8,440 results on '"Zhong and"'
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2. Honey bee (Apis cerana) queen rearing methods influence queen morphological characteristics and reproductive related gene expression
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Zhong, Wei-Lai, Ding, Gui-Ling, Yuan, Chun-Ying, Huang, Jia-Xing, and Feng, Mao
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- 2024
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3. A gene silencing screen uncovers diverse tools for targeted gene repression in Arabidopsis.
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Wang, Ming, Zhong, Zhenhui, Gallego-Bartolomé, Javier, Li, Zheng, Feng, Suhua, Kuo, Hsuan Yu, Kan, Ryan L, Lam, Hoiyan, Richey, John Curtis, Tang, Linli, Zhou, Jessica, Liu, Mukun, Jami-Alahmadi, Yasaman, Wohlschlegel, James, and Jacobsen, Steven E
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Arabidopsis ,Histones ,Arabidopsis Proteins ,Gene Expression ,Gene Expression Regulation ,Plant ,Gene Silencing ,Biotechnology ,Human Genome ,Genetics ,Plant Biology ,Crop and Pasture Production - Abstract
DNA methylation has been utilized for target gene silencing in plants. However, it is not well understood whether other silencing pathways can be also used to manipulate gene expression. Here we performed a gain-of-function screen for proteins that could silence a target gene when fused to an artificial zinc finger. We uncovered many proteins that suppressed gene expression through DNA methylation, histone H3K27me3 deposition, H3K4me3 demethylation, histone deacetylation, inhibition of RNA polymerase II transcription elongation or Ser-5 dephosphorylation. These proteins also silenced many other genes with different efficacies, and a machine learning model could accurately predict the efficacy of each silencer on the basis of various chromatin features of the target loci. Furthermore, some proteins were also able to target gene silencing when used in a dCas9-SunTag system. These results provide a more comprehensive understanding of epigenetic regulatory pathways in plants and provide an armament of tools for targeted gene manipulation.
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- 2023
4. A novel approach to assess the health risk of aryl hydrocarbon receptor-bound contaminants via inhalation exposure using CYP1A1 expression as a biomarker
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Huixia Zhong, Lili Yu, Xiaomei Lv, Yingxin Yu, and Junjie Hu
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Dose-response curve ,Gene expression ,Toxic equivalence factor ,Contributor ,Environmental pollution ,TD172-193.5 ,Environmental sciences ,GE1-350 - Abstract
Polycyclic aromatic hydrocarbons (PAHs) and dioxins are potential causes of multiple diseases by activating the aryl hydrocarbon receptor (AhR) pathway. Health risk assessment of chemicals primarily relies on the relative potency factor (RPF), although its accuracy may be limited when solely using EC50 values. The induction of cytochrome P4501A1 (CYP1A1) serves as a biomarker for AhR activation and is an integrator of dioxin-like toxicity. Here, we present a method for evaluating the risks associated with AhR activation using mathematical models of dose-CYP1A1 induction. The dose-effect curves for certain PAHs and dioxins, including Ant, BghiP, 1,2,3,4,7,8-HxCDD, and others, exhibited a non-classical S-shaped form. The toxic equivalent factor (TEF) profiles revealed a broad range of toxic equivalent factor values. The TEFs for PAHs ranged from approximately 0.01 to 6, with higher values being observed when the concentration was less than 10−10 M, with the exceptions of Ace, Phe, and BghiP. Most congeners of dioxins got the lowest TEF value at around 10−10 M, ranging from 0.04 to 1.00. The binding affinity of AhR to ligands did not display a strong correlation with the EC50 of CYP1A1 expression, suggesting that the AhR-mediated effects of PAHs and dioxins are not fixed but instead fluctuate with the dose. Air samples acquired from a parking area were used to compare the proficiency of RPF and our current approach. In the current method, naphthalene and chrysene were the primary contributors of PAHs to AhR-mediated risks in parking lots air samples, respectively. However, the contributions of naphthalene and chrysene could be disregarded in the RPF approach.
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- 2024
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5. Statistical Genomics Analysis of Simple Sequence Repeats from the Paphiopedilum Malipoense Transcriptome Reveals Control Knob Motifs Modulating Gene Expression
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Yingyi Liang, Jing Hao, Jieyu Wang, Guoqiang Zhang, Yingjuan Su, Zhong‐Jian Liu, and Ting Wang
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full‐length transcriptomes ,gene expression ,motif types ,Paphiopedilum malipoense ,simple sequence repeats (SSRs) ,Science - Abstract
Abstract Simple sequence repeats (SSRs) are found in nonrandom distributions in genomes and are thought to impact gene expression. The distribution patterns of 48 295 SSRs of Paphiopedilum malipoense are mined and characterized based on the first full‐length transcriptome and comprehensive transcriptome dataset from 12 organs. Statistical genomics analyses are used to investigate how SSRs in transcripts affect gene expression. The results demonstrate the correlations between SSR distributions, characteristics, and expression level. Nine expression‐modulating motifs (expMotifs) are identified and a model is proposed to explain the effect of their key features, potency, and gene function on an intra‐transcribed region scale. The expMotif‐transcribed region combination is the most predominant contributor to the expression‐modulating effect of SSRs, and some intra‐transcribed regions are critical for this effect. Genes containing the same type of expMotif‐SSR elements in the same transcribed region are likely linked in function, regulation, or evolution aspects. This study offers novel evidence to understand how SSRs regulate gene expression and provides potential regulatory elements for plant genetic engineering.
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- 2024
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6. Selection on the promoter regions plays an important role in complex traits during duck domestication
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Zhong-Tao Yin, Xiao-Qin Li, Yun-Xiao Sun, Jacqueline Smith, Maxwell Hincke, Ning Yang, and Zhuo-Cheng Hou
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Promoter ,Accumulated variants ,Gene expression ,Domestication ,Duck ,Biology (General) ,QH301-705.5 - Abstract
Abstract Background Identifying the key factors that underlie complex traits during domestication is a great challenge for evolutionary and biological studies. In addition to the protein-coding region differences caused by variants, a large number of variants are located in the noncoding regions containing multiple types of regulatory elements. However, the roles of accumulated variants in gene regulatory elements during duck domestication and economic trait improvement are poorly understood. Results We constructed a genomics, transcriptomics, and epigenomics map of the duck genome and assessed the evolutionary forces that have been in play across the whole genome during domestication. In total, 304 (42.94%) gene promoters have been specifically selected in Pekin duck among all selected genes. Joint multi-omics analysis reveals that 218 genes (72.01%) with selected promoters are located in open and active chromatin, and 267 genes (87.83%) with selected promoters were highly and differentially expressed in domestic trait-related tissues. One important candidate gene ELOVL3, with a strong signature of differentiation on the core promoter region, is known to regulate fatty acid elongation. Functional experiments showed that the nearly fixed variants in the top selected ELOVL3 promoter in Pekin duck decreased binding ability with HLF and increased gene expression, with the overexpression of ELOVL3 able to increase lipid deposition and unsaturated fatty acid enrichment. Conclusions This study presents genome resequencing, RNA-Seq, Hi-C, and ATAC-Seq data of mallard and Pekin duck, showing that selection of the gene promoter region plays an important role in gene expression and phenotypic changes during domestication and highlights that the variants of the ELOVL3 promoter may have multiple effects on fat and long-chain fatty acid content in ducks.
