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Salinity Acclimation Induces Reduced Energy Metabolism,Osmotic Pressure Regulation and Transcriptional Reprogramming in Hypotrichida Ciliate Gastrostyla setifera

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Journal of Ocean University of China 2024年第2期23卷 539-549页

作者： JI Xin BI Luping ZOU Songbao LI Wenlu JI Daode ZHANG Qianqian School of Ocean Yantai UniversityYantai 264005China Key Laboratory of Coastal Environmental Processes and Ecological Remediation Yantai Institute of Coastal Zone ResearchChinese Academy of SciencesYantai 264003China Zhejiang Institute of Freshwater Fisheries Huzhou 313001China Muping Coastal Environment Research Station Yantai Institute of Coastal Zone ResearchChinese Academy of SciencesYantai 264117China

Coastal and estuarine protists are frequently exposed to salinity undulation.While the tolerance and stress responses of microalgae to salinity have been extensively studied,there have been scarce studies on the physiological response of heterotrophic protists to salinity stressing.In this study,we investigated the physiological response of the heterotrophic ciliate Gastrostyla setifera to a salinity of 3,via a transcriptomic approach.The first transcriptome of genus Gastrostyla was obtained utilizing a group of manually isolated ciliate individuals(cells)and RNA-seq technique.The completeness of the transcriptome was verified.differentially expressed gene(DEG)analysis was performed among the transcriptomes of G.setifera acclimated in saline water(salinity 3)and those cultured in fresh water.The results demonstrated a significant alternation in gene transcription,in which the ciliate exhibits a transcripttomic acclimation in responding salinity stressing.The up-regulated DEGs were enriched in the pathways of cytoskeleton proteins,membrane trafficking,protein kinases and protein phosphatases.These may represent enhanced functions of ion transport,stress response and cell protections.Pathways involved in energy metabolism and biosynthesis were markedly down-regulated,reflecting decreased cell activity.Particularly,we detected significantly down-regulated genes involved in several pathways of amino acid catabolism,which may lead to accumulation of amino acids in the ciliate cell.Amino acid could act as compatible solutes in the cytoplasm to maintain the osmotic balance in saline water.Overall,this work is an initial exploration to the molecular basis of the heterotrophic protist responding to salinity stressing.The result sheds light on the mechanisms of enhancement of cell protection,reduction of cell activity,and osmotic pressure regulation in ciliates acclimated to salinity.

关键词： salinity stress heterotrophic protist ciliate Gastrostyla setifera transcriptome differentially expressed gene

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Constructing cDNA Microarray to Isolate Novel differentially expressed genes Related to Human Glioma and Characterizations of Novel Full-length gene PPIL-3

Constructing cDNA Microarray to Isolate Novel Differentially...

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中国抗癌协会神经肿瘤专业委员会第八届学术会议

作者： Zhen-Yu Qi1,Wang zhong,Yao Li2,Zong-Xiang Zhou2,Guo-Zhen Hui1,Yi Xie2 1.Department of Neurosurgery,The First Affiliated Hospital of Suzhou University,Suzhou,215006,People''s Republic of China 2.State Key Laboratory of genetic Engineering,Institute of genetics,Fudan University,220 Han Dan Rd.,Shanghai,200433,P.R.China

Identification of the genes that are differentially expressed between brain tumor and normal brain tissues is important for understanding the molecular basis of these nerve system tumors and for defining possible targets for therapeutic intervention.The objective of my research is to investigate the differentially expressed genes related to human glioma using cDNA microarray and study the characterization of one novel full-length gene.Total RNA was extracted from human glioma tissues and normal brain tissues,and mRNA was used to make probes.After hybridization and washing procedure,the results of hybridization were scanned using computer system.The gene named 681F05 clone was one differentially expressed gene to human glioma through four times hybridizations and scanning.Subsequently 681F05 clone was performed by northern blot,in situ hybridization,5’RACE,chromosome mapping and bioinformatics.Fifteen differentially expressed genes to human glioma were through four times hybridizations and scanning.We demonstrated that 681F05 clone was low-expression in human brain tissue and over-expression in human glioma tissues.The analysis of BLASTn and BLASTx showed that 681F05 clone is two cDNA clones encoding two novel proteins that are higher identity to the cyclophilin isoform 10 of C.Elgans,respectively.Sequence analysis revealed the two cDNA clones are two different splicing variants of a novel cycophilin-like gene（PPIL3a and PPIL3b）.According to the Nomenclature Committee of Human Genome Organization（HUGO）,the gene was named as peptidylprolyl isomerase（cyclophilin）-like 3（approved symbol,PPIL3）.Two nucleotide sequences found in this study have been submitted to the GenBankTM with accession numbers:AF251049 and AF271652.Furthermore,PPIL3 was located in chromosome 2q33 between STS marker stSG2762（proximal） and SHGC-3074（distal）.We experienced that cDNA microarray technology can be successfully applied to identify differentially expressed genes in human glioma.This approach is superior to routine representational differe

