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Age-related driving mechanisms of retinal diseases and neuroprotection by transcription factor EB-targeted therapy
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作者 Samuel Abokyi Dennis Yan-yin Tse 《Neural Regeneration Research》 SCIE CAS 2025年第2期366-377,共12页
Retinal aging has been recognized as a significant risk factor for various retinal disorders,including diabetic retinopathy,age-related macular degeneration,and glaucoma,following a growing understanding of the molecu... Retinal aging has been recognized as a significant risk factor for various retinal disorders,including diabetic retinopathy,age-related macular degeneration,and glaucoma,following a growing understanding of the molecular underpinnings of their development.This comprehensive review explores the mechanisms of retinal aging and investigates potential neuroprotective approaches,focusing on the activation of transcription factor EB.Recent meta-analyses have demonstrated promising outcomes of transcription factor EB-targeted strategies,such as exercise,calorie restriction,rapamycin,and metformin,in patients and animal models of these common retinal diseases.The review critically assesses the role of transcription factor EB in retinal biology during aging,its neuroprotective effects,and its therapeutic potential for retinal disorders.The impact of transcription factor EB on retinal aging is cell-specific,influencing metabolic reprogramming and energy homeostasis in retinal neurons through the regulation of mitochondrial quality control and nutrient-sensing pathways.In vascular endothelial cells,transcription factor EB controls important processes,including endothelial cell proliferation,endothelial tube formation,and nitric oxide levels,thereby influencing the inner blood-retinal barrier,angiogenesis,and retinal microvasculature.Additionally,transcription factor EB affects vascular smooth muscle cells,inhibiting vascular calcification and atherogenesis.In retinal pigment epithelial cells,transcription factor EB modulates functions such as autophagy,lysosomal dynamics,and clearance of the aging pigment lipofuscin,thereby promoting photoreceptor survival and regulating vascular endothelial growth factor A expression involved in neovascularization.These cell-specific functions of transcription factor EB significantly impact retinal aging mechanisms encompassing proteostasis,neuronal synapse plasticity,energy metabolism,microvasculature,and inflammation,ultimately offering protection against retinal aging and diseases.The review emphasizes transcription factor EB as a potential therapeutic target for retinal diseases.Therefore,it is imperative to obtain well-controlled direct experimental evidence to confirm the efficacy of transcription factor EB modulation in retinal diseases while minimizing its risk of adverse effects. 展开更多
关键词 age-related macular degeneration anti-aging interventions autophagy calorie restriction diabetic retinopathy exercise glaucoma NEUROMODULATION PHAGOCYTOSIS photoreceptor outer segment degradation retinal aging transcription factor EB
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Transcription factor OsSPL10 interacts with OsJAmyb to regulate blast resistance in rice 被引量:1
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作者 Zaofa Zhong Lijing Zhong +4 位作者 Xiang Zhu Yimin Jiang Yihong Zheng Tao Lan Haitao Cui 《The Crop Journal》 SCIE CSCD 2024年第1期301-307,共7页
Transcription factors(TFs)play essential roles in transcriptional reprogramming during activation of plant immune responses to pathogens.OsSPL10(SQUAMOSA promoter binding protein-like10)is an important TF regulating t... Transcription factors(TFs)play essential roles in transcriptional reprogramming during activation of plant immune responses to pathogens.OsSPL10(SQUAMOSA promoter binding protein-like10)is an important TF regulating trichome development and salt tolerance in rice.Here we report that knockout of OsSPL10 reduces whereas its overexpression enhances rice resistance to blast disease.OsSPL10 positively regulates chitin-induced immune responses including reactive oxygen species(ROS)burst and callose deposition.We show that OsSPL10 physically associates with OsJAmyb,an important TF involved in jasmonic acid(JA)signaling,and positively regulates its protein stability.We then prove that OsJAmyb positively regulates resistance to blast.Our results reveal a molecular module consisting of OsSPL10 and OsJAmyb that positively regulates blast resistance. 展开更多
关键词 IMMUNITY JASMONATE Oryza sativa OsSPL10 transcription factor
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Phase separation and transcriptional regulation in cancer development 被引量:1
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作者 Yan Gu Ke Wei Jun Wang 《Journal of Biomedical Research》 CAS CSCD 2024年第4期307-321,共15页
