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The dual-action mechanism of Arabidopsis cryptochromes

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Journal of Integrative Plant Biology 2024年第5期66卷 883-896页

作者： Gao-Ping Qu Bochen Jiang Chentao Lin Basic Forestry and Plant proteomics Research center Fujian Agriculture and Forestry UniversityFuzhou 350002China Department of Chemistry Department of Biochemistry and Molecular BiologyInstitute for Biophysical DynamicsThe University of ChicagoChicagoIL 60637USA

Photoreceptor cryptochromes (CRYs) mediate blue-light regulation of plant growth and development. It has been reported that Arabidopsis CRY1and CRY2 function by physically interacting with at least 84 proteins, including transcription factors or co-factors, chromatin regulators, splicing factors, messenger RNA methyltransferases, DNA repair proteins, E3 ubiquitin ligases, protein kinases and so on. Of these 84 proteins, 47 have been reported to exhibit altered binding affinity to CRYs in response to blue light, and 41 have been shown to exhibit condensation to CRY photobodies. The blue light-regulated composition or condensation of CRY complexes results in changes of gene expression and developmental programs. In this mini-review, we analyzed recent studies of the photoregulatory mechanisms of Arabidopsis CRY complexes and proposed the dual mechanisms of action, including the “Lock-and-Key” and the “Liquid-Liquid Phase Separation (LLPS)” mechanisms. The dual CRY action mechanisms explain, at least partially, the structural diversity of CRY-interacting proteins and the functional diversity of the CRY photoreceptors.

关键词： Arabidopsis blue light cryptochrome CRY1 CRY2 phaseseparation

Genetic mapping of plasma proteome on brain structure

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Journal of Genetics and Genomics 2024年第7期51卷 774-777页

作者： Shengyi Ma Fengzhe Xu Yuanqing Fu Ju-Sheng Zheng Fudan University Shanghai 200433China School of Life Sciences Westlake UniversityHangzhouZhejiang 310030China Westlake center for Intelligent proteomics Westlake Laboratory of Life Sciences and BiomedicineHangzhouZhejiang 310030China

The emergence of high-throughput techniques for proteomics measurement has led to an increasing number of proteogenomic studies that aim to reveal protein quantitative trait loci(pQTL)based on large cohorts(Suhre et a... 详细信息

关键词： mapping structure throughput

Chromosomal-level genome and metabolome analyses of highly heterozygous allohexaploid Dendrocalamus brandisii elucidate shoot quality and developmental characteristics

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Journal of Integrative Plant Biology 2024年第6期66卷 1087-1105页

作者： Jutang Jiang Zeyu Zhang Yucong Bai Xiaojing Wang Yuping Dou Ruiman Geng Chongyang Wu Hangxiao Zhang Cunfu Lu Lianfeng Gu Jian Gao Key Laboratory of National Forestry and Grassland Administration Beijing for Bamboo&Rattan Science and TechnologyInstitute of Gene Science and Industrialization for Bamboo and Rattan ResourcesInternational Center for Bamboo and RattanBeijing 100102China College of Forestry Basic Forestry and Proteomics Research CenterFujian Agriculture and Forestry UniversityFuzhou 350002China School of Life Science Peking UniversityBeijing 100871China College of Biological Sciences and Biotechnology Beijing Forestry UniversityBeijing 100083China

Dendrocalamus brandisii(Munro)Kurz is a sympodial bamboo species with inimitable taste and flavorful *** rapid growth and use as high-quality material make this bamboo species highly valued for both food processing and wood ***,genome information for *** is lacking,primarily due to its polyploidy and large genome ***,we assembled a high-quality genome for hexaploid ***,which comprises 70chromosomes with a total size of 2,756 Mb,using long-read Hi Fi ***,we accurately separated the genome into its three constituent *** used Oxford Nanopore Technologies long reads to construct a transcriptomic dataset covering 15 tissues for gene annotation to complement our genome assembly,revealing differential gene expression and post-transcriptional *** integrating metabolome analysis,we unveiled that well-balanced lignin formation,as well as abundant flavonoid and fructose contents,contribute to the superior quality of *** *** genomic,transcriptomic,and metabolomic datasets provided a solid foundation for enhancing bamboo shoot quality and developing efficient gene-editing *** study should facilitate research on *** and enhance its use as a food source and wood material by providing crucial genomic resources.