关键词： differentially expressed gene Glioma Microarray Novel Full-length gene

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Identification of functional genes regulating gastric cancer progression using integrated bioinformatics analysis

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World Journal of Clinical Cases 2023年第21期11卷 5023-5034页

作者： Kun Yu Dong Zhang Qiang Yao Xing Pan Gang Wang Hai-Yang Qian Yao Xiao Qiong Chen Ke Mei Department of Radiology Shanghai Xuhui Dahua HospitalShanghai 200090China Department of Spinal Surgery Yueyang Hospital of Integrated Traditional Chinese and Western MedicineShanghai University of Traditional Chinese MedicineShanghai 200090China Division of Chemistry and Ionizing Radiation Measurement Technology Shanghai Institute of Measurement and Testing TechnologyShanghai 200090China

BACKGROUND Gastric cancer(GC)is one of the most common cancers and has a poor prognosis.Treatment of GC has remained unchanged over the past few years.AIM To investigate the potential therapeutic targets and related regulatory biomarkers of GC.METHODS We obtained the public GC transcriptome sequencing dataset from the gene Expression Omnibus database.The datasets contained 348 GC tissues and 141 healthy tissues.In total,251 differentially expressed genes(DEGs)were identified,including 187 down-regulated genes and 64 up-regulated genes.The DEGs’enriched functions and pathways include Progesterone-mediated oocyte maturation,cell cycle,and oocyte meiosis,Hepatitis B,and the Hippo signaling pathway.Survival analysis showed that BUB1,MAD2L1,CCNA2,CCNB1,and BIRC5 may be associated with regulation of the cell cycle phase mitotic spindle checkpoint pathway.We selected 26 regulated genes with the aid of the protein-protein interaction network analyzed by Molecular Complex Detection.RESULTS We focused on three critical genes,which were highly expressed in GC,but negatively related to patient survival.Furthermore,we found that knockdown of Yu K et al.Biochemical analysis in GC WJCC https://*** 5024 July 26,2023 Volume 11 Issue 21 BIRC5,TRIP13 or UBE2C significantly inhibited cell proliferation and induced cell apoptosis.In addition,knockdown of BIRC5,TRIP13 or UBE2C increased cellular sensitivity to cisplatin.CONCLUSION Our study identified significantly upregulated genes in GC with a poor prognosis using integrated bioinformatics methods.

关键词： Gastric cancer Bioinformatics analysis differentially expressed gene Protein-protein interaction network Cisplatin resistance

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Dissecting the genetic basis of maize deep-sowing tolerance by combining association mapping and gene expression analysis

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Journal of Integrative Agriculture 2022年第5期21卷 1266-1277页

作者： YANG Yue MA Yu-ting LIU Yang-yang Demar LYLE LI Dong-dong WANG Ping-xi XU Jia-liang ZHEN Si-han LU Jia-wen PENG Yun-ling CUI Yu FU Jun-jie DU Wan-li ZHANG Hong-wei WANG Jian-hua Agronomy College Shenyang Agricultural UniversityShenyang 110161P.R.China National Key Facility for Crop gene Resources and genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081P.R.China Center for Seed Science and Technology College of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100193P.R.China Gansu Provincial Key Laboratory for Aridland Crop Science/Agronomy College Gansu Agricultural UniversityLanzhou 730070P.R.China