Liquid-liquid phase separation,a novel biochemical phenomenon,has been increasingly studied for its medical applications.It underlies the formation of membrane-less organelles and is involved in many cellular and biol... Liquid-liquid phase separation,a novel biochemical phenomenon,has been increasingly studied for its medical applications.It underlies the formation of membrane-less organelles and is involved in many cellular and biological processes.During transcriptional regulation,dynamic condensates are formed through interactions between transcriptional elements,such as transcription factors,coactivators,and mediators.Cancer is a disease characterized by uncontrolled cell proliferation,but the precise mechanisms underlying tumorigenesis often remain to be elucidated.Emerging evidence has linked abnormal transcriptional condensates to several diseases,especially cancer,implying that phase separation plays an important role in tumorigenesis.Condensates formed by phase separation may have an effect on gene transcription in tumors.In the present review,we focus on the correlation between phase separation and transcriptional regulation,as well as how this phenomenon contributes to cancer development. 展开更多
关键词 phase separation transcription regulation CANCER super-enhancer CONDENSATES
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Diabetic retinopathy identification based on multi-sourcefree domain adaptation 被引量:1
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作者 Guang-Hua Zhang Guang-Ping Zhuo +3 位作者 Zhao-Xia Zhang Bin Sun Wei-Hua Yang Shao-Chong Zhang 《International Journal of Ophthalmology(English edition)》 SCIE CAS 2024年第7期1193-1204,共12页
AIM:To address the challenges of data labeling difficulties,data privacy,and necessary large amount of labeled data for deep learning methods in diabetic retinopathy(DR)identification,the aim of this study is to devel... AIM:To address the challenges of data labeling difficulties,data privacy,and necessary large amount of labeled data for deep learning methods in diabetic retinopathy(DR)identification,the aim of this study is to develop a source-free domain adaptation(SFDA)method for efficient and effective DR identification from unlabeled data.METHODS:A multi-SFDA method was proposed for DR identification.This method integrates multiple source models,which are trained from the same source domain,to generate synthetic pseudo labels for the unlabeled target domain.Besides,a softmax-consistence minimization term is utilized to minimize the intra-class distances between the source and target domains and maximize the inter-class distances.Validation is performed using three color fundus photograph datasets(APTOS2019,DDR,and EyePACS).RESULTS:The proposed model was evaluated and provided promising results with respectively 0.8917 and 0.9795 F1-scores on referable and normal/abnormal DR identification tasks.It demonstrated effective DR identification through minimizing intra-class distances and maximizing inter-class distances between source and target domains.CONCLUSION:The multi-SFDA method provides an effective approach to overcome the challenges in DR identification.The method not only addresses difficulties in data labeling and privacy issues,but also reduces the need for large amounts of labeled data required by deep learning methods,making it a practical tool for early detection and preservation of vision in diabetic patients. 展开更多
关键词 diabetic retinopathy multisource-free domain adaptation pseudo-label generation softmaxconsistence minimization
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Transcriptional regulation in the development and dysfunction of neocortical projection neurons 被引量:1
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作者 Ningxin Wang Rong Wan Ke Tang 《Neural Regeneration Research》 SCIE CAS CSCD 2024年第2期246-254,共9页
Glutamatergic projection neurons generate sophisticated excitatory circuits to integrate and transmit information among different cortical areas,and between the neocortex and other regions of the brain and spinal cord... Glutamatergic projection neurons generate sophisticated excitatory circuits to integrate and transmit information among different cortical areas,and between the neocortex and other regions of the brain and spinal cord.Appropriate development of cortical projection neurons is regulated by certain essential events such as neural fate determination,proliferation,specification,differentiation,migration,survival,axonogenesis,and synaptogenesis.These processes are precisely regulated in a tempo-spatial manner by intrinsic factors,extrinsic signals,and neural activities.The generation of correct subtypes and precise connections of projection neurons is imperative not only to support the basic cortical functions(such as sensory information integration,motor coordination,and cognition)but also to prevent the onset and progression of neurodevelopmental disorders(such as intellectual disability,autism spectrum disorders,anxiety,and depression).This review mainly focuses on the recent progress of transcriptional regulations on the development and diversity of neocortical projection neurons and the clinical relevance of the failure of transcriptional modulations. 展开更多
关键词 autism spectrum disorders COGNITION DIFFERENTIATION excitatory circuits intellectual disability NEOCORTEX neurodevelopmental disorders projection neuron specification transcriptional regulation
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Transcriptomic and physiological analyses identifying Lanzhou lily(Lilium davidii var.unicolor)drought adaptation strategies 被引量:7
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作者 Wenmei Li Yajun Wang +4 位作者 Heng Ren Zhihong Guo Na Li Chengzheng Zhao Zhongkui Xie 《Horticultural Plant Journal》 SCIE CAS CSCD 2023年第1期145-157,共13页