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- 2023
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7. Selection on the promoter regions plays an important role in complex traits during duck domestication
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Yin, Zhong-Tao, Li, Xiao-Qin, Sun, Yun-Xiao, Smith, Jacqueline, Hincke, Maxwell, Yang, Ning, and Hou, Zhuo-Cheng
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- 2023
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8. Regulatory mechanism of LncRNAs in gonadal differentiation of hermaphroditic fish, Monopterusalbus
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Hu, Qiaomu, Xia, Xueping, Lian, Zitong, Tian, Haifeng, and Li, Zhong
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- 2023
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9. Von Hippel Lindau tumor suppressor controls m6A-dependent gene expression in renal tumorigenesis
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Zhang, Cheng, Yu, Miaomiao, Hepperla, Austin J., Zhang, Zhao, Raj, Rishi, Zhong, Hua, Zhou, Jin, Hu, Lianxin, Fang, Jun, Liu, Hongyi, Liang, Qian, Jia, Liwei, Liao, Chengheng, Xi, Sichuan, Simon, Jeremy M., Xu, Kexin, Liu, Zhijie, Nam, Yunsun, Kapur, Payal, and Zhang, Qing
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Thermo Fisher Scientific Inc. ,Scientific equipment and supplies industry ,Gene expression ,Genetic research ,RNA sequencing ,Messenger RNA ,Ligases ,Cancer ,Methyltransferases ,Health care industry - Abstract
N6-Methyladenosine (m6A) is the most abundant posttranscriptional modification, and its contribution to cancer evolution has recently been appreciated. Renal cancer is the most common adult genitourinary cancer, approximately 85% of which is accounted for by the clear cell renal cell carcinoma (ccRCC) subtype characterized by VHL loss. However, it is unclear whether VHL loss in ccRCC affects m6A patterns. In this study, we demonstrate that VHL binds and promotes METTL3/METTL14 complex formation while VHL depletion suppresses m6A modification, which is distinctive from its canonical E3 ligase role. m6A RNA immunoprecipitation sequencing (RIP-Seq) coupled with RNA-Seq allows us to identify a selection of genes whose expression may be regulated by VHL-m6A signaling. Specifically, PIK3R3 is identified to be a critical gene whose mRNA stability is regulated by VHL in a m6A-dependent but HIF-independent manner. Functionally, PIK3R3 depletion promotes renal cancer cell growth and orthotopic tumor growth while its overexpression leads to decreased tumorigenesis. Mechanistically, the VHL-m6A-regulated PIK3R3 suppresses tumor growth by restraining PI3K/AKT activity. Taken together, we propose a mechanism by which VHL regulates m6A through modulation of METTL3/METTL14 complex formation, thereby promoting PIK3R3 mRNA stability and protein levels that are critical for regulating ccRCC tumorigenesis., Introduction Estimated new cases and deaths from renal cancer in the US for 2020 were 73,750 and 14,830 respectively (1). Kidney cancer incidence has been steadily increasing over the past [...]
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- 2024
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10. METTL14-mediated m6A epitranscriptomic modification contributes to chemotherapy-induced neuropathic pain by stabilizing GluN2A expression via IGF2BP2
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Lu, Weicheng, Yang, Xiaohua, Zhong, Weiqiang, Chen, Guojun, Guo, Xinqi, Ye, Qingqing, Xu, Yixin, Qi, Zhenhua, Ye, Yaqi, Zhang, Jingyun, Wang, Yuge, Wang, Xintong, Wang, Shu, Zhao, Qiyue, Zeng, Weian, Huang, Junting, Ma, Huijie, and Xie, Jingdun
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Thermo Fisher Scientific Inc. ,Methyl aspartate ,Genes ,Aspartate ,Chemotherapy ,Pain -- Care and treatment ,Cancer -- Chemotherapy ,Neurons ,Scientific equipment and supplies industry ,Gene expression ,Methylation ,Methyltransferases ,Epigenetic inheritance ,Neurophysiology ,Health care industry - Abstract
Epigenetics is a biological process that modifies and regulates gene expression, affects neuronal function, and contributes to pain. However, the mechanism by which epigenetics facilitates and maintains chronic pain is poorly understood. We aimed to determine whether [N.sup.6]-methyladenosine (m6A) specifically modified by methyltransferase-like 14 (METTL14) alters neuronal activity and governs pain by sensitizing the GluN2A subunit of the N-methyl-D-aspartate receptor (NMDAR) in the dorsal root ganglion (DRG) neurons in a model of chemotherapy-induced neuropathic pain (CINP). Using dot blotting, immunofluorescence, gain/loss-of-function, and behavioral assays, we found that m6A levels were upregulated in L4-L6 DRG neurons in CINP in a DBP/METTL14-dependent manner, which was also confirmed in human DRGs. Blocking METTL14 reduced m6A methylation and attenuated pain hypersensitivity. Mechanistically, METTL14-mediated m6A modification facilitated the synaptic plasticity of DRG neurons by enhancing the GluN2A subunit of NMDAR, and inhibiting METTL14 blocked this effect. In contrast, overexpression of METTL14 upregulated m6A modifications, enhanced presynaptic NMDAR activity in DRG neurons, and facilitated pain sensation. Our findings reveal a previously unrecognized mechanism of METTL14-mediated m6A modification in DRG neurons to maintain neuropathic pain. Targeting these molecules may provide a new strategy for pain treatment., Introduction Chemotherapy-induced neuropathic pain (CINP) is a debilitating complication caused by damage to the peripheral nervous system by chemotherapeutic agents, including paclitaxel (1). CINP occurs in approximately 50% to 90% [...]
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- 2024
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11. Regulatory mechanism of LncRNAs in gonadal differentiation of hermaphroditic fish, Monopterus albus
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Qiaomu Hu, Xueping Xia, Zitong Lian, Haifeng Tian, and Zhong Li
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Monopterus albus ,LncRNA ,DNA methylation ,Sex reversal ,Gene expression ,Medicine ,Physiology ,QP1-981 - Abstract
Abstract Background Monopterus albus is a hermaphroditic fish with sex reversal from ovaries to testes via the ovotestes in the process of gonadal development, but the molecular mechanism of the sex reversal was unknown. Methods We produced transcriptomes containing mRNAs and lncRNAs in the crucial stages of the gonad, including the ovary, ovotestis and testis. The expression of the crucial lncRNAs and their target genes was detected using qRT‒PCR and in situ hybridization. The methylation level and activity of the lncRNA promoter were analysed by applying bisulfite sequencing PCR and dual-luciferase reporter assays, respectively. Results This effort revealed that gonadal development was a dynamic expression change. Regulatory networks of lncRNAs and their target genes were constructed through integrated analysis of lncRNA and mRNA data. The expression and DNA methylation of the lncRNAs MSTRG.38036 and MSTRG.12998 and their target genes Psmβ8 and Ptk2β were detected in developing gonads and sex reversal gonads. The results showed that lncRNAs and their target genes exhibited consistent expression profiles and that the DNA methylation levels were negatively regulated lncRNA expression. Furthermore, we found that Ptk2β probably regulates cyp19a1 expression via the Ptk2β/EGFR/STAT3 pathway to reprogram sex differentiation. Conclusions This study provides novel insight from lncRNA to explore the potential molecular mechanism by which DNA methylation regulates lncRNA expression to facilitate target gene transcription to reprogram sex differentiation in M. albus, which will also enrich the sex differentiation mechanism of teleosts.
