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Food Science and Human Wellness 2024年

作者： Xinyi Zhang Changzheng Shi Zhaoxin Lu Fanqiang Meng Moutong Chen Xiaomei Bie College of Food Science and Technology， Nanjing Agricultural University Guangdong Provincial key laboratory of Microbial Safety and Health， state key laboratory of Applied Microbiology Southern China， Institute of Microbiology， Guangdong Academy of Sciences

In the food industry， bacterial cells usually adhere to equipment surfaces， forming biofilms that may cause persistent contamination. This study aimed to identify the key genes responsible for the stronger biofilm-forming capability of the LMB 33426 strain compared to that of the CICC 21662 strain through comparative genomics. Additionally， the expression of genes and related metabolic pathways of LMB 33426 and CICC 21662 strains were analyzed at the transcriptional level by high-throughput sequencing technology to uncover key differentially expressed genes between planktonic and biofilm cells of those two strains. Subsequently， the key genes found to present differences that were uncovered by those genome-wide and transcriptomic analyses were used to construct gene deletion strains. The crystalline violet assay and motility assay showed that GL002291， GL002712 and lmo1438 genes were involved in the regulation of biofilm formation as well as motility. The hydrophobicity and auto-aggregation ability assay results demonstrated an association between the clpB， lmo1438， and lmo0294 genes and bacterial adhesion. However， no significant differences were found regarding this association in the GL002291 and GL002712 genes. This study elucidates some potential regulatory genes associated with biofilm formation in L. monocytogenes， and laying a theoretical foundation for future research.

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Plant-based meat analogues aggravated lipid accumulation by regulating lipid metabolism homeostasis in mice

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Food Science and Human Wellness 2024年第2期13卷 946-960页

作者： Yunting Xie Linlin Cai Zhiji Huang Kai Shan Xinglian Xu Guanghong Zhou Chunbao Li key laboratory of Meat Processing and Quality Control MOEKey Laboratory of Meat ProcessingMARAJiangsu Innovative Center of Meat ProductionProcessing and Quality ControlCollege of Food Science and TechnologyNanjing Agricultural UniversityNanjing 210095China

To determine the effects of plant-based meat analogues on the metabolic health and the possible mechanisms,mice were fed with a real pork diet(AP),a real beef diet(AB),a plant-based pork analogue diet(PP)and plant-based beef analogue diet(PB)for 68 *** with real meat,the plant-based meat analogues increased food and energy intake,body weight,white fat and liver weight and caused adipocyte hypertrophy,hepatic lipid droplet accumulation,and inflammatory responses in *** revealed that plantbased meat analogues altered the composition of serum metabolites,which regulated lipid metabolism *** PB diet upregulated gene expression related to lipid synthesis,lipolysis and adipocyte differentiation while the PP diet upregulated expression of lipolysis-related genes but downregulated expression of adipocyte differentiation-related genes in white adipose ***,both PP and PB diets upregulated lipid influx-and synthesis-related genes but downregulated lipid oxidation-related genes in *** specific metabolite biomarkers may affect fat accumulation mainly by direct lipid metabolism pathways or indirect amino acid metabolism,protein digestion and absorption,bile secretion,aminoacyl-tRNA biosynthesis,neuroactive ligand-receptor interaction and ABC transporters *** findings provide a new insight into understanding the differences in nutritional functions of meat and plant-based meat analogues.

关键词： Meat analogues Metabolomics Lipid metabolism Adipose tissue dysfunction Ectopic fat deposition

RebL1 is required for macronuclear structure stability and gametogenesis in Tetrahymena thermophila

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Marine Life Science & Technology 2024年第2期6卷 183-197页

作者： Huijuan Hao Yinjie Lian Chenhui Ren Sitong Yang Min Zhao Tao Bo Jing Xu Wei Wang key laboratory of Chemical Biology and Molecular Engineering of Ministry of Education Institute of BiotechnologyShanxi UniversityTaiyuan 030006China School of Life Science Shanxi UniversityTaiyuan 030006China Shanxi key laboratory of Biotechnology Taiyuan 030006China