Drought stress is the main limiting plant growth factor in arid and semiarid regions.The Lanzhou lily(Lilium davidii var.unicolor)is the only sweet-tasting lily grown in these regions of China that offers highly edibl... Drought stress is the main limiting plant growth factor in arid and semiarid regions.The Lanzhou lily(Lilium davidii var.unicolor)is the only sweet-tasting lily grown in these regions of China that offers highly edible,medicinal,health,and ornamental value.The Tresor lily is an ornamental flower known for its strong resistance.Plants were grown under three different drought intensity treatments,namely,being watered at intervals of 5,15,and 25 d(either throughout the study or during specific growth stages).We measured the biomass,leaf area,photosynthetic response,chlorophyll content(SPAD value),and osmoregulation of both the Lanzhou lily and the Tresor lily(Lilium‘Tresor’).Additionally,we employed RNA sequencing(RNA-Seq)and qRT-PCR to investigate transcriptomic changes of the Lanzhou lily in response to drought stress.Results showed that under drought stress,the decreasing rate in the Lanzhou lily bulb weight was lower than the corresponding Tresor lily bulb rate;the net photosynthetic rate,transpiration rate,and stomatal conductance of the Lanzhou lily were all higher compared to the Tresor lily;osmoregulation constituents,such as glucose,fructose,sucrose,trehalose,and soluble sugar,in the Lanzhou lily were comparatively higher;PYL,NCED,and ERS genes were significantly expressed in the Lanzhou lily.Under moderate drought,the biosynthesis of flavonoids,circadian rhythms,and the tryptophan metabolism pathway of the Lanzhou lily were all significant.Under severe drought stress,fatty acid elongation,photosynthetic antenna protein,plant hormone signal transduction,flavone and flavonol biosynthesis,and the carotenoid biosynthesis pathway were all significant.The Lanzhou lily adapted to drought stress by coordinating its organs and the unique role of its bulb,regulating photosynthesis,increasing osmolyte content,activating circadian rhythms,signal transduction,fatty acid elongation metabolism,and phenylalanine and flavonoid metabolic pathways,which may collectively be the main adaptation strategy and mechanisms used by the Lanzhou lily under drought stress. 展开更多
关键词 Drought stress adaptation strategy OSMOLYTES Lanzhou lily Physiological characterization transcription profiles
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The BEL1-like transcription factor GhBLH5-A05 participates in cotton response to drought stress
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作者 Jing-Bo Zhang Yao Wang +4 位作者 Shi-Peng Zhang Fan Cheng Yong Zheng Yang Li Xue-Bao Li 《The Crop Journal》 SCIE CSCD 2024年第1期177-187,共11页
Drought stress impairs crop growth and development.BEL1-like family transcription factors may be involved in plant response to drought stress,but little is known of the molecular mechanism by which these proteins regu... Drought stress impairs crop growth and development.BEL1-like family transcription factors may be involved in plant response to drought stress,but little is known of the molecular mechanism by which these proteins regulate plant response and defense to drought stress.Here we show that the BEL1-like transcription factor GhBLH5-A05 functions in cotton(Gossypium hirsutum)response and defense to drought stress.Expression of GhBLH5-A05 in cotton was induced by drought stress.Overexpression of GhBLH5-A05 in both Arabidopsis and cotton increased drought tolerance,whereas silencing GhBLH5-A05 in cotton resulted in elevated sensitivity to drought stress.GhBLH5-A05 binds to cis elements in the promoters of GhRD20-A09 and GhDREB2C-D05 to activate the expression of these genes.GhBLH5-A05 interacted with the KNOX transcription factor GhKNAT6-A03.Co-expression of GhBLH5-A05 and GhKNAT6-A03 increased the transcription of GhRD20-A09 and GhDREB2C-D05.We conclude that GhBLH5-A05 acts as a regulatory factor with GhKNAT6-A03 functioning in cotton response to drought stress by activating the expression of the drought-responsive genes GhRD20-A09 and GhDREB2C-D05. 展开更多
关键词 Cotton(Gossypium hirsutum) BEL1-like transcription factor Drought stress transcriptional regulation Drought tolerance
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Comprehensive analysis of coding and non-coding RNA transcriptomes related to hypoxic adaptation in Tibetan chickens 被引量:7
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作者 Ying Zhang Woyu Su +3 位作者 Bo Zhang Yao Ling Woo Kyun Kim Hao Zhang 《Journal of Animal Science and Biotechnology》 SCIE CAS CSCD 2021年第4期1309-1322,共14页