关键词： bamboo shoots Dendrocalamus brandisii(Munro)Kurz flavonoid genome lignin

Optimizing ABA-based chemically induced proximity for enhanced intracellular transcriptional activation and modification response to ABA

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Science China Life Sciences 2024年

作者： Zeng Zhou Yue-Qi Wang Xu-Nan Zheng Xiao-Hong Zhang Lu-Yao Ji Jun-You Han Ze-Cheng Zuo Wei-Liang Mo Li Zhang College of Life Sciences Fujian Agriculture and Forestry University Basic Forestry and proteomics Research center Fujian Agriculture and Forestry University Jilin Province Engineering Laboratory of Plant Genetic Improvement College of Plant Science Jilin University

Abscisic acid(ABA)-based chemically induced proximity(CIP) is primarily mediated by the interaction of the ABA receptor pyrabactin resistance 1-like 1(PYL1) and the 2C-type protein phosphatase ABI1, which confers ABA-induced proximity to their fusion proteins, and offers precise temporal control of a wide array of biological processes. However, broad application of ABA-based CIP has been limited by ABA response intensity. In this study, we demonstrated that ABA-induced interaction between another ABA receptor pyrabactin resistance 1(PYR1) and ABI1 exhibited higher ABA response intensity than that between PYL1 and ABI1 in HEK293T cells. We engineered PYR1-ABI1and PYL1-ABI1 into ABA-induced transcriptional activation tools in mammalian cells by integration with CRISPR/dCas9 and found that the tool based on PYR1-ABI1 demonstrated better ABA response intensity than that based on PYL1-ABI1 for both exogenous and endogenous genes in mammalian cells. We further achieved ABA-induced RNA m6A modification installation and erasure by combining ABA-induced PYR1-ABI1 interaction with CRISPR/dCas13, successfully inhibiting tumor cell proliferation. We subsequently improved the interaction of PYR1-ABI1 through phage-assisted continuous evolution(PACE), successfully generating a PYR1 mutant(PYR1m) whose interaction with ABI1 exhibited a higher ABA response intensity than that of the wild-type. In addition, we tested the transcriptional activation tool based on PYRm-ABI1 and found that it also showed a higher ABA response intensity than that of the wild type. These results demonstrate that we have developed a novel ABA-based CIP and further improved upon it using PACE, providing a new approach for the modification of other CIP systems.

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Multiomics analysis reveals metabolic subtypes and identifies diacylglycerol kinase α (DGKA) as a potential therapeutic target for intrahepatic cholangiocarcinoma

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Cancer Communications 2024年第2期44卷 226-250页

作者： Weiren Liu Huqiang Wang Qianfu Zhao Chenyang Tao Weifeng Qu Yushan Hou Run Huang Zimei Sun Guiqi Zhu Xifei Jiang Yuan Fang Jun Gao Xiaoling Wu Zhixiang Yang Rongyu Ping Jiafeng Chen Rui Yang Tianhao Chu Jian Zhou Jia Fan Zheng Tang Dong Yang Yinghong Shi Department of Liver Surgery and Transplantation Liver Cancer InstituteZhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP.R.China Research Unit of Liver cancer Recurrence and Metastasis Chinese Academy of Medical SciencesBeijingP.R.China State Key Laboratory of Medical proteomics Beijing Proteome Research CenterNational Center for Protein Sciences(Beijing)Beijing Institute of LifeomicsBeijingP.R.China

Background:Intrahepatic cholangiocarcinoma(iCCA)is a highly heteroge-neous and lethal hepatobiliary tumor with few therapeutic *** metabolic reprogramming of tumor cells plays an essential role in the develop-ment of tumors,while the metabolic molecular classification of iCCA is largely ***,we performed an integrated multiomics analysis and metabolic classification to depict differences in metabolic characteristics of iCCA patients,hoping to provide a novel perspective to understand and treat ***:We performed integrated multiomics analysis in 116 iCCA samples,including whole-exome sequencing,bulk RNA-sequencing and proteome *** on the non-negative matrix factorization method and the protein abundance of metabolic genes in human genome-scale metabolic models,the metabolic subtype of iCCA was *** and prognostic gene analy-ses were used to compare overall survival(OS)differences between metabolic *** proliferation analysis,5-ethynyl-2’-deoxyuridine(EdU)assay,colony formation assay,RNA-sequencing and Western blotting were performed to investigate the molecular mechanisms of diacylglycerol kinaseα(DGKA)in iCCA ***:Three metabolic subtypes(S1-S3)with subtype-specific biomarkers of iCCA were *** metabolic subtypes presented with distinct prog-noses,metabolic features,immune microenvironments,and genetic *** S2 subtype with the worst survival showed the activation of some special metabolic processes,immune-suppressed microenvironment and Kirsten ratsar-coma viral oncogene homolog(KRAS)/AT-rich interactive domain 1A(ARID1A)*** the S2 subtype-specific upregulated proteins,DGKA was further identified as a potential drug target for iCCA,which promoted cell proliferation by enhancing phosphatidic acid(PA)metabolism and activating mitogen-activated protein kinase(MAPK)***:Viamultiomics analyses,we identified three metabolic subtypes of iCCA,revealing