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- 2023
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12. Manganese-superoxide dismutase (MnSOD) rescues redox balance and mucosal barrier function in midgut of hybrid fish (Carassius cuvieri ♀ × Carassius auratus red var ♂) infected with Aeromonas hydrophila and Edwardsiella tarda
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Jie Ou, Wei-Sheng Luo, Zi-Rou Zhong, Qing Xie, Fei Wang, Ning-Xia Xiong, and Sheng-Wei Luo
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Crucian carp ,MnSOD ,Gut immunity ,Gene expression ,Genetics ,QH426-470 ,Reproduction ,QH471-489 ,Animal biochemistry ,QP501-801 - Abstract
MnSOD is a ubiquitous metalloenzyme that constitutes the first line of antioxidant defense against oxidative stress. In this study, full length sequence of MnSOD was identified from hybrid crucian carp (WR, Carassius cuvieri ♀ × Carassius auratus red var ♂). Tissue-specific analysis revealed that the highest expression of WR-MnSOD was detected in kidney. Aeromonas hydrophila challenge could dramatically enhance WR-MnSOD mRNA expression in tissues. In vivo administration of purified WR-MnSOD peptide could maintain gut mucosal barrier function, rescue redox balance as well as decrease apoptotic cell death in midgut upon bacterial infection, suggesting that WR-MnSOD is playing a crucial role in gut mucosal barrier function and could be used as feed additive to improve gut immunity in fish.
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- 2023
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13. Effect of Three Novel Thiazolidiones on the Development, Reproduction, and Trehalase Activity of Spodoptera frugiperda (Lepidoptera: Noctuidae)
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Liuhe Yu, Fan Zhong, Xinyi Jiang, Biner He, Haoyu Fu, Xiangyu Liu, Qixuan Mao, Ying Zhao, Shigui Wang, Yan Wu, Hongxia Duan, and Bin Tang
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trehalase inhibitors ,gene expression ,insect physiology ,chitin ,piperine compounds ,Agriculture - Abstract
Spodoptera frugiperda was used to investigate its role as a trehalase inhibitor of three new thiothiazolidone compounds—6d, 6e, and 6f. The development and reproduction of S. frugiperda were investigated to evaluate the potential of these compounds as a novel pesticide for pest control. Compounds 6d, 6e, and 6f were injected into larvae and female pupae. Molecular changes in trehalose and chitin metabolism genes were monitored. Pupal trehalase activity, the female pupal emergence rate, ovarian development, and SfVg and SfVgR gene expression levels were assessed. The results revealed that all three compounds significantly inhibited trehalase activity in the larvae. The expression of TRE was significantly downregulated, and compounds 6d and 6f significantly downregulated the expression of TRE2. Treated larvae exhibited significantly decreased survival rates and a higher incidence of abnormalities. The egg production and hatching rates were markedly diminished by the inhibitors, and the ovaries displayed blackening and clumping. These compounds exhibit promise as eco-friendly insecticides, but further experiments are required to test their multifaceted capabilities.
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- 2024
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14. Nonadditive and allele-specific expression of ghrelin in hybrid tilapia
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Huan Zhong, Bingxin Ren, Chenyi Lou, Yi Zhou, Yongju Luo, and Jun Xiao
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ghrelin ,hybrid tilapia ,nonadditive expression ,gene expression ,heterosis ,Diseases of the endocrine glands. Clinical endocrinology ,RC648-665 - Abstract
BackgroundInterspecies hybridization is an important breeding method to generate fishes with heterosis in aquaculture. Using this method, hybrid Nile tilapia (Oreochromis niloticus, ♀) × blue tilapia (Oreochromis aureus, ♂) has been produced and widely farmed due to its growth and appetite superiorities. However, the genetic mechanism of these advanced traits is still not well understood. Ghrelin is a crucial gene that regulates growth and appetite in fishes. In the present study, we focused on the expression characteristics and its regulation of ghrelin in the hybrid.ResultsThe tissue distribution analysis showed that ghrelin was predominantly expressed in the stomach in the hybrid. Ghrelin was more highly expressed in the stomach in the hybrid and Nile tilapia, compared to blue tilapia, showing a nonadditive pattern. Two single-nucleotide polymorphism (SNP) sites were identified including T/C and C/G from the second exon in the ghrelin gene from Nile tilapia and blue tilapia. By pyrosequencing based on the SNP sites, the allele-specific expression (ASE) of ghrelin in the hybrid was assayed. The result indicated that ghrelin in the hybrid showed higher maternal allelic transcript ratios. Fasting significantly increased ghrelin overall expression at 4, 8, 12, 24, and 48 h. In addition, higher maternal allelic transcript ratios were not changed in the fasting hybrids at 48 h. The cis and trans effects were determined by evaluating the overall expression and ASE values in the hybrid. The expression of ghrelin was mediated by compensating cis and trans effects in hybrid.ConclusionIn summary, the present lines of evidence showed the nonadditive expression of ghrelin in the hybrid tilapia and its regulation by subgenomes, offering new insight into gene expression characteristics in hybrids.
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- 2023
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15. Short-term warming-induced increase in non-microbial carbon emissions from semiarid abandoned farmland soils
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Zekun Zhong, Xing Wang, Gaihe Yang, Xinhui Han, Lin Zhu, and Rentao Liu
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Climate change ,Carbon emission ,Soil metagenomics ,Gene expression ,Microbial metabolism ,Ecology ,QH540-549.5 - Abstract
Soil warming is expected to accelerate microbial carbon (C) degradation, increasing carbon dioxide (CO2) emissions. This process greatly contributes to global warming. To validate this positive feedback loop in semiarid restored ecosystems, we examined the effects of 2 years of open-top chamber warming on soil CO2 efflux (soil respiration) and microbial metabolic characteristics in abandoned farmland on the Chinese Loess Plateau. Soil warming of 1.3 °C above ambient at 10 cm depth significantly stimulated CO2 emissions by 40.5 %. Despite short-term warming alleviating the C (energy) limitation on microbial activity, no substantial differences in microbial C use efficiency or biomass turnover rate were noted compared to those in the control. Importantly, we found little evidence that warming altered the expression levels of carbohydrate metabolism genes annotated using the eggNOG, KEGG, and CAZy databases. All expressed genes targeting the degradation of diverse carbonaceous components were assigned to bacterial taxa unaffected by warming. Therefore, short-term warming stimulated soil CO2 emissions from non-microbial sources but did not drive the abandoned farmland in the reverse direction to a C source. Our findings highlight the importance of conducting long-term comparisons of microbial metabolic profiles and soil respiration components to elucidate the mechanisms underlying changes in C-cycling in ecosystems that have undergone restoration and experienced warming.