Background:Tibetan chickens,a unique native breed in the Qinghai-Tibet Plateau of China,possess a suite of adaptive features that enable them to tolerate the high-altitude hypoxic environment.Increasing evidence sugge... Background:Tibetan chickens,a unique native breed in the Qinghai-Tibet Plateau of China,possess a suite of adaptive features that enable them to tolerate the high-altitude hypoxic environment.Increasing evidence suggests that long non-coding RNAs(lncRNAs)and microRNAs(miRNAs)play roles in the hypoxic adaptation of high-altitude animals,although their exact involvement remains unclear.Results:This study aimed to elucidate the global landscape of mRNAs,lncRNAs,and miRNAs using transcriptome sequencing to construct a regulatory network of competing endogenous RNAs(ceRNAs)and thus provide insights into the hypoxic adaptation of Tibetan chicken embryos.In total,354 differentially expressed genes(DE genes),389 differentially expressed lncRNAs(DE lncRNAs),and 73 differentially expressed miRNAs(DE miRNAs)were identified between Tibetan chickens(TC)and control Chahua chickens(CH).GO and KEGG enrichment analysis revealed that several important DE miRNAs and their target DE lncRNAs and DE genes are involved in angiogenesis(including blood vessel development and blood circulation)and energy metabolism(including glucose,carbohydrate,and lipid metabolism).The ceRNA network was then constructed with the predicted DE gene-DE miRNA-DE lncRNA interactions,which further revealed the regulatory roles of these differentially expressed RNAs during hypoxic adaptation of Tibetan chickens.Conclusions:Analysis of transcriptomic data revealed several key candidate ceRNAs that may play high-priority roles in the hypoxic adaptation of Tibetan chickens by regulating angiogenesis and energy metabolism.These results provide insights into the molecular mechanisms of hypoxic adaptation regulatory networks from the perspective of coding and non-coding RNAs. 展开更多
关键词 ceRNA Hypoxic adaptation Non-coding RNA Tibetan chicken transcriptOME
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Wild soybean(Glycine soja)transcription factor GsWRKY40 plays positive roles in plant salt tolerance
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作者 Minglong Li Man Xue +7 位作者 Huiying Ma Peng Feng Tong Chen Xiaohuan Sun Qiang Li Xiaodong Ding Shuzhen Zhang Jialei Xiao 《The Crop Journal》 SCIE CSCD 2024年第3期766-775,共10页
Wild soybean(Glycine soja),a relative of cultivated soybean,shows high adaptability to adverse environmental conditions.We identified and characterized a wild soybean transcription factor gene,GsWRKY40,that promotes p... Wild soybean(Glycine soja),a relative of cultivated soybean,shows high adaptability to adverse environmental conditions.We identified and characterized a wild soybean transcription factor gene,GsWRKY40,that promotes plant salt stress.GsWRKY40 was highly expressed in wild soybean roots and was up-regulated by salt treatment.GsWRKY40 was localized in nucleus and demonstrated DNA-binding activities but without transcriptional activation.Mutation and overexpression of GsWRKY40 altered salt tolerance of Arabidopsis plants.To understand the molecular mechanism of GsWRKY40 in regulating plant salt resistance,we screened a cDNA library and identified a GsWRKY40 interacting protein GsbHLH92 by using yeast two-hybrid approach.The physical interaction of GsWRKY40 and GsbHLH92 was confirmed by co-immunoprecipitation(co-IP),GST pull-down,and bimolecular fluorescence complementation(BiFC)techniques.Intriguingly,co-overexpression of GsWRKY40 and GsbHLH92 resulted in higher salt tolerance and lower ROS levels than overexpression of GsWRKY40 or GsbHLH92 in composite soybean plants,suggesting that GsWRKY40 and GsbHLH92 may synergistically regulate plant salt resistance through inhibiting ROS production.qRT-PCR data indicated that the expression level of GmSPOD1 gene encoding peroxidase was cooperatively regulated by GsWRKY40 and GsbHLH92,which was confirmed by using a dual luciferase report system and yeast one-hybrid experiment.Our study reveals a pathway that GsWRKY40 and GsbHLH92 collaboratively up-regulate plant salt resistance through impeding GmSPOD1 expression and reducing ROS levels,providing a novel perspective on the regulatory mechanisms underlying plant tolerance to abiotic stresses. 展开更多
关键词 Wild soybean transcription factor Salt stress ROS
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Roles of NAC transcription factors in cotton
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作者 XU Yuewei ZHAO Yunlei +3 位作者 CHEN Wei SANG Xiaohui ZHAO Pei WANG Hongmei 《Journal of Cotton Research》 CAS 2024年第3期289-301,共13页
Climate deterioration,water shortages,and abiotic stress are the main threats worldwide that seriously affect cotton growth,yield,and fiber quality.Therefore,research on improving cotton yield and tolerance to biotic ... Climate deterioration,water shortages,and abiotic stress are the main threats worldwide that seriously affect cotton growth,yield,and fiber quality.Therefore,research on improving cotton yield and tolerance to biotic and abiotic stresses is of great importance.The NAC proteins are crucial and plant-specific transcription factors(TFs)that are involved in cotton growth,development,and stress responses.The comprehensive utilization of cotton NAC TFs in the improvement of cotton varieties through novel biotechnological methods is feasible.Based on cotton genomic data,genome-wide identification and analyses have revealed potential functions of cotton NAC genes.Here,we comprehensively summarize the recent progress in understanding cotton NAC TFs roles in regulating responses to drought,salt,and Verticillium wilt-related stresses,as well as leaf senescence and the development of fibers,xylem,and glands.The detailed regulatory network of NAC proteins in cotton is also elucidated.Cotton NAC TFs directly bind to the promoters of genes associated with ABA biosynthesis and secondary cell-wall formation,participate in several biological processes by interacting with related proteins,and regulate the expression of downstream genes.Studies have shown that the overexpression of NAC TF genes in cotton and other model plants improve their drought or salt tolerance.This review elucidates the latest findings on the functions and regulation of cotton NAC proteins,broadens our understanding of cotton NAC TFs,and lays a fundamental foundation for further molecular breeding research in cotton. 展开更多