Histone modification and nucleosome assembly play important roles in chromatin-related *** chaperones form different complexes and coordinate histone transportation and *** histone chaperone complexes have been identified in different *** ciliate protozoa(ciliates)have various chromatin structures and different nuclear ***,histone chaperone components and functions of different subunits remain unclear in ***-rahymema thermophila contains a transcriptionally active macronucleus(MAC)and a transcriptionally inactive micronu-cleus(MIC)which exhibit multiple replication and various chromatin remodeling progresses during vegetative growth and sexual developmental ***,we found histone chaperone RebL1 not only localized evenly in the transcriptionally active MAC but also dynamically changed in the MIC during vegetative growth and sexual developmental ***1 knockdown inhibited cellular *** macronuclear morphology became bigger in growing *** abnormal macronuclear structure also occurred in the starvation ***,micronuclear meiosis was disturbed during sexual development,leading to a failure to generate new gametic ***1 potentially interacted with various factors involved in histone-modifying complexes and chromatin remodeling complexes in different developmental ***1 knockdown affected expression levels of the genes involved in chromatin organization and *** together,RebL1 plays a vital role in maintaining macronuclear structure stability and gametogenesis in ***.

关键词： Gametogenesis Histone chaperone Macronuclear structure RebL1 Tetrahymena thermophilaIntroduction

Sugarcane transcription factor ScWRKY4 negatively regulates resistance to pathogen infection through the JA signaling pathway

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The Crop Journal 2024年第1期12卷 164-176页

作者： Dongjiao Wang Wei Wang Shoujian Zang Liqian Qin Yanlan Liang Peixia Lin Yachun Su Youxiong Que key laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture and Rural AffairsKey Laboratory of GeneticsBreeding and Multiple Utilization of CropsMinistry of EducationCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhou 350002FujianChina National key laboratory for Tropical Crop Breeding Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesSanya 572024HainanChina

WRKY transcription factors,transcriptional regulators unique to plants,play an important role in defense response to pathogen ***,the resistance mechanisms of WRKY genes in sugarcane remain *** the present study,gene ontology(GO)enrichment analysis revealed that WRKY gene family in sugarcane was extensively involved in the response to biotic stress and in defense *** identified gene ScWRKY4,a classⅡc member of the WRKY gene family,in sugarcane cultivar *** gene was induced by salicylic acid(SA)and methyl jasmonate(MeJA)***,expression of ScWRKY4 was down-regulated in smut-resistant sugarcane cultivars but up-regulated in smutsusceptible sugarcane cultivars infected with Sporisorium ***,stable overexpression of the ScWRKY4 gene in Nicotiana benthamiana enhanced susceptibility to Fusarium solani *** and caused down-regulated expression of immune marker-related *** analysis indicated suppressed expression of most JAZ genes in the signal transduction ***4 interacted with ScJAZ13 to repress its *** thus hypothesized that the ScWRKY4 gene was involved in the regulatory network of plant disease resistance,most likely through the JA signaling *** present study depicting the molecular involvement of ScWRKY4 in sugarcane disease resistance lays a foundation for future investigation.

关键词： Disease resistance Expression profile Transcriptome analysis WRKY transcription factors

Combined ATAC-seq,RNA-seq,and GWAS analysis reveals glycogen metabolism regulatory network in Jinjiang oyster(Crassostrea ariakensis)

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Zoological Research 2024年第1期45卷 201-214页

作者： Biao Wu Xi Chen Jie Hu Zhen-Yuan Wang Yan Wang Da-You Xu Hao-Bing Guo Chang-Wei Shao Li-Qing Zhou Xiu-Jun Sun Tao Yu Xiao-Mei Wang Yan-Xin Zheng Guang-Yi Fan Zhi-Hong Liu state key laboratory of Mariculture Biobreeding and Sustainable Goods Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoShandong 266071China laboratory for Marine Fisheries Science and Food Production Processes Laoshan LaboratoryQingdaoShandong 266071China BGI-Qingdao BGI-ShenzhenQingdaoShandong 266426China National Demonstration Center for Experimental Fisheries Science Education Shanghai Ocean UniversityShanghai 201306China Changdao Enhancement and Experiment Station Chinese Academy of Fishery SciencesYantaiShandong 265800China state key laboratory of Agricultural Genomics BGI-ShenzhenShenzhenGuangdong 518083China

Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of *** Jinjiang oyster(Crassostrea ariakensis)is an economically and ecologically important species in *** the present study,RNA sequencing(RNA-seq)and assay for transposase-accessible chromatin using sequencing(ATAC-seq)were performed to investigate gene expression and chromatin accessibility variations in oysters with different glycogen *** identified 9483 differentially expressed genes(DEGs)and 7215 genes with significantly differential chromatin accessibility(DCAGs)were obtained,with an overlap of 2600 genes between ***,a significant proportion of these genes were enriched in pathways related to glycogen metabolism,including“Glycogen metabolic process”and“Starch and sucrose metabolism”.In addition,genome-wide association study(GWAS)identified 526 single nucleotide polymorphism(SNP)loci associated with glycogen *** loci corresponded to 241 genes,63 of which were categorized as both DEGs and *** study enriches basic research data and provides insights into the molecular mechanisms underlying the regulation of glycogen metabolism in ***.

