciliates, including dicer-like proteins, Hsp90 proteins, RNA polymerase Ⅱ and transcription elongation factors, ribosomal-associated proteins, and ubiquitin-related proteins. Four of these homologs belong to the PIWI family, each with different expression patterns identified and confirmed by RT-qPCR,which may function in small RNA-mediated genome rearrangement. Proteins involved in the nonhomologous end-joining pathway are induced early during meiosis and accumulate in the developing new somatic nucleus, where more than 80% of the germline sequences are eliminated from the somatic genome. A number of new candidate genes and proteins likely t

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Interannual variability of boreal summer intraseasonal oscillation over the northwestern Pacific influenced by the Pacific Meridional Mode

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Atmospheric and Oceanic Science Letters 2025年第1期18卷 6-11页

作者： Haoyu Zhou Pang-Chi Hsu Lin Chen Yitian Qian key laboratory of Meteorological Disaster Ministry of Education/Joint International Research Laboratory of Climate and Environmental Change/Collaborative Innovation Center on Forecast and Evaluation of Meteorological DisastersNanjing University of Information Science and TechnologyNanjingChina

During the boreal summer,intraseasonal oscillations exhibit significant interannual variations in intensity over two key regions:the central-western equatorial Pacific(5°S-5°N,150°E-150°W)and the subtropical Northwestern Pacific(10°-20°N,130°E-175°W).The former is well-documented and considered to be influenced by the ENSO,while the latter has received comparatively less attention and is likely influenced by the Pacific Meridional Mode(PMM),as suggested by partial correlation analysis *** elucidate the physical processes responsible for the enhanced(weakened)intraseasonal convection over the subtropical northwestern Pacific during warm(cold)PMM years,the authors employed a moisture budget *** findings reveal that during warm PMM years,there is an increase in summer-mean moisture over the subtropical northwestern *** increase interacts with intensified vertical motion perturbations in the region,leading to greater vertical moisture advection in the lower troposphere and consequently resulting in convective *** a process is pivotal in amplifying intraseasonal convection *** observational findings were further verified by model experiments forced by PMM-like sea surface temperature patterns.

关键词： Boreal summer intraseasonal oscillation Interannual variability Pacific Meridional Mode Moisture budget analysis

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Recombinant chitinase-3-like protein 1 alleviates learning and memory impairments via M2 microglia polarization in postoperative cognitive dysfunction mice

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Neural Regeneration Research 2025年第9期20卷 2727-2736页

作者： Yujia Liu Xue Han Yan Su Yiming Zhou Minhui Xu Jiyan Xu Zhengliang Ma Xiaoping Gu Tianjiao Xia Department of Anesthesiology Nanjing Drum Tower HospitalAffiliated Hospital of Medical SchoolNanjing UniversityNanjingJiangsu ProvinceChina Medical School Nanjing UniversityNanjingJiangsu ProvinceChina Jiangsu key laboratory of Molecular Medicine Nanjing UniversityNanjingJiangsu ProvinceChina State key laboratory of Pharmaceutical biotechnology Nanjing UniversityNanjingJiangsu ProvinceChina Department of Anesthesiology Zhongshan HospitalFudan UniversityShanghaiChina

Postoperative cognitive dysfunction is a seve re complication of the central nervous system that occurs after anesthesia and surgery,and has received attention for its high incidence and effect on the quality of life of *** date,there are no viable treatment options for postoperative cognitive *** identification of postoperative cognitive dysfunction hub genes could provide new research directions and therapeutic targets for future *** identify the signaling mechanisms contributing to postoperative cognitive dysfunction,we first conducted Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses of the Gene Expression Omnibus GSE95426 dataset,which consists of mRNAs and long non-coding RNAs differentially expressed in mouse hippocampus3 days after tibial *** dataset was enriched in genes associated with the biological process"regulation of immune cells,"of which Chill was identified as a hub ***,we investigated the contribution of chitinase-3-like protein 1 protein expression changes to postoperative cognitive dysfunction in the mouse model of tibial fractu re *** were intraperitoneally injected with vehicle or recombinant chitinase-3-like protein 124 hours post-surgery,and the injection groups were compared with untreated control mice for learning and memory capacities using the Y-maze and fear conditioning *** addition,protein expression levels of proinflammatory factors(interleukin-1βand inducible nitric oxide synthase),M2-type macrophage markers(CD206 and arginase-1),and cognition-related proteins(brain-derived neurotropic factor and phosphorylated NMDA receptor subunit NR2B)were measured in hippocampus by western *** with recombinant chitinase-3-like protein 1 prevented surgery-induced cognitive impairment,downregulated interleukin-1βand nducible nitric oxide synthase expression,and upregulated CD206,arginase-1,pNR2B,and brain-derived neurotropic factor expr