关键词 COTTON NAC transcription factor STRESS Regulatory network
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Meiotic transcriptional reprogramming mediated by cell-cell communications in humans and mice revealed by scATACseq and scRNA-seq
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作者 Hai-Quan Wang Xiao-Long Wu +6 位作者 Jing Zhang Si-Ting Wang Yong-Juan Sang Kang Li Chao-Fan Yang Fei Sun Chao-Jun Li 《Zoological Research》 SCIE CSCD 2024年第3期601-616,共16页
Meiosis is a highly complex process significantly influenced by transcriptional regulation.However,studies on the mechanisms that govern transcriptomic changes during meiosis,especially in prophase I,are limited.Here,... Meiosis is a highly complex process significantly influenced by transcriptional regulation.However,studies on the mechanisms that govern transcriptomic changes during meiosis,especially in prophase I,are limited.Here,we performed single-cell ATAC-seq of human testis tissues and observed reprogramming during the transition from zygotene to pachytene spermatocytes.This event,conserved in mice,involved the deactivation of genes associated with meiosis after reprogramming and the activation of those related to spermatogenesis before their functional onset.Furthermore,we identified 282 transcriptional regulators(TRs)that underwent activation or deactivation subsequent to this process.Evidence suggested that physical contact signals from Sertoli cells may regulate these TRs in spermatocytes,while secreted ENHO signals may alter metabolic patterns in these cells.Our results further indicated that defective transcriptional reprogramming may be associated with non-obstructive azoospermia(NOA).This study revealed the importance of both physical contact and secreted signals between Sertoli cells and germ cells in meiotic progression. 展开更多
关键词 Single-cell RNA-seq Single-cell ATAC-seq SPERMATOGENESIS MEIOSIS transcriptional reprogramming Cell-cell communication
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Sugarcane transcription factor ScWRKY4 negatively regulates resistance to pathogen infection through the JA signaling pathway
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作者 Dongjiao Wang Wei Wang +5 位作者 Shoujian Zang Liqian Qin Yanlan Liang Peixia Lin Yachun Su Youxiong Que 《The Crop Journal》 SCIE CSCD 2024年第1期164-176,共13页
WRKY transcription factors,transcriptional regulators unique to plants,play an important role in defense response to pathogen infection.However,the resistance mechanisms of WRKY genes in sugarcane remain unclear.In th... WRKY transcription factors,transcriptional regulators unique to plants,play an important role in defense response to pathogen infection.However,the resistance mechanisms of WRKY genes in sugarcane remain unclear.In 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 response.We identified gene ScWRKY4,a classⅡc member of the WRKY gene family,in sugarcane cultivar ROC22.This gene was induced by salicylic acid(SA)and methyl jasmonate(MeJA)stress.Interestingly,expression of ScWRKY4 was down-regulated in smut-resistant sugarcane cultivars but up-regulated in smutsusceptible sugarcane cultivars infected with Sporisorium scitamineum.Moreover,stable overexpression of the ScWRKY4 gene in Nicotiana benthamiana enhanced susceptibility to Fusarium solani var.coeruleum and caused down-regulated expression of immune marker-related genes.Transcriptome analysis indicated suppressed expression of most JAZ genes in the signal transduction pathway.ScWRKY4 interacted with ScJAZ13 to repress its expression.We thus hypothesized that the ScWRKY4 gene was involved in the regulatory network of plant disease resistance,most likely through the JA signaling pathway.The present study depicting the molecular involvement of ScWRKY4 in sugarcane disease resistance lays a foundation for future investigation. 展开更多
关键词 Disease resistance Expression profile transcriptome analysis WRKY transcription factors
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Cu Stress-Induced Transcriptome Alterations in Sorghum and Expression Analysis of the Transcription Factor-Encoding Gene SbWRKY24
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作者 Mingchuan Yang Jia Zheng +4 位作者 Wenhui Yu Yanghua Li YaliWang Zilu Zhang Zhenhui Kang 《Phyton-International Journal of Experimental Botany》 SCIE 2024年第7期1503-1521,共19页
