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Metabolomics and gene expression levels reveal the positive effects of teaseed oil on lifespan and aging process in Caenorhabditis elegans

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Food Science and Human Wellness 2023年第4期12卷 1391-1401页

作者： Yanan Wang Jiachen Shi Kun Liu Yu Wang Yongjiang Xu Yuanfa Liu State Key Laboratory of Food Science and Technology National Engineering Research Center for Functional FoodNational Engineering Laboratory for Cereal Fermentation TechnologyCollaborative Innovation Center of Food Safety and Quality Control in Jiangsu ProvinceSchool of Food Science and TechnologyJiangnan UniversityWuxi 214122China

As an irreplaceable dietary constituent,lipids play a vital important role in health,but their effects on aging process and longevity are still not well known *** this paper,the metabolic profiling and gene expression levels of Caenorhabditis elegans were investigated to explore the effects of different edible oils on senescence and *** results showed that teaseed oil(TO)could prolong the life expectancy and slow down the aging process of *** to the control group,the intake of lard oil(LO)and TO increased the expression levels of genes related to inhibition of protein aggregation(akt-1,daf-16,hsf-1,hsp-16.2)and lipid metabolism(daf-7,daf-1,mdt-15,lipl-4,fat-5,fat-6,fat-7),with a more significant alteration in TO *** revealed that palm oil can upregulated plenty of fatty acids(palmitic acid,stearic acid,tetracosanoic acid),together with some amino acids(tryptophan,L-aspartate,L-valine)and carbohydrate(D-glucose),while the trend was opposite in TO ***,moderate-to-strong correlations were found between differential metabolites and changed *** general,this paper claimed that TO could prolong lifespan and slow down aging process via regulating the lipids,amino acids and carbohydrates metabolism.

关键词： Caenorhabditis elegans Lipids Lifespan Food omics gene expression

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Crosslink among cyclin-dependent kinase 9,ATP binding cassette transporter G2 and Beclin 1 in colorectal cancer

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World Journal of Gastrointestinal Oncology 2024年第12期16卷 4778-4781页

作者： Zhong-Bao Shao Ke He Yu-Bin Su Zhi Shi Cancer Minimally Invasive Therapies Centre Guangdong Second Provincial General HospitalJinan UniversityGuangzhou 510632Guangdong ProvinceChina Department of Cell Biology&Institute of Biomedicine Guangdong Provincial Biotechnology&Engineering Technology Research CenterGuangdong Provincial Key Laboratory of Bioengineering MedicineGenomic Medicine Engineering Research Center of Ministry of EducationMOE Key Laboratory of Tumor Molecular BiologyNational Engineering Research Center of Genetic MedicineState Key Laboratory of Bioactive Molecules and Druggability AssessmentCollege of Life Science and TechnologyJinan UniversityGuangzhou 510632Guangdong ProvinceChina

Colorectal cancer(CRC)ranks third in the number of cancers mainly because of the inability to diagnose it at an early *** pathogenesis of CRC is complicated,which is the result of the complex interaction of multiple genetic and environmental ***,one of the main treatments for CRC is *** the primary cause of CRC treatment failure is drug *** expression of cyclin-dependent kinase 9(CDK9)was correlated with elevated autophagy levels in colon cancer,and high expression of CDK9 indicates a poor prognosis in *** incidence of autophagy and the expressions of Beclin 1 and ATP binding cassette transporter G2 are different in left and right colon cancer,and autophagy may be involved in the occurrence of chemotherapy *** this article,the roles of CDK9,ATP binding cassette transporter G2 and Beclin 1 in CRC were elucidated,emphasizing the linkages among them and providing potential therapeutic targets of CRC.