Deep-sowing is an important method for avoiding drought stress in crop species,including maize.Identifying candidate genes is the groundwork for investigating the molecular mechanism underlying maize deep-sowing tolerance.This study evaluated four traits(mesocotyl length at 10 and 20 cm planting depths and seedling emergence rate on days 6 and 12)related to deep-sowing tolerance using a large maize population containing 386 inbred lines genotyped with 0.5 million high-quality single nucleotide polymorphisms(SNPs).The genomewide association study detected that 273 SNPs were in linkage disequilibrium(LD)with the genetic basis of maize deep-sowing tolerance.The RNA-sequencing analysis identified 1944 and 2098 differentially expressed genes(DEGs)in two comparisons,which shared 281 DEGs.By comparing the genomic locations of the 273 SNPs with those of the 281 DEGs,we identified seven candidate genes,of which GRMZM2G119769 encoded a sucrose non-fermenting 1 kinase interactor-like protein.GRMZM2G119769 was selected as the candidate gene because its homologs in other plants were related to organ length,auxin,or light response.Candidate gene association mapping revealed that natural variations in GRMZM2G119769 were related to phenotypic variations in maize mesocotyl length.gene expression of GRMZM2G119769 was higher in deep-sowing tolerant inbred lines.These results suggest that GRMZM2G119769 is the most likely candidate gene.This study provides information on the deep-sowing tolerance of maize germplasms and identifies candidate genes,which would be useful for further research on maize deep-sowing tolerance.

关键词： maize mesocotyl length association mapping differentially expressed gene SNF1 kinase interactor-like protein

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Transcriptome analysis reveals potential genes associated with plant height in rice

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BIOCELL 2023年第2期47卷 409-421页

作者： CAN CHEN RUI FENG ZONGQIONG ZHANG XIUZHONG XIA BAOXUAN NONG YU ZENG HUI GUO XINGHAI YANG DANTING LI Guangxi Key Laboratory of Rice genetics and Breeding Rice Research InstituteGuangxi Academy of Agricultural SciencesNanning530007China

Plant height(PH)is a complex trait regulated by the environment and multiple genes.PH directly affects crop yield,harvest index,and lodging resistance.From plant dwarf mutants,many genes related to PH have been identified and described.Nonetheless,the molecular mechanism of height regulation in high-culm rice mutants has not been well studied.By using transcriptome and weighted gene co-expression network analysis(WGCNA),we identified the differentially expressed genes(DEGs)between high-culm rice mutants(MUT)and wild-type(WT)and explored the key pathways and potential candidate genes involved in PH regulation.Transcriptome analysis identified a total of 2,184 DEGs,of which 1,317 were identified at the jointing stage and 1,512 were identified at the heading stage.Kyoto Encyclopedia of genes and Genomes enrichment showed that the enrichment pathways were mainly involved in plant hormone signal transduction,ABC transportation,and steroid hormone biosynthesis.Among these metabolic pathways,LOC_Os05g43910 and LOC_Os01g35030 were auxin(IAA)-related genes,up-regulated in MUT and LOC_Os02g08500(LEPTO1),LOC_Os11g04720,and LOC_Os12g04500 were cytokinin(CK)-related genes,downregulated in MUT.The WGCNA identified four modules(light cyan,dark grey,grey,and pale turquoise)closely related to PH,and seven key genes were screened from these modules,of which two were up-regulated cell wallrelated genes(LOC_Os01g26174(OsWAK5),LOC_Os06g05050)in MUT,and one gibberellic acid(GA)gene(LOC_Os06g37364,OsKO2)was also up-regulated.These genes might be closely related to PH regulation.These findings help us better understand the transcriptional regulation of rice plant growth and development and provide a theoretical basis for mapping and cloning the PH regulatory genes.