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- 2023
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16. Consecutive Pruning Enhances Leaf Flavonoids, Leaf Yield, and Cutting Rooting in Ginkgo biloba
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Lei Zhong, Shiyuan Xu, Shuwen Xu, Wanxiang Zhou, Zhaogeng Lu, Biao Jin, and Li Wang
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pruning intensity ,cutting rooting ,gene expression ,flavonoid compounds ,plant regeneration ,Plant ecology ,QK900-989 - Abstract
Ginkgo biloba L. is a valuable medicinal plant known for its high content of flavonoids and terpenoids in the leaves of young trees. Pruning can increase leaf yield in ginkgo plantations; however, it is unclear how the intensity of pruning affects leaf yield and quality. In addition, G. biloba exhibits low cutting rooting rates, which limits its efficiency in asexual propagation. In our study, we compared consecutive pruning with varying levels of intensity, including top pruning, light pruning, and heavy pruning, to evaluate the effects of pruning on leaf yield and cutting rooting. The results showed that these three pruning methods all contributed to an increase in the number of new branches, the leaf weight, and the flavonoid content in five-year-old trees. Among them, the effect of light pruning was the best, with a 150% increase in branch number, a 130% increase in leaf weight, and a 40.6% increase in flavonoid content. The secondary pruning further increased leaf area by 22.3%, indicating that secondary pruning further enhanced the rejuvenation of plants and increased leaf yield. At the transcriptional level, pruning can significantly change the expression of genes related to bud sprouting, resulting in a particularly significant increase in SHR expression in the buds. Pruning also promoted the expression of important genes related to flavonoid synthesis, including chalcone synthase (CHS), flavonoid 3′-hydroxylase (F3′H), flavonol synthase (FLS), and dihydroflavonol reductase (DFR). Furthermore, we demonstrated a significant increase in the rooting rate of these second-pruned branch cuttings and screened the optimal hormone ratio for rooting, which is 1.5 μM MeJA + 400 mg/L NAA + 100 mg/L Uniconazole-P. These results suggest that secondary pruning can effectively rejuvenate plants to promote cutting rooting in G. biloba. This method can not only be used to improve the yield and quality of ginkgo leaves, but also for cutting propagation.
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- 2024
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17. Characterization of the Ovarian Development and Associated Factors during the Breeding Migration of Coilia nasus in the Yangtze River
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Shuwei Wei, Zhong Hua, Yanping Yang, Fengjiao Ma, Wei Han, Wei Zhang, Congping Ying, Yanmin Deng, and Kai Liu
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Coilia nasus ,ovarian development ,organizational observation ,sex steroid hormones ,gene expression ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
Coilia nasus is a typical anadromous migratory fish found in the lower reaches of the Yangtze River. Every year, C. nasus clusters offshore and swims upstream along the Yangtze River into the tributaries and lakes in the middle and lower reaches of the Yangtze River to breed. In this study, female C. nasus were collected as study subjects from the Chongming section of Shanghai, the Taizhou section of Jiangsu, and the Anqing section of Anhui. Their ovaries were used to examine tissue sections and investigate gene expression, including the follicle-stimulating hormone receptor (fshr), the luteinizing hormone receptor (lhr), kisspeptin-1 (kiss1), and forkhead box l2 (foxl2), which are related to reproductive development, while the serum levels of estrogen (including estradiol, E2) and progestins (including 17α,20β-dihydroxy-4-pregenen-3-one, 17α,20β-DHP) were also analyzed. Our results showed that, first, the growth period of the oocytes was small in stage II of ovarian development, in which both E2 and 17α,20β-DHP levels and gene expression were low. Then, in stage III, the growth period of the oocytes became large, and the yolk granules and oil droplets began to appear. Simultaneously, E2 and the expression of kiss1 and foxl2 were significantly elevated. Finally, stage IV was the period of a large amount of accumulation of nutrients in the oocytes, and 17α,20β-DHP levels and the expression of fshr and lhr were significantly elevated. These results enrich the theoretical study of ovarian development in the natural population of C. nasus, supplementing the biological basis of C. nasus reproduction and scientifically supporting the study of C. nasus population ecology and resource conservation.
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- 2024
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18. Fosthiazate exposure induces oxidative stress, nerve damage, and reproductive disorders in nontarget nematodes
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Liu, Shiling, Wu, Qiqi, Zhong, Yanru, He, Zongzhe, Wang, Zhen, Li, Rui, and Wang, Minghua
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- 2023
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19. The molecular regulation mechanism of dmrt1—based on the establishment of the testis cell line derived from two-spot puffer Takifugu bimaculatus
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Zhong, Zhaowei, Wang, Yilei, Feng, Yan, Xu, Yan, Zhao, Liping, Jiang, Yonghua, and Zhang, Ziping
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- 2022
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20. Understanding the responses of tillering to 2,4-D isooctyl ester in Setaria viridis L.
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Xiong, Wangdan, Jia, Xinfeng, Wang, Qixin, Zhong, Nina, Gao, Hanchi, Zhang, Lingxin, and Sun, Juan
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- 2024
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21. A Cytokinin Analog Thidiazuron Suppresses Shoot Growth in Potted Rose Plants via the Gibberellic Acid Pathway
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Çelikel, Fisun G, Zhang, Qingchun, Zhang, Yanlong, Reid, Michael S, and Jiang, Cai-Zhong
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Agricultural ,Veterinary and Food Sciences ,Horticultural Production ,Stem Cell Research ,ethylene ,GA oxidase enzymes ,gene expression ,internode length and thickness ,microscopy ,miniature rose ,plant height ,thidiazuron ,Plant Biology ,Crop and pasture production ,Plant biology - Abstract
Application of thidiazuron (N-phenyl-N'-1,2,3-thiadiazol-5-ylurea, TDZ), a cytokinin analog, to inhibit the leaf yellowing that occurs after pinching potted rose plants, resulted in compact plants with shorter shoots and thicker internodes. Two weeks after treatment with 100 μM of TDZ, new shoots were half as long as those in control plants, and stem diameters were about 40% greater. This effect of TDZ is associated with changes in cell architecture. Although TDZ treatment stimulated ethylene production by the plants, inhibitors of ethylene biosynthesis (2-aminoethoxyvinyl glycine) or action (silver thiosulfate) did not affect the response of plants to TDZ. We found that TDZ treatment significantly suppressed the expression of bioactive gibberellic acid (GA) biosynthesis genes encoding GA3 and GA20 oxidases and slightly increased the expression of GA catabolism genes encoding GA2 oxidase. Application of GA3 and TDZ together resulted in normal elongation growth, although stem diameters were still somewhat thicker. Our results suggest that TDZ regulates shoot elongation and stem enlargement in potted rose plants through the modulation of bioactive GA biosynthesis.
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- 2021
22. A Combinatorial Single-Molecule Real-Time and Illumina Sequencing Analysis of Postembryonic Gene Expression in the Asian Citrus Psyllid Diaphorina citri.