关键词： Cyclin-dependent kinase 9 ATP binding cassette transporter G2 Beclin 1 Colorectal cancer Chemotherapy

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Integrating crop models,single nucleotide polymorphism,and climatic indices to develop genotype-environment interaction model:A case study on rice flowering time

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植物表型组学（英文） 2025年第1期7卷 66-76页

作者： Jinhan Zhang Shaoyuan Zhang Yubin Yang Wenliang Yan Xiaomao Lin Lloyd T.Wilson Bing Liu Leilei Liu Liujun Xiao Yan Zhu Weixing Cao Liang Tang National Engineering and Technology Center for Information Agriculture Engineering Research Center of Smart AgricultureMinistry of EducationKey Laboratory for Crop System Analysis and Decision MakingMinistry of AgricultureNanjing Agricultural UniversityNanjingJiangsu 210095China Texas A&M AgriLife Research Center at Beaumont USA Department of Agronomy Kansas State University2108 Throckmorton Plant Sciences CenterManhattanKS 66506USA

Genotype-environment interaction(G × E)models have potential in digital breeding and crop phenotype *** genotype-specific parameters(GSPs)as a bridge,crop growth models can capture G × E and simulate plant growth and development *** this study,a dataset containing multi-environmental planting and flowering data for 169 genotypes,each with 700K single nucleotide polymorphism(SNP)markers was *** rice growth models(ORYZA,CERES-Rice,and RiceGrow),SNPs,and climatic indices were in-tegrated for flowering time *** associations between GSPs and quantitative trait nucleotides(QTNs)were investigated using genome-wide association study(GWAS)*** GSPs were associated with previously reported rice flowering genes,including DTH2,DTH3 and OsCOL15,demonstrating the genetic interpretability of the *** rice models driven by SNPs-based GSPs showed a decrease in goodness of fit as reflected by increased root mean square errors(RMSE),compared to the traditional model *** predictions of crop model were further modified using the machine learning(ML)methods and climate *** accuracy of the modified predictions were comparable to what was achieved using the traditional calibration *** addition,the Multi-model ensemble(MME)was comparable to that of the best individual *** of our findings can potentially facilitate molecular breeding and phenotypic prediction of rice.

关键词： Crop models SNPs Climatic indices Genotype-environment interaction Flowering time

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A Novel Intelligent System for Dynamic Observation of Cotton Verticillium Wilt

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Plant Phenomics 2023年第1期5卷 73-84页

作者： Chenglong Huang Zhongfu Zhang Xiaojun Zhang Li Jiang Xiangdong Hua Junli Ye Wanneng Yang Peng Song Longfu Zhu College of Engineering Huazhong Agricultural UniversityWuhan 430070PR China College of Plant Science&Technology Huazhong Agricultural UniversityWuhan 430070PR China National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene Research(Wuhan)Huazhong Agricultural UniversityWuhan 430070PR China

Verticillium wilt is one of the most critical cotton diseases,which is widely distributed in cotton-producing ***,the conventional method of verticillium wilt investigation is still manual,which has the disadvantages of subjectivity and low *** this research,an intelligent vision-based system was proposed to dynamically observe cotton verticillium wilt with high accuracy and high ***,a 3-coordinate motion platform was designed with the movement range 6,100 mm×950 mm×500 mm,and a specific control unit was adopted to achieve accurate movement and automatic ***,the verticillium wilt recognition was established based on 6 deep learning models,in which the VarifocalNet(VFNet)model had the best performance with a mean average precision(mAP)of ***,deformable convolution,deformable region of interest pooling,and soft non-maximum suppression optimization methods were adopted to improve VFNet,and the mAP of the VFNet-Improved model improved by 1.8%.The precision–recall curves showed that VFNet-Improved was superior to VFNet for each category and had a better improvement effect on the ill leaf category than fine *** regression results showed that the system measurement based on VFNet-Improved achieved high consistency with manual ***,the user software was designed based on VFNet-Improved,and the dynamic observation results proved that this system was able to accurately investigate cotton verticillium wilt and quantify the prevalence rate of different resistant *** conclusion,this study has demonstrated a novel intelligent system for the dynamic observation of cotton verticillium wilt on the seedbed,which provides a feasible and effective tool for cotton breeding and disease resistance research.