Sorghum is not only an important bio-energy crop but also a vital raw material for brewing.Exogenous copper affects the growth and metabolism of crops in specific ways.This study identified 8475 differentially expressed... Sorghum is not only an important bio-energy crop but also a vital raw material for brewing.Exogenous copper affects the growth and metabolism of crops in specific ways.This study identified 8475 differentially expressed genes(DEGs)by high-throughput transcriptome sequencing in the sorghum cultivar‘Jinnuoliang 2’after 24 h of treatment with 10 mM CuSO4.Using GO analysis,476 genes were functionally annotated,which were mainly related to catabolism and biosynthetic processes.Additionally,90 pathways were annotated by employing the KEGG analysis.Among them,glutathione metabolism and peroxisome were induced,while photosynthesis,photosynthesis-antenna protein,and carbon sequestration of photosynthetic organisms were inhibited.Of the DEGs,399 were identified to encode transcription factors belonging to 49 families.This study also identified a WRKY transcription factor-encoding gene SbWRKY24 from the transcriptome data.For studying its function,the relative expression levels of SbWRKY24 in roots and leaves post-treatment with different growth hormones and exposure to a variety of abiotic stresses were detected by RT-qPCR.SbWRKY24 showed treatment-and tis-sue-specific expression patterns,indicating its unique role in stress tolerance.This study lays a theoretical basis for the functional exploration of SbWRKY24,elucidating the mechanism of copper resistance,and elaborating on the stress responses in sorghum.It also guides the exploration of the molecular mechanism of copper ions inducing intracellular signal transduction pathways. 展开更多
关键词 SORGHUM copper stress transcriptOME transcription factor SbWRKY24
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Gene expression,transcription factor binding and histone modification predict leaf adaxial-abaxial polarity related genes
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作者 Wei Sun Zhicheng Zhang +2 位作者 Guusje Bonnema Xiaowu Wang Aalt Dirk Jan van Dijk 《Horticultural Plant Journal》 SCIE CAS CSCD 2024年第4期971-982,共12页
Leaf adaxial-abaxial(ad-abaxial)polarity is crucial for leaf morphology and function,but the genetic machinery governing this process remains unclear.To uncover critical genes involved in leaf ad-abaxial patterning,we... Leaf adaxial-abaxial(ad-abaxial)polarity is crucial for leaf morphology and function,but the genetic machinery governing this process remains unclear.To uncover critical genes involved in leaf ad-abaxial patterning,we applied a combination of in silico prediction using machine learning(ML)and experimental analysis.A Random Forest model was trained using genes known to influence ad-abaxial polarity as ground truth.Gene expression data from various tissues and conditions as well as promoter regulation data derived from transcription factor chromatin immunoprecipitation sequencing(ChIP-seq)was used as input,enabling the prediction of novel ad-abaxial polarity-related genes and additional transcription factors.Parallel to this,available and newly-obtained transcriptome data enabled us to identify genes differentially expressed across leaf ad-abaxial sides.Based on these analyses,we obtained a set of 111 novel genes which are involved in leaf ad-abaxial specialization.To explore implications for vegetable crop breeding,we examined the conservation of expression patterns between Arabidopsis and Brassica rapa using single-cell transcriptomics.The results demonstrated the utility of our computational approach for predicting candidate genes in crop species.Our findings expand the understanding of the genetic networks governing leaf ad-abaxial differentiation in agriculturally important vegetables,enhancing comprehension of natural variation impacting leaf morphology and development,with demonstrable breeding applications. 展开更多
关键词 Machine learning Leaf polarity Arabidopsis thaliana Brassica rapa transcription factor
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The Magnaporthe oryzae effector Avr-PikD suppresses rice immunity by inhibiting an LSD1-like transcriptional activator
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作者 Jiayuan Guo Yiling Wu +8 位作者 Jianqiang Huang Kaihui Yu Meilian Chen Yijuan Han Zhenhui Zhong Guodong Lu Yonghe Hong Zonghua Wang Xiaofeng Chen 《The Crop Journal》 SCIE CSCD 2024年第2期482-492,共11页
Avirulence effectors(Avrs),encoded by plant pathogens,can be recognized by plants harboring the corresponding resistance proteins,thereby initiating effector-triggered immunity(ETI).In susceptible plants,however,Avrs ... Avirulence effectors(Avrs),encoded by plant pathogens,can be recognized by plants harboring the corresponding resistance proteins,thereby initiating effector-triggered immunity(ETI).In susceptible plants,however,Avrs can function as effectors,facilitating infection via effector-triggered susceptibility(ETS).Mechanisms of Avr-mediated ETS remain largely unexplored.Here we report that the Magnaporthe oryzae effector Avr-PikD enters rice cells via the canonical cytoplasmic secretion pathway and suppresses rice basal defense.Avr-PikD interacts with an LSD1-like transcriptional activator AKIP30 of rice,and AKIP30 is also a positive regulator of rice immunity,whereas Avr-PikD impedes its nuclear localization and suppresses its transcriptional activity.In summary,M.oryzae delivers Avr-PikD into rice cells to facilitate ETS by inhibiting AKIP30-mediated transcriptional regulation of immune response against M.oryzae. 展开更多
关键词 Magnaporthe oryzae Avirulence effector Avr-PikD Effector-triggered susceptibility Rice immunity transcriptional activator