关键词： diacylglycerol kinaseα intrahepatic cholangiocarcinoma MAPK signaling metabolic classifi-cation multiomics analysis phosphatidic acid metabolism

TCM-HIN2Vec:A strategy for uncovering biological basis of heart qi deficiency pattern based on network embedding and transcriptomic experiment

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Journal of Traditional Chinese Medical Sciences 2024年第3期11卷 264-274页

作者： Lihong Diao Xinyi Fan Jiang Yu Kai Huang Edouard C.Nice Chao Liu Dong Li Shuzhen Guo School of Traditional Chinese Medicine Beijing University of Chinese MedicineBeijing 102488China Department of Biochemistry and Molecular Biology Monash UniversityClayton VIC 3800Australia Beijing Institute of Lifeomics Beijing 102206China State Key Laboratory of Medical proteomics Beijing 102206China National center for Protein Sciences(Beijing) Beijing 102206China Beijing Proteome Research center Beijing 102206China

Objective To elucidate the biological basis of the heart qi deficiency(HQD)pattern,an in-depth understanding of which is essential for improving clinical herbal *** We predicted and characterized HQD pattern genes using the new strategy,TCM-HIN2Vec,which involves heterogeneous network embedding and transcriptomic ***,a heterogeneous network of traditional Chinese medicine(TCM)patterns was constructed using public ***,we predicted HQD pattern genes using a heterogeneous network-embedding *** then analyzed the functional characteristics of HQD pattern genes using gene enrichment analysis and examined gene expression levels using ***,we identified TCM herbs that demonstrated enriched interactions with HQD pattern genes via herbal enrichment *** Our TCM-HIN2Vec strategy revealed that candidate genes associated with HQD pattern were significantly enriched in energy metabolism,signal transduction pathways,and immune ***,we found that these candidate genes were significantly differentially expressed in the transcriptional profile of mice model with heart failure with a qi deficiency ***,herbal enrichment analysis identified TCM herbs that demonstrated enriched interactions with the top 10 candidate genes and could potentially serve as drug candidates for treating *** Our results suggested that TCM-HIN2Vec is capable of not only accurately identifying HQD pattern genes,but also deciphering the basis of HQD *** our finding indicated that TCM-HIN2Vec may be further expanded to develop other patterns,leading to a new approach aimed at elucidating general TCM patterns and developing precision medicine.

关键词： Qi deficiency pattern Heart failure Biological basis Network embedding Transcriptome

Hypoxia-inducible factor-1αin myocardial infarction

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World Journal of Cardiology 2024年第4期16卷 181-185页

作者： IvanaŠkrlec Sergey N Kolomeichuk Faculty of Dental Medicine and Health Josip Juraj Strossmayer University of OsijekOsijek 31000Croatia Institute of Biology Karelia Research Center of Russian Academy of SciencesPetrozavodsk 185910Russia Laboratory for Genomics Proteomicsand MetabolomicsResearch Institute of Biomedicine and Biomedical TechnologiesTyumen State Medical UniversityTyumen 625023Russia

Hypoxia-inducible factor 1(HIF1)has a crucial function in the regulation of oxygen levels in mammalian cells,especially under hypoxic *** importance in cardiovascular diseases,particularly in cardiac ischemia,is because of its ability to alleviate cardiac *** oxygen-responsive subunit,HIF1α,plays a crucial role in this process,as it has been shown to have cardioprotective effects in myocardial infarction through regulating the expression of genes affecting cellular survival,angiogenesis,and ***,HIF1αexpression induced reperfusion in the ischemic skeletal muscle,and hypoxic skin wounds in diabetic animal models showed reduced HIF1α*** expression of HIF1αhas been shown to reduce apoptosis and oxidative stress in cardiomyocytes during acute myocardial *** variations in HIF1αhave also been found to correlate with altered responses to ischemic cardiovascular *** addition,a link has been established between the circadian rhythm and hypoxic molecular signaling pathways,with HIF1αfunctioning as an oxygen sensor and circadian genes such as period circadian regulator 2 responding to changes in *** editorial analyzes the relationship between HIF1αand the circadian rhythm and highlights its significance in myocardial adaptation to *** the changes in molecular signaling pathways associated with diseases,specifically cardiovascular diseases,provides the opportunity for innovative therapeutic interventions,especially in low-oxygen environments such as myocardial infarction.