关键词： Chil1 hippocampus learning and memory M2 microglia neuroinflammation postoperative cognitive dysfunction(POCD) recombinant CHI3L1

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Resting-state brain network remodeling after different nerve reconstruction surgeries:a functional magnetic resonance imaging study in brachial plexus injury rats

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Neural Regeneration Research 2025年第5期20卷 1495-1504页

作者： Yunting Xiang Xiangxin Xing Xuyun Hua Yuwen Zhang Xin Xue Jiajia Wu Mouxiong Zheng He Wang Jianguang Xu School of Rehabilitation Science Shanghai University of Traditional Chinese MedicineShanghaiChina Engineering Research Center of Traditional Chinese Medicine Intelligent Rehabilitation Ministry of EducationShanghaiChina Department of Rehabilitation Medicine Yueyang Hospital of Integrated Traditional Chinese and Western MedicineShanghai University of Traditional Chinese MedicineShanghaiChina Department of Traumatology and Orthopedics Yueyang Hospital of Integrated Traditional Chinese and Western MedicineShanghai University of Traditional Chinese MedicineShanghaiChina Institute of Science and Technology for Brain-Inspired Intelligence Fudan UniversityShanghaiChina key laboratory of Computational Neuroscience and Brain-Inspired Intelligence(Fudan University) Ministry of EducationShanghaiChina Human Phenome Institute Fudan UniversityShanghaiChina

Distinct brain remodeling has been found after different nerve reconstruction strategies,including motor representation of the affected ***,differences among reconstruction strategies at the brain network level have not been *** study aimed to explore intranetwork changes related to altered peripheral neural pathways after different nerve reconstruction surgeries,including nerve repair,endto-end nerve transfer,and end-to-side nerve ***–Dawley rats underwent complete left brachial plexus transection and were divided into four equal groups of eight:no nerve repair,grafted nerve repair,phrenic nerve end-to-end transfer,and end-to-side transfer with a graft sutured to the anterior upper ***-state brain functional magnetic resonance imaging was obtained 7 months after *** independent component analysis algorithm was utilized to identify group-level network components of interest and extract resting-state functional connectivity values of each voxel within the *** in intra-network resting-state functional connectivity were compared among the *** muscle reinnervation was assessed by behavioral observation(elbow flexion)and *** results showed that alterations in the sensorimotor and interoception networks were mostly related to changes in the peripheral neural *** repair was related to enhanced connectivity within the sensorimotor network,while end-to-side nerve transfer might be more beneficial for restoring control over the affected limb by the original motor *** thalamic-cortical pathway was enhanced within the interoception network after nerve repair and end-to-end nerve *** areas related to cognition and emotion were enhanced after end-to-side nerve *** study revealed important brain networks related to different nerve *** networks may be potential targets for enhancing motor recovery.

关键词： brain functional networks end-to-end nerve transfer end-to-side nerve transfer independent component analysis nerve repair peripheral plexus injury resting-state functional connectivity

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De novo synthesis of atropisomeric benzofurans via Cu/SPDO complex catalyzed asymmetric formal [3 + 2] annulation

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Science China Chemistry 2025年第1期 174-180页

作者： Fan-Xiao Meng Xing-Yu Wang Ka Lu Ju-Song Yang Fu-Min Zhang Ai-Jun Ma Bao Du Yong-Qiang Tu State key laboratory of Applied Organic Chemistry College of Chemistry and Chemical Engineering Lanzhou University School of Chemistry and Chemical Engineering Shanghai Jiao Tong University School of biotechnology and Health Sciences Wuyi University

Herein, the de novo synthesis of atropisomeric benzofurans through the Cu/spirocyclic-pyrrolidine-oxazoline(SPDO) complex catalyze asymmetric formal [3 + 2] cycloaddition between quinones and ynamides is explored, producing a range of structurally diverse axially chiral benzofurans in satisfactory yields with good to excellent enantioselectivities. Furthermore, density functional theory calculations were applied to explain the possible reaction mechanism.