关键词： Crassostrea ariakensis Glycogen Transcriptome ATAC GWAS

ADAMTS12 promotes migration and epithelial-mesenchymal transition and predicts poor prognosis for pancreatic cancer

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Hepatobiliary & Pancreatic Diseases International 2023年第2期22卷 169-178页

作者： Rui-Zhe He Jia-Hao Zheng Hong-Fei Yao Da-Peng Xu Min-Wei Yang De-Jun Liu Yong-Wei Sun Yan-Miao Huo state key laboratory of oncogenes and related genes Department of Biliary-Pancreatic SurgeryRenji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina

Background: ADAMTS(a disintegrin and metalloproteinase with thrombospondin-like motifs) family, a group of extracellular multifunctional enzymes, has been proven to play a pivotal role in the tumor. In pancreatic cancer, the role and mechanism of this family remain unclear. The present study aimed to figure out the hub gene of ADAMTSs and explore the exact roles in the prognosis and biological functions in pancreatic ductal adenocarcinoma(PDAC). Methods: We used several databases to analyze the ADAMTS family and then screen out the hub genes. The expression of ADAMTS12 in 106 pairs of PDAC tumors and adjacent normal tissues was examined by immunohistochemistry, and its correlations with clinical parameters were further analyzed. The impacts of ADAMTS12 on the migration of PDAC cells were predicted by gene set enrichment analysis and confirmed by transwell assays. The potential impacts of ADAMTS12 on the epithelial-mesenchymal transition(EMT) were identified by database analysis and experimental proof of real-time quantitative polymerase chain reaction(q PCR) and Western blotting. Results: Our study found that ADAMTS12 was a crucial gene in PDAC, and it was highly expressed in tumor tissues when compared to that in the adjacent tissues. ADATMS12 had predictive value of a poor prognosis for PDAC. The elevation of ADAMTS12 was parallel to the progression of PDAC. Inhibition of ADAMTS12 suppressed the migration of PDAC cells and interfered with the process of EMT. Conclusions: ADAMTS12 is a crucial member of ADAMTSs in PDAC and a predictor of poor prognosis. Additionally, based on its impacts on migration and metastasis in PDAC and the relationship with EMT, ADAMTS12 plays a role of an oncogene in PDAC and may be a promising target for treatment.

关键词： ADAMTS12 Pancreatic ductal adenocarcinoma Prognosis Migration Epithelial-mesenchymal transition

MicroRNAs in hypoxia and acidic tumor microenvironment

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Chinese Science Bulletin 2014年第19期59卷 2223-2231页

作者： Haojie Jin Ning Wang Cun Wang Wenxin Qin state key laboratory of oncogenes and related genes Shanghai Cancer Institute Renji Hospital Shanghai Jiao Tong University School of Medicine

MicroRNAs(miRNAs)are short non-coding RNAs of*22 nucleotides that play important roles in diverse biological functions including tumor adaption,survival,and metabolism homeostasis in specific tumor microenvironment,such as hypoxia and low *** is a unique physiological condition during tumor development and progression,which alters a set of hypoxia-mediated miRNAs *** hypoxia-mediated miRNAs may exhibit either oncogenic activities or tumor-suppressive activities,mainly through the regulation of cellular pathways including hypoxia-inducible factors *** tumor microenvironment develops in hypoxic solid tumors due to a combination of predominant glycolytic metabolism(Warburg effect)and poor fluid clearance due to incomplete *** this review,we summarize our current understanding of the emerging roles of miRNAs in hypoxia and acidic tumor microenvironment.