关键词： system category cotton

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A highly efficient method for genomic deletion across diverse lengths in thermophilic Parageobacillus thermoglucosidasius

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Synthetic and Systems Biotechnology 2024年第4期9卷 658-666页

作者： Zhiheng Yang Bixiao Li Ruihong Bu Zhengduo Wang Zhenguo Xin Zilong Li Lixin Zhang Weishan Wang State Key Laboratory of Bioreactor Engineering School of BiotechnologyEast China University of Science and Technology(ECUST)200237ShanghaiChina Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials Key Laboratory of Cluster ScienceMinistry of EducationFrontiers Science Center for High Energy MaterialAdvanced Research Institute of Multidisciplinary ScienceSchool of Chemistry and Chemical EngineeringBeijing Institute of TechnologyBeijing100081China State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing100101China

Parageobacillus thermoglucosidasius is emerging as a highly promising thermophilic organism for metabolic *** utilization of CRISPR-Cas technologies has facilitated programmable genetic manipulation in ***,the absence of thermostable NHEJ enzymes limited the capability of the endogenous type I CRISPR-Cas system to generate a variety of extensive genomic ***,two thermophilic NHEJ enzymes were identified and combined with the endogenous type I CRISPR-Cas system to develop a genetic manipulation tool that can achieve long-range genomic deletion across various *** optimizing this tool—through adjusting the expression level of NHEJ enzymes and leveraging our discovery of a negative correlation between GC content of the guide RNA(gRNA)and deletion efficacy—we streamlined a comprehensive gRNA selection manual for whole-genome editing,achieving a 100%success rate in randomly selecting ***,using just one gRNA,we achieved genomic deletions spanning diverse length,exceeding 200 *** tool will facilitate the genomic manipulation of *** for both fundamental research and applied engineering studies,further unlocking its potential as a thermophilic cell factory.

关键词： Type I CRISPR system Thermostable NHEJ enzymes Thermophile Long-range genomic deletions

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A review of structure-activity relationship， enzymatic and genetic modulation of exopolysaccharides from lactic acid bacteria

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Food Science and Human Wellness 2024年

作者： Jingyan Zhang Tao Hu Qingshen Sun Engineering Research Center of Agricultural Microbiology Technology， Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology， College of Heilongjiang Province & School of Life Sciences， Heilongjiang University

Lactic acid bacteria (LAB) exopolysaccharides (EPS) reveal high safety and multiple activities， and are typical postbiotics produced by LAB during fermentation. In this paper， 6583 articles on LAB-EPS from web of science and ELSEVIER databases were retrieved， and 236 articles related to this review were screened. The EPS from 90 LAB strains were summarized in terms of their extraction methods， yield， molecular weight， monosaccharide composition， glycosidic bond configuration and the structural and activity relationships (SARs). However， there exist great challenges as for the low yield and high cost in EPS production. Therefore， this review further elaborated the mechanism of EPS secretion， the anabolic pathway of EPS， the structure and mechanism of key enzymes involving in EPS synthesis process， the prospect of gene regulation for EPS secretion， and proposed the engineering strategies for increasing EPS yield or tailored EPS design in recent years. In addition， CRISPR/Cas9 gene editing technology was also discussed in the production control of EPS in LAB. Finally， the engineering strategy of increasing EPS yield in recent years was proposed. This work might provide important theoretical support for the production and application of LAB-based EPS.

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LncRNA-AP006284.1 promotes prostate cancer cell growth and motility by forming RNA-DNA triplexes and recruiting GNL3/SFPQ complex to facilitate RASSF7 transcription

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genes & Diseases 2023年第2期10卷 317-320页