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The effect of pmpR on the type Ⅲ secretion system in Pseudomonas aeruginosa

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Chinese Science Bulletin 2012年第19期57卷 2413-2418页

作者： LIANG HaiHua KONG WeiNa SHEN Tuo DUAN JiaLi DUAN KangMin key laboratory of resources biology and biotechnology in western China Ministry of EducationFaculty of Life SciencesNorthwest UniversityXi'anShaanxi 710069China

The type III secretion system(T3SS) plays important roles in Pseudomonas aeruginosa ***,we reported that the uncharacterized protein PmpR could regulate pqsR,an important regulator in the quorum-sensing system,by directly binding to its promoter *** the T3SS is controlled by the quorum-sensing system,here,we investigated the relationship between PmpR and the *** data showed that expression of the T3SS genes exoS,exoY,exoT,and exsD was dramatically increased in a pmpR-deletion mutant compared with that in the wild-type *** strain *** from DNA mobility assays indicated that PmpR affects the T3SS *** is unlikely that PmpR controls the T3SS via the Pseudomonas quinolone signal(PQS) because the PQS negatively regulates the T3SS,while pmpR negatively regulates the *** effect of PmpR on the T3SS seems to be independent of the PQS;further investigation is required to uncover the underlying regulatory pathways.

关键词：分泌系统绿脓杆菌类型缺失突变体传感系统感应系统假单胞菌数据表

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The immunophilin CYCLOPHILIN28 affects PSII-LHCII supercomplex assembly and accumulation in Arabidopsis thaliana

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Journal of Integrative Plant biology 2022年第4期64卷 915-929页

作者： Weining Zhu Linqing Xu Xiaoxia Yu Ying Zhong Chinese education Ministry's key laboratory of western resources and Modern biotechnology Key Laboratory of Biotechnology Shaanxi ProvinceCollege of Life SciencesNorthwest UniversityXi'an 710069China

In plant chloroplasts,photosystem II(PSII)complexes,together with light-harvesting complex II(LHCII),form various PSII-LHCII supercomplexes(SCs).This process likely involves immunophilins,but the underlying regulatory mechanisms are ***,by comparing Arabidopsis thaliana mutants lacking the chloroplast lumen-localized immunophilin CYCLOPHILIN28(CYP28)to wildtype and transgenic complemented lines,we determined that CYP28 regulates the assembly and accumulation of PSII-LHCII *** to the wild type,cyp28 plants showed accelerated leaf growth,earlier flowering time,and enhanced accumulation of high molecular weight PSII-LHCII SCs under normal light *** lack of CYP28 also significantly affected the electron transport *** native-polyacrylamide gel electrophoresis analysis revealed more Lhcb6 and less Lhcb4 in M-LHCII-Lhcb4-Lhcb6 complexes in cyp28 versus wild-type ***-prolyl cis/trans isomerase(PPIase)activity assays revealed that CYP28 exhibits weak PPIase activity and that its K113 and E187 residues are critical for this *** analysis suggested that CYP28 may regulate PSIILHCII SC accumulation by altering the configuration of Lhcb6 via its PPIase ***,the Lhcb6-P139 residue is critical for PSII-LHCII SC assembly and ***,our findings suggest that CYP28 likely regulates PSII-LHCII SC assembly and accumulation by altering the configuration of P139 of Lhcb6 via its PPIase activity.

关键词： cyclophilin28 immunophilin peptidyl-prolyl cis/trans isomerase activity photosynthesis PSII-LHCII supercomplexes thylakoid lumen

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Effect of Denaturant Concentration on Hen-egg White Lysozyme Renaturation

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Chinese Journal of Chemistry 2006年第5期24卷 653-659页

作者：边六交杨晓燕 key laboratory of Ministry of education for Resource biology and biotechnology in western China Northwest University Xi' an Shaanxi 710069 China

Based on three-state renaturation process of denatured proteins, an equation describing the effect of denaturant concentration on renaturation yield of denatured proteins was presented. By this equation, two parameters n（m1 -m2） and Ka can be obtained. The former indicates the difference in the number of denaturant molecules between the renaturation process of n number of refolding intermediates from refolding intermediate state to native state and their aggregate process from refolding intermediate state to aggregate state, the latter denotes the apparent aggregate equilibrium constant for protein molecules aggregated from native state to aggregate state, and from them, the characteristics of the renaturation process of denatured proteins in denaturant solution can be identified. This equation was tested by the renaturation processes of denatured egg white lysozyme in guanidine hydrochloride and urea solutions, with the results to show that when guanidine hydrochloride and urea concentrations were separately higher than 1.25 and 3.00 mol/L or separately lower than 1.00 and 3.00 mol/L, the refolding intermediates of egg white lysozymes were more easily aggregated to aggregate state or more easily renatured to native state, respectively. Under different initial total egg white lysozyme concentrations in urea solution, the refolding egg white lysozyme intermediates could be deduced to have a tendency to form a bimolecular intermediate aggregate, and this inference was further confirmed by their nonreducing SDS-PAGE and size exclusion chromatography.