关键词：肿瘤发生 microRNA 缺氧症微环境酸性 miRNA 低氧诱导因子非编码RNA

Cross-species transmission and host range genes in poxviruses

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Virologica Sinica 2024年第2期39卷 177-193页

作者： Chen-Hui Yang A-Ling Song Ye Qiu Xing-Yi Ge College of Biology Hunan Provincial Key Laboratory of Medical VirologyHunan UniversityChangsha410012China

The persistent epidemic of human mpox, caused by mpox virus (MPXV), raises concerns about the future spread ofMPXV and other poxviruses. MPXV is a typical zoonotic virus which can infect human and cause smallpox-likesymptoms. MPXV belongs to the Poxviridae family, which has a relatively broad host range from arthropods tovertebrates. Cross-species transmission of poxviruses among different hosts has been frequently reported andresulted in numerous epidemics. Poxviruses have a complex linear double-strand DNA genome that encodeshundreds of proteins. genes related to the host range of poxvirus are called host range genes (HRGs). This reviewbriefly introduces the taxonomy, phylogeny and hosts of poxviruses, and then comprehensively summarizes thecurrent knowledge about the cross-species transmission of poxviruses. In particular, the HRGs of poxvirus aredescribed and their impacts on viral host range are discussed in depth. We hope that this review will provide acomprehensive perspective about the current progress of researches on cross-species transmission and HRGvariation of poxviruses, serving as a valuable reference for academic studies and disease control in the future.

关键词： Poxvirus Host range gene(HRG) Host spectrum Cross-species transmission

Natural killer cells in hepatocellular carcinoma： current status and perspectives for future immunotherapeutic approaches

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Frontiers of Medicine 2017年第4期11卷 509-521页

作者： Min Yu Zonghai Li state key laboratory of oncogenes and related genes Shanghai Cancer Institute Renji Hospital Shanghai Jiao Tong University School ofMedicine Shanghai 200032 China

Hepatocellular carcinoma （HCC） is currently the fifth most common malignancy and the third leading cause of cancer-related mortalities worldwide. In the last few years, treatments for HCC have significantly improved from a mere surgical resection to a series of minimally invasive therapies and targeted drugs. However, recurrence frequently occurs even upon curative therapeutics, and drug therapies generally produce disappointing results, with the overall prognosis dismal. This challenging clinical scenario warrants new effective and life-prolonging strategies for patients with HCC. Compelling evidence suggests that NK cells play a critical role in the immune function of the fiver and in the immune defenses against HCC, indicating that HCC might be an ideal target for NK cell-based immunotherapies. To obtain comprehensive insights into the putative influence of NK cells on HCC, this paper summarizes current knowledge on NK cells in HCC and discusses the usefulness and prospects of NK cell-based immunotherapies. Critical issues that require consideration for the successful clinical translation of NK cell-based therapies are also addressed. If appropriately used and further optimized, NK cell- based therapies could dominate important roles in the future immunotherapeutic market of HCC.

关键词： natural killer cell hepatocellular carcinoma immunotherapy

Type I interferon pathway in pediatric systemic lupus erythematosus

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World Journal of Pediatrics 2024年第7期20卷 653-668页

作者： Yu Zhou Hong‑Mei Song Department of Pediatrics Peking Union Medical College HospitalChinese Academy of Medical SciencesBeijingChina state key laboratory of Complex Severe and Rare Diseases Peking Union Medical College HospitalBeijingChina

Background The role of type I interferon(IFN-I)signaling in systemic lupus erythematosus(SLE)has been well ***,unanswered questions remain regarding the applicability of these findings to pediatric-onset *** aim of this review is to provide an overview of the novel discoveries on IFN-I signaling in pediatric-onset *** sources A literature search was conducted in the PubMed database using the following keywords:“pediatric systemic lupus erythematosus”and“type I interferon”.Results IFN-I signaling is increased in pediatric SLE,largely due to the presence of plasmacytoid dendritic cells and pathways such as cyclic GMP-AMP synthase–stimulator of interferon genes–TANK-binding kinase 1 and Toll-like receptor(TLR)4/*** extracellular traps and oxidative DNA damage further stimulate IFN-I *** variants in IFN-I-related genes,such as IFN-regulatory factor 5 and tyrosine kinase 2,are linked to SLE susceptibility in pediatric *** addition,type I interferonopathies,characterized by sustained IFN-I activation,can mimic SLE symptoms and are thus important to *** on interferonopathies also contribute to exploring the pathogenesis of *** IFN-I activation is crucial for SLE diagnosis and *** IFNstimulated gene expression and serum IFN-α2 levels are common *** cytometry markers such as CD169 and galectin-9 are promising ***-IFN therapies,such as sifalimumab and anifrolumab,show promise in adult patients with SLE,but their efficacy in pediatric patients requires further *** kinase inhibitors are another treatment option for severe pediatric SLE *** This review presents an overview of the IFN-I pathway in pediatric *** the intricate relationship between IFN-I and pediatric SLE may help to identify potential diagnostic markers and targeted therapies,paving the way for improved patient care and outcomes.

关键词： Interferonopathies Pediatric systemic lupus erythematosus Type I interferon