关键词： Rice Plant height Transcriptome Weighted gene co-expression network analysis differentially expressed gene

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Transcriptome Analysis of a Wild Eggplant Germplasm M239 in Response to Verticillium dahliae Infection

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Phyton-International Journal of Experimental Botany 2023年第2期92卷 591-609页

作者： Liyan Wu Jie Cheng Yaju Gong Rui Bao Zhibin Li Min Gui Guanghui Du Institute of Horticultural Crops Yunnan Academy of Agricultural SciencesKunming650205China Institute of Plant Resources Yunnan UniversityKunming650500China

In this study,wild eggplant germplasm No.M239,which is highly susceptible to Verticillium wilt,was used as the experimental material.The physiological and biochemical indices(SOD,PAL,MDA and soluble protein)of M239 roots were measured at different times(0,12,24,36,48,60 and 72 h)post inoculation with Verticillium dahliae,and the key time points for the M239 response to Verticillium wilt infection were screened.Then,RNA-Seq technology was used to screen the differentially expressed genes(DEGs)in M239 roots at 0,12 and 48 h post-inoculation(hpi).The transcriptional results of M239 were also compared with those resistance genes from some reported wild relative Solanum species(S.sisymbriifolium and S.aculeatissimum).Then some DEGs were chosen for validation by qRT–PCR.The results showed that 12 and 48 hpi were the turning points in the changes in all physiological and biochemical indices.A total of 6,783 DEGs were identified by RNA-Seq,including 6,141 DEGs(3,046 upregulated and 3,095 downregulated)at the M_12 h vs.M_0 h,1,903 DEGs(792 upregulated and 1,111 downregulated)at M_48 h vs.M_12 h,and 1,261 DEGs that appeared simultaneously in both stages.KEGG enrichment analysis showed that there were 5 metabolic pathways enriched from DEGs,which were mostly related to primary metabolism,such as glycolysis,amino acid and ribosome biogenesis.Compared with the NCBI non-redundant protein(NR)database,one Ve2 homologous gene and 8 PR protein-related genes were screened.Transcription factor analysis showed that there were a large number of DEGs,such as MYB,AP2-EREBP,bHLH,NAC and Orphans in the two stages.Compared with the reported Verticillium wilt-resistant wild eggplant species,it was found that there were fewer genes and enriched metabolic pathways in the M239 response to Verticillium wilt infection,and it also lacked the response of some known key resistance genes.These results proved that the above resistance genes and metabolic pathways played a key role in the wild eggplant response to V.dahliae infection.

关键词： Wild eggplant Verticillium wilt transcriptome sequencing differentially expressed gene KEGG pathway

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Transcriptomic Responses of Garlic(Allium sativum L.)to Heat and Drought Stresses

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Phyton-International Journal of Experimental Botany 2023年第11期92卷 3077-3090页

作者： Seung Hee Eom Tae Kyung Hyun Department of Industrial Plant Science and Technology Chungbuk National UniversityCheongju28644Korea

Heat and drought are prominent abiotic stressors that limit crop productivity and yield,particularly concerning climate change;therefore,understanding the molecular mechanisms underlying plant stress responses is crucial for stress-tolerant crop production.This study conducted a transcriptomic analysis to elucidate how garlic(Allium sativum L.)responds to drought and heat stress conditions.Transcriptome libraries were generated to identify differentially expressed genes(DEGs)induced by drought and heat stresses.Functional classification and clustering analysis of DEGs revealed stress-specific gene expression patterns.Notably,cell wall-related genes were implicated in the drought response,whereas heat stress was associated with heat stress transcription factors and heat shock proteins.Our results provide essential information for future studies on stress tolerances in garlic.

关键词： differentially expressed gene drought heat garlic transcriptome

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Reexploring the Possible Roles of Some genes Associated with Nasopharyngeal Carcinoma Using Microarray-based Detection

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Acta Biochimica et Biophysica Sinica 2005年第8期37卷 541-546页

作者： Wei-Yi FANG~(1,2#) Teng-Fei LIU~(1#) Wei-Bing XIE~2 Xu-Yu YANG~1 Shuang WANG~2 Cai-Ping REN~1 Xin DENG~2 Qiu-Zhen LIU~2 Zhong-Xi HUANG~2 Xin LI~2 Yan-Qing DING~2 Kai-Tai YAO~(1,2*) ~1 Cancer Research Institute.Xiangya Medical School,Central South University,Changsha 410078.China ~2 Cancer Research Institute.Nanfang Medical University Guangahou 510515,China Cancer Research Institute Xiangya Medical School Central South UniversityChangsha 410078 China Cancer Research Institute Nanfang Medical UniversityGuangzhou 510515 China