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Prognostic significance of oligodendrocyte transcription factor 2 expression in glioma patients:A systematic review and metaanalys
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作者 Peng-Cheng Li De-Bo Yun +1 位作者 Ya-Xin Huang Qian-Yi Huang 《World Journal of Clinical Cases》 SCIE 2024年第25期5739-5748,共10页
BACKGROUND Gliomas are the most common primary central nervous system neoplasm.Despite recent advances in the diagnosis and treatment of gliomas,patient prognosis remains dismal.Therefore,it is imperative to identify ... BACKGROUND Gliomas are the most common primary central nervous system neoplasm.Despite recent advances in the diagnosis and treatment of gliomas,patient prognosis remains dismal.Therefore,it is imperative to identify novel diagnostic biomarkers and therapeutic targets of glioma to effectively improve treatment outcomes.AIM To investigate the association between oligodendrocyte transcription factor 2(Olig2)expression and the outcomes of glioma patients.METHODS The PubMed,Embase,Cochrane Library,and China National Knowledge Infrastructure databases were searched for studies(published up to October 2023)that investigated the relationship between Olig2 expression and prognosis of glioma patients.The quality of the studies was assessed using the Newcastle Ottawa Scale.Data analyses were performed using Stata Version 12.0 software.RESULTS A total of 1205 glioma patients from six studies were included in the metaanalysis.High Olig2 expression was associated with better outcomes in glioma patients[hazard ratio(HR):0.81;95%(confidence interval)CI:0.51-1.27;P=0.000].Furthermore,the results of subgroup meta-analysis showed that high expression of Olig2 was associated with poor overall survival in European patients(HR:1.34;95%CI:0.79-2.27)and better prognosis in Asian patients(HR:0.43;95%CI:0.22-0.84).The sensitivity analysis showed that no single study had a significant effect on pooled HR,and there was also no indication of publication bias according to the Egger’s and Begger’s P value test or funnel plot test.CONCLUSION High Olig2 expression may have a positive impact on the prognosis of glioma patients,and should be investigated further as a prognostic biomarker and therapeutic target for glioma. 展开更多
关键词 GLIOMA Oligodendrocyte transcription factor 2 PROGNOSIS BIOMARKER META-ANALYSIS
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Population genomic data reveal low genetic diversity,divergence and local adaptation among threatened Reeves's Pheasant(Syrmaticus reevesii)
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作者 Qi Lu Pengcheng Wang +4 位作者 Jiang Chang De Chen Shenghan Gao Jacob Hoglund Zhengwang Zhang 《Avian Research》 SCIE CSCD 2024年第1期1-11,共11页
Population genomic data could provide valuable information for conservation efforts;however,limited studies have been conducted to investigate the genetic status of threatened pheasants.Reeves’s Pheasant(Syrmaticus r... Population genomic data could provide valuable information for conservation efforts;however,limited studies have been conducted to investigate the genetic status of threatened pheasants.Reeves’s Pheasant(Syrmaticus reevesii)is facing population decline,attributed to increases in habitat loss.There is a knowledge gap in understanding the genomic status and genetic basis underlying the local adaptation of this threatened bird.Here,we used population genomic data to assess population structure,genetic diversity,inbreeding patterns,and genetic divergence.Furthermore,we identified candidate genes linked with adaptation across the current distribution of Reeves’s Pheasant.The present study assembled the first de novo genome sequence of Reeves’s Pheasant and annotated 19,458 genes.We also sequenced 30 individuals from three populations(Dabie Mountain,Shennongjia,Qinling Mountain)and found that there was clear population structure among those populations.By comparing with other threatened species,we found that Reeves’s Pheasants have low genetic diversity.Runs of homozygosity suggest that the Shennongjia population has experienced serious inbreeding.The demographic history results indicated that three populations experienced several declines during the glacial period.Local adaptative analysis among the populations identified 241 candidate genes under directional selection.They are involved in a large variety of processes,including the immune response and pigmentation.Our results suggest that the three populations should be considered as three different conservation units.The current study provides genetic evidence for conserving the threatened Reeves’s Pheasant and provides genomic resources for global biodiversity management. 展开更多
关键词 Conservation genetics Local adaptation PHEASANT Whole-genome sequencing
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Irrigated Agriculture Facing the Challenge of Climate Change: Adaptation Strategies for Farmers in the Irrigated Perimeters of Môle Saint-Nicolas, Haiti
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作者 Frantz Mial Jean-François Bissonnette +1 位作者 Marc-André Bourgault Meryem Qacami 《American Journal of Climate Change》 2024年第3期477-498,共22页