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Zhang, Qin, Zhang, Can, Zhong, Hong, He, Qing, Xia, Zhao-Ying, Hu, Yu, Liao, Yu-Xin, Yi, Long, Lu, Zhan-Jun, and Yu, Hai-Zhong
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GENE expression ,CITRUS greening disease ,HIPPO signaling pathway ,CANDIDATUS liberibacter asiaticus ,REVERSE transcriptase polymerase chain reaction ,ALTERNATIVE RNA splicing - Abstract
Simple Summary: Diaphorina citri is an important transmission vector of Candidatus Liberibacter asiaticus (CLas), the causal agent of citrus Huanglongbing (HLB). The control of HLB mainly depends on the management of D. citri. The efficiency of D. citri nymphs in acquiring CLas bacteria is significantly higher than that of the adults, while the transmission efficiency of CLas bacteria by adults is significantly higher than that of nymphs. Therefore, it is of great significance to research the functions of key genes during the molting of fifth-instar nymphs. In this study, SMRT and Illumina sequencing were performed on D. citri fifth-instar nymphs and adults. SMRT-Seq-generated full-length transcripts provide valuable information for improving functional gene research in D. citri. Additionally, Illumina sequencing revealed that the Hippo pathway played an important role in regulating the transition of D. citri from fifth-instar nymphs to adults. Our findings provide useful reference information and lay a foundation for controlling D. citri. Huanglongbing (HLB) is a systemic plant disease caused by 'Candidatus Liberibacter asiaticus (CLas)' and transmitted by Diaphorina citri. D. citri acquires the CLas bacteria in the nymph stage and transmits it in the adult stage, indicating that molting from the nymph to adult stages is crucial for HLB transmission. However, the available D. citri reference genomes are incomplete, and gene function studies have been limited to date. In the current research, PacBio single-molecule real-time (SMRT) and Illumina sequencing were performed to investigate the transcriptome of D. citri nymphs and adults. In total, 10,641 full-length, non-redundant transcripts (FLNRTs), 594 alternative splicing (AS) events, 4522 simple sequence repeats (SSRs), 1086 long-coding RNAs (lncRNAs), 281 transcription factors (TFs), and 4459 APA sites were identified. Furthermore, 3746 differentially expressed genes (DEGs) between nymphs and adults were identified, among which 30 DEGs involved in the Hippo signaling pathway were found. Reverse transcription–quantitative PCR (RT-qPCR) further validated the expression levels of 12 DEGs and showed a positive correlation with transcriptome data. Finally, the spatiotemporal expression pattern of genes involved in the Hippo signaling pathway exhibited high expression in the D. citri testis, ovary, and egg. Silencing of the D. citri transcriptional co-activator (DcYki) gene significantly increased D. citri mortality and decreased the cumulative molting. Our results provide useful information and a reliable data resource for gene function research of D. citri. [ABSTRACT FROM AUTHOR]
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- 2024
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23. Stress-induced RNA-chromatin interactions promote endothelial dysfunction.
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Calandrelli, Riccardo, Xu, Lixia, Luo, Yingjun, Wu, Weixin, Fan, Xiaochen, Nguyen, Tri, Chen, Chien-Ju, Sriram, Kiran, Tang, Xiaofang, Burns, Andrew B, Natarajan, Rama, Chen, Zhen Bouman, and Zhong, Sheng
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Chromatin ,Endothelial Cells ,Humans ,Diabetes Mellitus ,Glucose ,Tumor Necrosis Factor-alpha ,Plasminogen Activator Inhibitor 1 ,DNA ,RNA ,Gene Expression ,Gene Regulatory Networks ,Stress ,Physiological ,Epigenomics ,Human Umbilical Vein Endothelial Cells ,Stress ,Physiological - Abstract
Chromatin-associated RNA (caRNA) has been proposed as a type of epigenomic modifier. Here, we test whether environmental stress can induce cellular dysfunction through modulating RNA-chromatin interactions. We induce endothelial cell (EC) dysfunction with high glucose and TNFα (H + T), that mimic the common stress in diabetes mellitus. We characterize the H + T-induced changes in gene expression by single cell (sc)RNA-seq, DNA interactions by Hi-C, and RNA-chromatin interactions by iMARGI. H + T induce inter-chromosomal RNA-chromatin interactions, particularly among the super enhancers. To test the causal relationship between H + T-induced RNA-chromatin interactions and the expression of EC dysfunction-related genes, we suppress the LINC00607 RNA. This suppression attenuates the expression of SERPINE1, a critical pro-inflammatory and pro-fibrotic gene. Furthermore, the changes of the co-expression gene network between diabetic and healthy donor-derived ECs corroborate the H + T-induced RNA-chromatin interactions. Taken together, caRNA-mediated dysregulation of gene expression modulates EC dysfunction, a crucial mechanism underlying numerous diseases.
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- 2020
24. Ellagic Acid and Its Microbial Metabolite Urolithin A Alleviate Diet‐Induced Insulin Resistance in Mice
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Yang, Jieping, Guo, Yuanqiang, Henning, Susanne M, Chan, Brenda, Long, Jianfeng, Zhong, Jin, Acin‐Perez, Rebeca, Petcherski, Anton, Shirihai, Orian, Heber, David, and Li, Zhaoping
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Agricultural ,Veterinary and Food Sciences ,Biomedical and Clinical Sciences ,Food Sciences ,Nutrition and Dietetics ,Diabetes ,Nutrition ,Obesity ,2.1 Biological and endogenous factors ,Aetiology ,Metabolic and endocrine ,Adiponectin ,Animals ,Blood Glucose ,Coumarins ,Cytokines ,Diet ,High-Fat ,Ellagic Acid ,Gene Expression ,Inflammation ,Insulin Resistance ,Lipid Metabolism ,Lipids ,Liver ,Male ,Mice ,Inbred DBA ,Mitochondria ,Liver ,Muscle ,Skeletal ,Sucrose ,ellagic acid ,insulin resistance ,mitochondria ,obesity ,urolithin A ,Public Health and Health Services ,Food Science ,Nutrition & Dietetics ,Food sciences ,Nutrition and dietetics - Abstract
ScopeThis work aims at evaluating the effect of dietary ellagic acid (EA) and its microbial metabolite urolithin A (UA) on glucose metabolism and insulin resistance (IR) in mice with diet-induced IR.Methods and resultsDBA2J mice are fed a high fat/high sucrose diet (HF/HS) for 8 weeks to induce IR and then 0.1% EA, UA, or EA and UA (EA+UA) are added to the HF/HS-diet for another 8 weeks. UA significantly decreases fasting glucose and increases adiponectin compared with HF/HS-controls. During intraperitoneal insulin tolerance test, EA+UA significantly improve insulin-mediated glucose lowering effects at 15 and 120 min and reduce blood triglycerides compared with HF/HS-controls. Serum free fatty acids are significantly decreased by EA, UA, and EA+UA. Differential expression of genes related to mitochondrial function by EA, UA, and EA+UA in liver and skeletal muscle is observed. Primary hepatocytes from IR-mice have higher proton leak, basal and ATP-linked oxygen consumption rates compared with healthy controls. EA and EA+UA but not UA reduce the proton leak in hepatocytes from IR-mice.ConclusionEA and UA induce different metabolic benefits in IR mice. The effects of EA and UA on mitochondrial function suggest a potentially novel mechanism modulating metabolism.