In gene expression profiling,nasopharyngeal carcinoma(NPC)5-8F cells differ from 6-10Bcells in terms of their high tumorigenicity and metastatic ability.differentially expressed genes from the twocell types were analyzed by combining with MILANO(the automatic custom annotation of microarray resultswhich is based on all the available published work in PubMed).The results showed that five genes,includingCTSD,P63,CSE1L,BPAG1 and EGR1,have been studied or mentioned in published work on NPC.Subsequently,we revaluated the roles of these genes in the pathogenesis of NPC by combining the data ofgene chips from NPCs versus NPs and pooled cells from 5-8F,6-10B and CNE2 versus NPs.The resultssuggested that the roles of BPAG1 and EGR1 are possibly different from those reported in previous NPCstudies.These five genes are likely to be involved in the proliferation,apoptosis,invasion and metastasis ofNPC.A reexploration of the genes will further define their roles in the pathogenesis of NPC.

关键词： nasopharynx(NP) nasopharyngeal carcinoma(NPC) MILANO differentially expressed gene

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Identification of differentially expressed genes in human uterine leiomyomas using differential display

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Cell Research 2002年第1期12卷 39-45页

作者： BIN LI, MEI SUN, BIN HE, JIN YU, You DUAN ZHANG, YONG LIAN ZHANG, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, 820, Yue- Yang Road, Shanghai, State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institute for Biological Science Chinese Academy of Sciences Shanghai China Room 3D16 Building 10 NINDS NIH Bethesda USA Laboratories for Reproductive Biology Department of pediatrics School of Medicine University of North Carolina Chapel Hill USA OB/GYN Hospital Shanghai (First) Medical University Shanghai China

In searching of differentially expressed genes in human uterine leiomyomas, differential display was used with twelve pairs of primers to compare human uterine leiomyomas with matched myometrium. False positives were eliminated by reverse Northern analysis. Positives were confirmed by Northern blot analysis. RESULTS: [1] Four of 69 cDNA fragments (3 up-regulated named L1, L2 and L3 and 1 down-regulated named Mi in leiomyoma) were confirmed by Northern analysis. [2] Sequence comparison and Northern analysis proved that Li is exactly the human ribosomal protein Si9. [3] It was present ubiquitously in i3 tissues tested but in various levels and even in different size. [4] Li was highly expressed in parotidean cystadenocarcinoma, pancreatic cancer and breast cancer examined. [5] No mutations have been found in human uterine leiomyomas (n=6). CONCLUSIONS: hRPSi9 overexpression might be a universal signal in rapid cell growth tissues.

关键词： Human uterine leiomyomas differentially expressed gene differential display (DD) human S19 ribosomal protein (hRPS19) up-regulated gene in human leiomyomas.

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Bioinformatics-based Identification of Key Pathways and Hub genes of Traumatic Brain Injury in a Rat Model

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Current Medical Science 2021年第3期41卷 610-617页

作者： Xin-yi CAO Xiao QIAN Guo-dong LIU Yu-hai WANG Wuxi Clinical College of Anhui Medical University(904th Hospital of the Joint Logistic Support Force of the Chinese People's Liberation Army) Wuxi 214000China

Traumatic brain injury(TBI)is a common injury caused by external forces that lead to damaged brain function or pathological changes in the brain tissue.To explore the molecular mechanism and the hub genes of TBI,we downloaded gene expression profiles of the TBI model of rat and the sham control for the subsequent gene set enrichment analysis,pathway analysis and protein-protein interactions analysis.The results of gene Ontology and Kyoto Encyclopedia of genes and Genomes analysis indicated that multiple biological pathways,including immune response,inflammatory response and cellular response to interleukin-1,as well as signaling pathways,such as tumor necrosis factor signaling pathway,chcmokine signaling pathway,cytokine-cytokine receptor interaction,Toll-like receptor signaling pathway and nuclear factor kappa B signaling pathway were implicated in the TBI.In conclusion,this study provides insights into the molecular mechanism of TBI by screening the differentially expressed genes and hub genes that can be used as biomarkers and therapeutic targets.

关键词： traumatic brain injury bioinformatics analysis differentially expressed gene hub gene signal pathway

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