Môle Saint-Nicolas, like all other communes in the Republic of Haiti, faces increasing climate variability, impacting agricultural production and water resources. Consequently, there is a pressing need for adapta... Môle Saint-Nicolas, like all other communes in the Republic of Haiti, faces increasing climate variability, impacting agricultural production and water resources. Consequently, there is a pressing need for adaptation to these climatic changes. This research aims to showcase the adaptation strategies deployed by farmers to cope with the increasing climate variability. Surveys were conducted through group and individual discussions with a randomly selected cohort of 150 farmers. Two types of analysis were performed: quantitative and qualitative. The quantitative data analysis was conducted using Statistical Package for the Social Sciences (SPSS) software. The findings reveal that farmers have perceived changes in rainfall patterns, temperature, wind, and their environment. These changes manifest as irregular rainfall, higher temperatures, prolonged drought periods, violent winds accompanied by rain, premature cessation of rains, and reduced flow from water sources. In response, the most common adaptation strategies adopted include selecting new cultivars, early-maturing varieties, crop rotation and diversification, canal dredging, new soil preparation methods, upstream water source protection, and micro-watershed management. The significance of this research lies in its contribution to enhancing farmers’ adaptive capacities by alerting stakeholders in the irrigated perimeters about the consequences of climate change, thereby incorporating the real needs of farmers in future projects. 展开更多
关键词 Climate Change Perception adaptation Agriculture Irrigated Perimeter
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The ABA synthesis enzyme allele OsNCED2^(T)promotes dryland adaptation in upland rice
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作者 Liyu Huang Yachong Bao +9 位作者 Shiwen Qin Min Ning Qinyan Li Qingmao Li Shilai Zhang Guangfu Huang Jing Zhang Wensheng Wang Binying Fu Fengyi Hu 《The Crop Journal》 SCIE CSCD 2024年第1期68-78,共11页
Upland rice shows dryland adaptation in the form of a deeper and denser root system and greater drought resistance than its counterpart,irrigated rice.Our previous study revealed a difference in the frequency of the O... Upland rice shows dryland adaptation in the form of a deeper and denser root system and greater drought resistance than its counterpart,irrigated rice.Our previous study revealed a difference in the frequency of the OsNCED2 gene between upland and irrigated populations.A nonsynonymous mutation(C to T,from irrigated to upland rice)may have led to functional variation fixed by artificial selection,but the exact biological function in dryland adaptation is unclear.In this study,transgenic and association analysis indicated that the domesticated fixed mutation caused functional variation in OsNCED2,increasing ABA levels,root development,and drought tolerance in upland rice under dryland conditions.OsNCED2-overexpressing rice showed increased reactive oxygen species-scavenging abilities and transcription levels of many genes functioning in stress response and development that may regulate root development and drought tolerance.OsNCED2^(T)-NILs showed a denser root system and drought resistance,promoting the yield of rice under dryland conditions.OsNCED2^(T)may confer dryland adaptation in upland rice and may find use in breeding dryland-adapted,water-saving rice. 展开更多
关键词 Upland rice Dryland adaptation ABA Root development Drought tolerance
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Exercise-induced adaptation of neurons in the vertebrate locomotor system
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作者 Yue Dai Yi Cheng +2 位作者 Renkai Ge Ke Chen Liming Yang 《Journal of Sport and Health Science》 SCIE CAS CSCD 2024年第2期160-171,共12页
Vertebrate neurons are highly dynamic cells that undergo several alterations in their functioning and physiologies in adaptation to various external stimuli.In particular,how these neurons respond to physical exercise... Vertebrate neurons are highly dynamic cells that undergo several alterations in their functioning and physiologies in adaptation to various external stimuli.In particular,how these neurons respond to physical exercise has long been an area of active research.Studies of the vertebrate locomotor system’s adaptability suggest multiple mechanisms are involved in the regulation of neuronal activity and properties during exercise.In this brief review,we highlight recent results and insights from the field with a focus on the following mechanisms:(a)alterations in neuronal excitability during acute exercise;(b)alterations in neuronal excitability after chronic exercise;(c)exercise-induced changes in neuronal membrane properties via modulation of ion channel activity;(d)exercise-enhanced dendritic plasticity;and(e)exercise-induced alterations in neuronal gene expression and protein synthesis.Our hope is to update the community with a cellular and molecular understanding of the recent mechanisms underlying the adaptability of the vertebrate locomotor system in response to both acute and chronic physical exercise. 展开更多
关键词 Dendritic plasticity EXCITABILITY Exercise Ion channel modulation Neuron adaptation
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