作者： Yali Lu Yan Lin Xiaoyang Zhang Jun Yan Zhe Kong Lu Zhang Chenji Wang Yan Huang Shimin Zhao Yao Li Obstetrics and Gynecology Hospital State Key Laboratory of Genetic EngineeringMOE Engineering Research Center of Gene TechnologySchool of Life ScienceFudan UniversityShanghai 200433China Shanghai Engineering Research Center of Industrial Microorganisms School of Life ScienceFudan UniversityShanghai 200433China Institute of Metabolism and Integrative Biology (IMIB) Key Laboratory of Reproduction Regulation of NPFPCFudan UniversityShanghai 200433China Institutes of Biomedical Sciences Fudan UniversityShanghai 200433China Department of Laboratory Animal Science Fudan UniversityShanghai 200032China

Long noncoding RNAs(lncRNAs)are known to be involved in transcriptional regulation and their deregulation is associated with the development of human diseases such as cancer.1,2 LncRNA can directly bind to purine-rich double-stranded DNA sequences through Hoogsteen base pairing to form an RNA-DNA triplex motifs and regulate gene expression.3,4,5 However,its regulatory mechanisms and functions in tumors remain ***,we report that the LMNTD2 antisense RNA 1(LMNTD2-AS1,also known as AP006284.1)is highly expressed in prostate cancer(PCa)and positively correlated with the expression of its adjacent coding gene N-terminal Ras-association domain family 7(RASSF7).Mechanistically,AP006284.1 tethers to the RASSF7 promoter via RNA-DNA triplexes in cis-acting manner,which enhances chromatin accessibility and recruits the transcription factor complex GNL3/SFPQ to activate the expression of RASSF7,a repressor of the Hippo signaling ***,overexpression of either AP006284.1 or RASSF7 inactivated the Hippo signaling and malignant proliferation of PCa cells.

关键词： expression LncRNA cancer

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ESCRT-Ⅲ component OsSNF7.2 modulates leaf rolling by trafficking and endosomal degradation of auxin biosynthetic enzyme OsYUC8 in rice

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Journal of Integrative Plant Biology 2023年第6期65卷 1408-1422页

作者： Liang Zhou Saihua Chen Maohong Cai Song Cui Yulong Ren Xinyue Zhang Tianzhen Liu Chunlei Zhou Xin Jin Limin Zhang Minxi Wu Shuyi Zhang Zhijun Cheng Xin Zhang Cailin Lei Qibing Lin Xiuping Guo Jie Wang Zhichao Zhao Ling Jiang Shanshan Zhu Jianmin Wan State Key Laboratory for Crop Genetics and Germplasm Enhancement Jiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing 210095China National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology Agricultural College of Yangzhou UniversityYangzhou 225009China

The endosomal sorting complex required for transport(ESCRT)is highly conserved in eukaryotic cells and plays an essential role in the biogenesis of multivesicular bodies and cargo degradation to the plant vacuole or *** ESCRT components affect a variety of plant growth and development processes,their impact on leaf development is rarely ***,we found that OsSNF7.2,an ESCRT-Ⅲ component,controls leaf rolling in rice(Oryza sativa).The Ossnf7.2 mutant rolled leaf 17(rl17)has adaxially rolled leaves due to the decreased number and size of the bulliform ***7.2is expressed ubiquitously in all tissues,and its protein is localized in the endosomal ***7.2 homologs,including OsSNF7,OsSNF7.3,and OsSNF7.4,can physically interact with OsSNF7.2,but their single mutation did not result in leaf *** ESCRT complex subunits,namely OsVPS20,OsVPS24,and OsBRO1,also interact with *** assays revealed that OsSNF7.2 interacts with OsYUC8 and aids its vacuolar *** Osyuc8and rl17 Osyuc8 showed rolled leaves,indicating that OsYUC8 and OsSNF7.2 function in the same pathway,conferring leaf *** study reveals a new biological function for the ESCRT-Ⅲcomponents,and provides new insights into the molecular mechanisms underlying leaf rolling.