关键词： egg white lysozyme urea guanidine hydrochloride renaturation yield denaturant concentration

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Transcriptome analysis of the endangered Notopterygium incisum: Coldtolerance gene discovery and identification of EST-SSR and SNP markers

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Plant Diversity 2019年第1期41卷 1-6页

作者： Yun Jia Ji-Qing Bai Mi-Li Liu Zhen-Fang Jiang Yan Wu Min-Feng Fang Zhong-Hu Li key laboratory of Resource biology and biotechnology in western China Ministry of Education College of Life Sciences Northwest University Shaanxi University of Chinese Medicine

Notopterygium incisum C. C. Ting ex H. T. Chang(Apiaceae) is an endangered perennial herb in China. The lack of transcriptomic and genomic resources for N. incisum greatly hinders studies of its population genetics and conservation. In this study, we employed RNA-seq technology to characterize transcriptomes for the flowers, leaves, and stems of this endangered herb. A total of 56 million clean reads were assembled into 120,716 unigenes with an N50 length of 850 bp. Among these unigenes, 70,245(58.19%) were successfully annotated and 65,965(54.64%) were identified as coding sequences based on their similarities with sequences in public databases. We identified 21 unigenes that had significant relationships with cold tolerance in N. incisum according to gene ontology(GO) annotation analysis. In addition, 13,149 simple sequence repeats(SSRs) and 85,681 single nucleotide polymorphisms were detected as potential molecular genetic markers. Ninety-six primer pairs of SSRs were randomly selected to validate their amplification efficiency and polymorphism. Nineteen SSR loci exhibited polymorphism in three natural populations of N. incisum. These results provide valuable resources to facilitate future functional genomics and conservation genetics studies of N. incisum.

关键词： Endangered species EST-SSR marker Notopterygium incisum Single nucleotide polymorphism Transcriptome

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A chromatographic method for pursuing potential GPCR ligands with the capacity to characterize their intrinsic activities of regulating downstream signaling pathway

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Chinese Chemical Letters 2024年第10期35卷 425-429页

作者： Ting Li Xinxin Zheng Lejing Qu Yuanyuan Ou Sai Qiao Xue Zhao Yajun Zhang Xinfeng Zhao Qian Li key laboratory of Resource biology and biotechnology in western China Ministry of EducationCollege of Life SciencesNorthwest UniversityXi'an 710069China

GPCRs are dominant targets for approved drugs and the discovery of lead compound targeting them is still ***-based screening technique is a promising platform to uncover GPCR ***,the intrinsic activities of them are seldom simultaneously determined during the *** beta2-adrenoceptor(β2AR)as a probe,this work created a strategy for screening GPCR ligands with simultaneous characterization of their downstream G protein binding responses associated with *** strategy included(i)the design and expression of a protein miniature formed byβ2AR and G proteinα-subunit(Gαs)using circularly permuted HaloTag(cpHalo)as a flexible linker;(ii)immobilization of the miniature onto silica gel by a click dehalogenation reaction;(iii)systematic characterization of the immobilized miniature by fluorescent and chromatographic studies,and(iv)simulating of ligand-inducedβ2AR-Gαs signaling cascade by chromatographic assays using GTP as an *** immobilized miniature exhibited specificity toβ2AR and Gαs antibodies and *** specificity is stable at least within fifteen days with the variation less than 1%.The intrinsic activities ofβ2AR ligands were distinguished by the changes of GTP chromatographic behaviors on Gαs-cpHalo-β2AR *** strengthened the binding affinity and kinetics of GTP with Gαs,while antagonist did not give any effect on *** the intrinsic activity evaluation,we believe,it will improve the attributes of chromatographic methods for drug discovery efforts with minimizing false-positive results.

关键词： Intrinsic efficacy GPCR-G protein miniature Circularly permuted HaloTag High-performance receptor chromatography GTP binding Agonist/antagonist

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