关键词： Cardiovascular pathologies Circadian genes Hypoxia-inducible factor 1 Hypoxia Gene-gene interaction

High-fat diet impairs gut barrier through intestinal microbiota-derived reactive oxygen species

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Science China(Life Sciences) 2024年第5期67卷 879-891页

作者： Nianyi Zeng Fan Wu Junqi Lu Xiang Li Shaomei Lin Lang Zhou Zhongwei Wang Guangyan Wu Qingfa Huang Daowen Zheng Jie Gao Shan Wu Xiaojiao Chen Muxuan Chen Fanguo Meng Haitao Shang Yan He Peng Chen Hong Wei Zhuang Li Hongwei Zhou Microbiome Medicine center Department of Laboratory MedicineZhujiang HospitalSouthern Medical UniversityGuangzhou 510282China Department of Environmental Health Guangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public Health and Tropical MedicineSouthern Medical UniversityGuangzhou 510515China Redox Medical center for Public Health Soochow UniversitySuzhou 215301China Precision Medicine Institute The First Affiliated HospitalSun Yat-sen UniversityGuangzhou 510080China Department of Pathophysiology Guangdong Provincial Key Laboratory of ProteomicsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou 510515China

Gut barrier disruption is a key event in bridging gut microbiota dysbiosis and high-fat diet(HFD)-associated metabolic ***,the underlying mechanism remains *** the present study,by comparing HFD-and normal diet(ND)-treated mice,we found that the HFD instantly altered the composition of the gut microbiota and subsequently damaged the integrity of the gut *** sequencing revealed that the HFD upregulates gut microbial functions related to redox reactions,as confirmed by the increased reactive oxygen species(ROS)levels in fecal microbiota incubation in vitro and in the lumen,which were detected using in vivo fluorescence *** microbial ROS-producing capability induced by HFD can be transferred through fecal microbiota transplantation(FMT)into germ-free(GF)mice,downregulating the gut barrier tight ***,mono-colonizing GF mice with an Enterococcus strain excelled in ROS production,damaged the gut barrier,induced mitochondrial malfunction and apoptosis of the intestinal epithelial cells,and exacerbated fatty liver,compared with other low-ROS-producing Enterococcus *** administration of recombinant high-stability-superoxide dismutase(SOD)significantly reduced intestinal ROS,protected the gut barrier,and improved fatty liver against the *** conclusion,our study suggests that extracellular ROS derived from gut microbiota play a pivotal role in HFD-induced gut barrier disruption and is a potential therapeutic target for HFD-associated metabolic diseases.

关键词： fatty liver disease gut microbiota gut barrier high-fat diet oxidative stress reactive oxygen species

A Pt/CeO_(2)Hybrid Nanozyme with Stable Peroxidase Activity for the Detection of Acetylcholine

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Chemical Research in Chinese Universities 2024年第2期40卷 268-271页

作者： CUI Xulian MA Baofu PAN Hui XIA Yu LIU Li ZHAO Baofeng LIANG Zhen ZHANG Lihua ZHANG Yukui State Key Laboratory of Medical proteomics Dalian Institute of Chemical PhysicsChinese Academy of ScienceDalian116023P.R.China The Research center for Medical Genomics Key Laboratory of Medical Cell BiologyMinistry of EducationSchool of Life ScienceChina Medical UniversityShenyang110001P.R.China River Fisheries Research Institute Chinese Academy of Fishery SciencesGuangzhou510000P.R.China

Acetylcholine(ACh)is a common neurotransmitterl)that is secreted by cholinergic neurons[2]and is found mainly in the peripheral and central nervous systems.[3]ACh transmits nerve signals from presynaptic to postsynapt... 详细信息

关键词： Acetylcholine/choline Nanozyme Hydrogen peroxide Alzheimer’s disease