关键词： bulliform cell leaf rolling OsSNF7.2 OsYUC8 rice(Oryza sativa) vacuolar degradation

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A novel semi-dominant allele of the transmembrane NAC transcription factor ZmNTL2 reduces the size of multiple maize organs

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The Crop Journal 2024年第3期12卷 676-687页

作者： Chuan Li Yun Bai Yuwei Hou Siyu Wang Yue Xin Tao Yu Jing Wang Xiaowei Liu Hongyang Yi Chao Xia Hai Lan Moju Cao State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China Maize Research InstituteSichuan Agricultural UniversityChengdu 611130SichuanChina Jilin Engineering Research Center for Crop Biotechnology Breeding College of Plant ScienceJilin UniversityChangchun 130012JilinChina

Maize plant architecture influences planting density and,in turn,grain *** of the plant architecture-related traits can be described as organ *** describe a miniature maize mutant,Tiny plant 4(Tip4),which exhibits reduced size of multiple organs and exhibits a semi-dominant monofactorial inheritance *** cloning confirmed that a 4-bp deletion in the NAC TF with transmembrane motif 1-Like(NTL)gene ZmNTL2,denoted as ZmNTL2^(Δ),confers the Tip4 ***-PCR showed that ZmNTL2 was expressed in all tested ***2 functions as a transcriptional activator and is located in both the nucleus and *** mutation does not affect the mRNA abundance of ZmNTL2 locus,but it does result in the loss of transmembrane domain and confines the ZmNTL2^(Δ)protein to the *** out ZmNTL2 has no effect on maize organ size development,indicating that the 4-bp deletion might be a gain-of-function mutation in organ size *** transcriptome sequencing with cytokinin and auxin content determination suggests that the decreased organ size may be possibly mediated by changes in hormone homeostasis.

关键词： Organ size c-ray mutagenesis Membrane-bound NAC TF Hormone homeostasis Maize

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Pan-cancer analysis identifies RNA helicase DDX1 as a prognostic marker

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Phenomics 2022年第1期2卷 33-49页

作者： Baocai Gao Xiangnan Li Shujie Li Sen Wang Jiaxue Wu Jixi Li State Key Laboratory of Genetic Engineering School of Life SciencesMOE Engineering Research Center of Gene TechnologyShanghai Engineering Research Center of Industrial MicroorganismsFudan UniversityShanghai 200438China Kunming Institute of Physics Kunming 650223China

The DEAD-box RNA helicase(DDX)family plays a critical role in the growth and development of multiple ***1 is involved in mRNA/rRNA processing and mature,virus replication and transcription,hormone metabolism,tumo-rigenesis,and tumor ***,how DDX1 functions in various cancers remains ***,we explored the potential oncogenic roles of DDX1 across 33 tumors with The Cancer Genome Atlas(TCGA)and the Genotype-Tissue Expression(GTEx)***1 is highly expressed in breast cancer(BRCA),cholangiocarcinoma(CHOL),and colon adenocarcinoma(COAD),but it is lowly expressed in renal cancers,including kidney renal clear cell carcinoma(KIRC),kidney chromophobe(KICH),and kidney renal papillary cell carcinoma(KIRP).Low expression of DDX1 in KIRC is cor-related with a good prognosis of overall survival(OS)and disease-free survival(DFS).Highly expressed DDX1 is linked to a poor prognosis of OS for adrenocortical carcinoma(ACC),bladder urothelial carcinoma(BLCA),KICH,and liver hepatocellular carcinoma(LIHC).Also,the residue Ser481 of DDX1 had an enhanced phosphorylation level in BRCA and ovarian cancer(OV)but decreased in *** infiltration analysis exhibited that DDX1 expression affected CD8+T cells,and it was significantly associated with MSI(microsatellite instability),TMB(tumor mutational burden),and ICT(immune checkpoint blockade therapy)in *** addition,the depletion of DDX1 dramatically affected the cell viability of human tumor-derived cell ***1 could affect the DNA repair pathway and the RNA transport/DNA replication processes during tumorigenesis by analyzing the CancerSEA ***,our pan-cancer analysis revealed that DDX1 had complicated impacts on different cancers and might act as a prognostic marker for cancers such as renal cancer.

关键词： RNA helicase DDX1 Pan-cancer analysis Survival analysis Prognostic marker

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