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- 2020
25. Characterization of the transcription factor Sox3 regulating the gonadal development of pearlscale angelfish (Centropyge vrolikii)
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Feng, Yan, Zhong, Zhao-wei, Xu, Yan, Zhang, Ze-yu, Ao, Lu-lu, Yang, Zhen, Wang, Yi-lei, and Jiang, Yong-hua
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- 2022
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26. The coordinated alterations in antioxidative enzymes, PeCu/ZnSOD and PeAPX2 expression facilitated in vitro Populus euphratica resistance to salinity stress
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Feng, Kai, Lu, Jinling, Chen, Ying, Luo, Yongya, Hu, Yuchen, Li, Xuexia, Zhong, Songzheng, and Cheng, Le
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- 2022
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27. A Comprehensive Analysis of Auxin Response Factor Gene Family in Melastoma dodecandrum Genome
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Yukun Peng, Kai Zhao, Ruiyue Zheng, Jiemin Chen, Xuanyi Zhu, Kai Xie, Ruiliu Huang, Suying Zhan, Qiuli Su, Mingli Shen, Muqi Niu, Xiuming Chen, Donghui Peng, Sagheer Ahmad, Zhong-Jian Liu, and Yuzhen Zhou
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Myrtales ,protein structure ,miRNA regulation ,gene expression ,IAA response and inhibition ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Auxin Response Factors (ARFs) mediate auxin signaling and govern diverse biological processes. However, a comprehensive analysis of the ARF gene family and identification of their key regulatory functions have not been conducted in Melastoma dodecandrum, leading to a weak understanding of further use and development for this functional shrub. In this study, we successfully identified a total of 27 members of the ARF gene family in M. dodecandrum and classified them into Class I–III. Class II–III showed more significant gene duplication than Class I, especially for MedARF16s. According to the prediction of cis-regulatory elements, the AP2/ERF, BHLH, and bZIP transcription factor families may serve as regulatory factors controlling the transcriptional pre-initiation expression of MedARF. Analysis of miRNA editing sites reveals that miR160 may play a regulatory role in the post-transcriptional expression of MeARF. Expression profiles revealed that more than half of the MedARFs exhibited high expression levels in the stem compared to other organs. While there are some specific genes expressed only in flowers, it is noteworthy that MedARF16s, MedARF7A, and MedARF9B, which are highly expressed in stems, also demonstrate high expressions in other organs of M. dodecandrum. Further hormone treatment experiments revealed that these MedARFs were sensitive to auxin changes, with MedARF6C and MedARF7A showing significant and rapid changes in expression upon increasing exogenous auxin. In brief, our findings suggest a crucial role in regulating plant growth and development in M. dodecandrum by responding to changes in auxin. These results can provide a theoretical basis for future molecular breeding in Myrtaceae.
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- 2024
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28. General Analysis of Heat Shock Factors in the Cymbidium ensifolium Genome Provided Insights into Their Evolution and Special Roles with Response to Temperature
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Ruiyue Zheng, Jiemin Chen, Yukun Peng, Xuanyi Zhu, Muqi Niu, Xiuming Chen, Kai Xie, Ruiliu Huang, Suying Zhan, Qiuli Su, Mingli Shen, Donghui Peng, Sagheer Ahmad, Kai Zhao, Zhong-Jian Liu, and Yuzhen Zhou
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orchid ,cis-elements ,gene expression ,abiotic stress ,floral scent regulation ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Heat shock factors (HSFs) are the key regulators of heat stress responses and play pivotal roles in tissue development and the temperature-induced regulation of secondary metabolites. In order to elucidate the roles of HSFs in Cymbidium ensifolium, we conducted a genome-wide identification of CeHSF genes and predicted their functions based on their structural features and splicing patterns. Our results revealed 22 HSF family members, with each gene containing more than one intron. According to phylogenetic analysis, 59.1% of HSFs were grouped into the A subfamily, while subfamily HSFC contained only two HSFs. And the HSF gene families were differentiated evolutionarily between plant species. Two tandem repeats were found on Chr02, and two segmental duplication pairs were observed on Chr12, Chr17, and Chr19; this provided evidence for whole-genome duplication (WGD) events in C. ensifolium. The core region of the promoter in most CeHSF genes contained cis-acting elements such as AP2/ERF and bHLH, which were associated with plant growth, development, and stress responses. Except for CeHSF11, 14, and 19, each of the remaining CeHSFs contained at least one miRNA binding site. This included binding sites for miR156, miR393, and miR319, which were responsive to temperature and other stresses. The HSF gene family exhibited significant tissue specificity in both vegetative and floral organs of C. ensifolium. CeHSF13 and CeHSF15 showed relatively significant expression in flowers compared to other genes. During flower development, CeHSF15 exhibited markedly elevated expression in the early stages of flower opening, implicating critical regulatory functions in organ development and floral scent-related regulations. During the poikilothermic treatment, CeHSF14 was upregulated over 200-fold after 6 h of heat treatment. CeHSF13 and CeHSF14 showed the highest expression at 6 h of low temperature, while the expression of CeHSF15 and CeHSF21 continuously decreased at a low temperature. The expression patterns of CeHSFs further confirmed their role in responding to temperature stress. Our study may help reveal the important roles of HSFs in plant development and metabolic regulation and show insight for the further molecular design breeding of C. ensifolium.
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- 2024
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29. Changes in Photosynthetic Characteristics between Green-Leaf Poplar Linn. '2025' and Its Bud-Sporting Colored-Leaf Cultivars
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Tao Wang, Donghuan Xu, Fan Zhang, Tengyue Yan, Yuhang Li, Zhong Wang, Yinfeng Xie, and Weibing Zhuang
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colored-leaf poplar ,photosynthetic light-response curve ,chlorophyll fluorescence ,chloroplast ultrastructure ,gene expression ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Colored-leaf poplar is increasingly popular due to its great ornamental values and application prospects. However, the photosynthetic characteristics of these colored-leaf cultivars have not been well understood. In this study, the photosynthetic differences between green-leaf poplar Populus deltoids Linn. “2025” (L2025) and colored-leaf cultivars ‘Zhonghong poplar’ (ZHP), ‘Quanhong poplar’ (QHP), and ‘Caihong poplar’ (CHP) were investigated on several levels, including chloroplast ultrastructure observation, photosynthetic physiological characteristics, and expression analysis of key genes. The results showed that the photosynthetic performance of ZHP was basically consistent with that of L2025, while the ranges of light energy absorption and efficiency of light energy utilization decreased to different degrees in CHP and QHP. A relatively low water use efficiency and high dark respiration rate were observed in QHP, suggesting a relatively weak environmental adaptability. The differences in chloroplast structure in different colored-leaf poplars were further observed by transmission electron microscopy. The disorganization of thylakoid in CHP was considered an important reason, resulting in a significant decrease in chlorophyll content compared with other poplar cultivars. Interestingly, CHP exhibited extremely high photosynthetic electron transport activity and photochemical efficiency, which were conductive to maintaining its relatively high photosynthetic performance. The actual quantum yield of PSII photochemistry of ZHP was basically the same as that of QHP, while the relatively high photosynthetic performance indexes in ZHP suggested a more optimized photosynthetic apparatus, which was crucial for the improvement of photosynthetic efficiency. The differential expressions of a series of key genes in different colored-leaf poplars provided a reasonable explanation for anthocyanin accumulation and specific photosynthetic processes.
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- 2024
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30. Corrigendum: Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrid
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Meng Ma, Wenying Zhong, Qing Zhang, Li Deng, Jing Wen, Bin Yi, Jinxing Tu, Tingdong Fu, Lun Zhao, and Jinxiong Shen
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Brassica napus ,heterosis ,gene expression ,epigenetic ,histone modification ,Plant culture ,SB1-1110 - Published
- 2023
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31. Genome-wide characterization of ascorbate peroxidase gene family in pepper (Capsicum annuum L.) in response to multiple abiotic stresses
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Xin Pang, Jun Chen, Yang Xu, Jia Liu, Yangmin Zhong, Linlin Wang, Jiaqiu Zheng, and Hongjian Wan
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pepper ,ascorbate peroxidase ,bioinformatics analysis ,gene expression ,phylogenetic relationship ,Plant culture ,SB1-1110 - Abstract
Pepper is widely grown all over the world, so it faces many abiotic stresses, such as drought, high temperature, low temperature, salt damage, and so on. Stresses causing the accumulation of reactive oxidative species (ROS) in plants are removed by antioxidant defense systems, and ascorbate peroxidase (APX) is an important antioxidant enzyme. Therefore, the present study performed genome-wide identification of the APX gene family in pepper. We identified nine members of the APX gene family in the pepper genome according to the APX proteins’ conserved domain in Arabidopsis thaliana. The physicochemical property analysis showed that CaAPX3 had the longest protein sequence and the largest molecular weight of all genes, while CaAPX9 had the shortest protein sequence and the smallest MW. The gene structure analysis showed that CaAPXs were composed of seven to 10 introns. The CaAPX genes were divided into four groups. The APX genes of groups I and IV were localized in the peroxisomes and chloroplasts, respectively; the group II genes were localized in the chloroplasts and mitochondria; and the group III genes were located in the cytoplasm and extracell. The conservative motif analysis showed that all APX genes in the pepper had motif 2, motif 3, and motif 5. The APX gene family members were distributed on five chromosomes (Chr. 2, 4, 6, 8, and 9). The cis-acting element analysis showed that most CaAPX genes contain a variety of cis-elements related to plant hormones and abiotic stress. RNA-seq expression analysis showed that the expression patterns of nine APXs were different in vegetative and reproductive organs at different growth and development stages. In addition, the qRT-PCR analysis of the CaAPX genes revealed significant differential expression in response to high temperature, low temperature, and salinity stresses in leaf tissue. In conclusion, our study identified the APX gene family members in the pepper and predicted the functions of this gene family, which would provide resources for further functional characterization of CaAPX genes.
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- 2023
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32. Gut microbiota composition and gene expression changes induced in the Apis cerana exposed to acetamiprid and difenoconazole at environmentally realistic concentrations alone or combined
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Wensu Han, Zheyuan Ye, Yifan Gu, Yihai Zhong, Jinglin Gao, Shan Zhao, and Shijie Wang
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Apis cerana ,acetamiprid ,difenoconazole ,gut microbiota ,gene expression ,Physiology ,QP1-981 - Abstract
Apis cerana is an important pollinator of agricultural crops in China. In the agricultural environment, A. cerana may be exposed to acetamiprid (neonicotinoid insecticide) and difenoconazole (triazole fungicide), alone or in combination because they are commonly applied to various crops. At present, our understanding of the toxicological effects of acetamiprid and difenoconazole on honey bee gut microbiomes is limited. The primary objective of this study was to explore whether these two pesticides affect honey bees’ gut microbiota and to analyze the transcriptional effects of these two pesticides on honey bees’ head and gut. In this study, adults of A. cerana were exposed to acetamiprid and/or difenoconazole by contaminated syrup at field-realistic concentrations for 10 days. Results indicated that acetamiprid and/or difenoconazole chronic exposure did not affect honey bees’ survival and food consumption, whereas difenoconazole decreased the weight of honey bees. 16S rRNA sequencing suggested that difenoconazole and the mixture of difenoconazole and acetamiprid decreased the diversity index and shaped the composition of gut bacteria microbiota, whereas acetamiprid did not impact the gut bacterial community. The ITS sequence data showed that neither of the two pesticides affected the fungal community structure. Meanwhile, we also observed that acetamiprid or difenoconazole significantly altered the expression of genes related to detoxification and immunity in honey bees’ tissues. Furthermore, we observed that the adverse effect of the acetamiprid and difenoconazole mixture on honey bees’ health was greater than that of a single mixture. Taken together, our study demonstrates that acetamiprid and/or difenoconazole exposure at field-realistic concentrations induced changes to the honey bee gut microbiome and gene expression.
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- 2023
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33. Dual antivascular function of human fibulin‐3 variant, a potential new drug discovery strategy for glioblastoma
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Ke, Chao, Luo, Jun‐ran, Cen, Zi‐wen, Li, Yanyan, Cai, Hai‐ping, Wang, Jing, Chen, Fu‐rong, Siegel, Eric R, Le, Kody N, Winokan, Jesica R, Gibson, Grace J, McSwain, Asia E, Afrasiabi, Kambiz, Linskey, Mark E, Zhou, You‐Xin, Chen, Zhong‐ping, and Zhou, Yi‐Hong
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Biotechnology ,Stem Cell Research - Nonembryonic - Human ,Neurosciences ,Brain Disorders ,Rare Diseases ,Brain Cancer ,Stem Cell Research ,Cancer ,2.1 Biological and endogenous factors ,Aetiology ,Animals ,Brain Neoplasms ,Cell Line ,Tumor ,Cell Proliferation ,Down-Regulation ,Drug Discovery ,Endothelial Cells ,ErbB Receptors ,Extracellular Matrix Proteins ,Female ,Gene Expression ,Glioblastoma ,Humans ,Mice ,Mice ,Inbred BALB C ,Mice ,Nude ,Neovascularization ,Pathologic ,Signal Transduction ,Xenograft Model Antitumor Assays ,extracellular compartment ,malignant glioma ,novel cancer therapeutic ,syngeneic primary culture ,vasculogenic mimicry ,Oncology and Carcinogenesis ,Pharmacology and Pharmaceutical Sciences ,Oncology & Carcinogenesis - Abstract
The ECM protein EFEMP1 (fibulin-3) is associated with all types of solid tumor through its cell context-dependent dual function. A variant of fibulin-3 was engineered by truncation and mutation to alleviate its oncogenic function, specifically the proinvasive role in glioblastoma multiforme (GBM) cells at stem-like state. ZR30 is an in vitro synthesized 39-kDa protein of human fibulin-3 variant. It has a therapeutic effect in intracranial xenograft models of human GBM, through suppression of epidermal growth factor receptor/AKT and NOTCH1/AKT signaling in GBM cells and extracellular MMP2 activation. Glioblastoma multiforme is highly vascular, with leaky blood vessels formed by tumor cells expressing endothelial cell markers, including CD31. Here we studied GBM intracranial xenografts, 2 weeks after intratumoral injection of ZR30 or PBS, by CD31 immunohistochemistry. We found a 70% reduction of blood vessel density in ZR30-treated xenografts compared with that of PBS-treated ones. Matrigel plug assays showed the effect of ZR30 on suppressing angiogenesis. We further studied the effect of ZR30 on genes involved in endothelial transdifferentiation (ETD), in 7 primary cultures derived from 3 GBMs under different culture conditions. Two GBM cultures formed mesh structures with upregulation of ETD genes shortly after culture in Matrigel Matrix, and ZR30 suppressed both. ZR30 also downregulated ETD genes in two GBM cultures with high expression of these genes. In conclusion, multifaceted tumor suppression effects of human fibulin-3 variant include both suppression of angiogenesis and vasculogenic mimicry in GBM.
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- 2020
34. CsIVP functions in vasculature development and downy mildew resistance in cucumber
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Yan, Shuangshuang, Ning, Kang, Wang, Zhongyi, Liu, Xiaofeng, Zhong, Yanting, Ding, Lian, Zi, Hailing, Cheng, Zhihua, Li, Xuexian, Shan, Hongyan, Lv, Qingyang, Luo, Laixin, Liu, Renyi, Yan, Liying, Zhou, Zhaoyang, Lucas, William John, and Zhang, Xiaolan
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Agricultural ,Veterinary and Food Sciences ,Plant Biology ,Biological Sciences ,Crop and Pasture Production ,Stem Cell Research - Nonembryonic - Non-Human ,Genetics ,Biotechnology ,Stem Cell Research ,Basic Helix-Loop-Helix Transcription Factors ,Cucumis sativus ,Disease Resistance ,Gene Expression ,Gene Expression Regulation ,Plant ,Indoleacetic Acids ,Morphogenesis ,Phylogeny ,Plant Diseases ,Plant Proteins ,Plant Vascular Bundle ,Plants ,Genetically Modified ,Protein Binding ,Salicylic Acid ,Signal Transduction ,Agricultural and Veterinary Sciences ,Medical and Health Sciences ,Developmental Biology ,Agricultural ,veterinary and food sciences ,Biological sciences ,Biomedical and clinical sciences - Abstract
Domesticated crops with high yield and quality are frequently susceptible to pathogen attack, whereas enhancement of disease resistance generally compromises crop yield. The underlying mechanisms of how plant development and disease resistance are coordinately programed remain elusive. Here, we showed that the basic Helix-Loop-Helix (bHLH) transcription factor Cucumis sativus Irregular Vasculature Patterning (CsIVP) was highly expressed in cucumber vascular tissues. Knockdown of CsIVP caused severe vasculature disorganization and abnormal organ morphogenesis. CsIVP directly binds to vascular-related regulators YABBY5 (CsYAB5), BREVIPEDICELLUS (CsBP), and AUXIN/INDOLEACETIC ACIDS4 (CsAUX4) and promotes their expression. Knockdown of CsYAB5 resulted in similar phenotypes as CsIVP-RNA interference (RNAi) plants, including disturbed vascular configuration and abnormal organ morphology. Meanwhile, CsIVP-RNAi plants were more resistant to downy mildew and accumulated more salicylic acid (SA). CsIVP physically interacts with NIM1-INTERACTING1 (CsNIMIN1), a negative regulator in the SA signaling pathway. Thus, CsIVP is a novel vasculature regulator functioning in CsYAB5-mediated organ morphogenesis and SA-mediated downy mildew resistance in cucumber.
- Published
- 2020
35. Mechanisms underlying genome instability mediated by formation of foldback inversions in Saccharomyces cerevisiae
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Li, Bin-zhong, Putnam, Christopher D, and Kolodner, Richard David
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Aetiology ,2.1 Biological and endogenous factors ,Chromosome Inversion ,Chromosomes ,Fungal ,DNA Breaks ,Double-Stranded ,Gene Rearrangement ,Genome ,Fungal ,Genomic Instability ,Homologous Recombination ,Saccharomyces cerevisiae ,Saccharomyces cerevisiae Proteins ,S. cerevisiae ,chromosomes ,dna repair ,gene expression ,genome rearrangement ,translocation ,whole genome sequencing ,Biochemistry and Cell Biology ,Biological sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
Foldback inversions, also called inverted duplications, have been observed in human genetic diseases and cancers. Here, we used a Saccharomyces cerevisiae genetic system that generates gross chromosomal rearrangements (GCRs) mediated by foldback inversions combined with whole-genome sequencing to study their formation. Foldback inversions were mediated by formation of single-stranded DNA hairpins. Two types of hairpins were identified: small-loop hairpins that were suppressed by MRE11, SAE2, SLX1, and YKU80 and large-loop hairpins that were suppressed by YEN1, TEL1, SWR1, and MRC1. Analysis of CRISPR/Cas9-induced double strand breaks (DSBs) revealed that long-stem hairpin-forming sequences could form foldback inversions when proximal or distal to the DSB, whereas short-stem hairpin-forming sequences formed foldback inversions when proximal to the DSB. Finally, we found that foldback inversion GCRs were stabilized by secondary rearrangements, mostly mediated by different homologous recombination mechanisms including single-strand annealing; however, POL32-dependent break-induced replication did not appear to be involved forming secondary rearrangements.
- Published
- 2020
36. NOS1 inhibits the interferon response of cancer cells by S-nitrosylation of HDAC2.
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Xu, Pengfei, Ye, Shuangyan, Li, Keyi, Huang, Mengqiu, Wang, Qianli, Zeng, Sisi, Chen, Xi, Gao, Wenwen, Chen, Jianping, Zhang, Qianbing, Zhong, Zhuo, Lin, Ying, Rong, Zhili, Xu, Yang, Hao, Bingtao, Peng, Anghui, Ouyang, Manzhao, and Liu, Qiuzhen
- Subjects
Cell Line ,Tumor ,Animals ,Mice ,Inbred BALB C ,Mice ,Inbred C57BL ,Humans ,Mice ,Mice ,Nude ,Melanoma ,Melanoma ,Experimental ,Lung Neoplasms ,Interferon-alpha ,Transfection ,Gene Expression ,Female ,Nitric Oxide Synthase Type I ,Histone Deacetylase 2 ,H4K16ac ,HDAC2 ,IFNα ,Metastasis ,NOS1 ,S-nitrosylation ,Genetics ,Brain Disorders ,Prevention ,Cancer ,Aetiology ,2.1 Biological and endogenous factors ,IFN alpha ,Oncology and Carcinogenesis ,Oncology & Carcinogenesis - Abstract
BACKGROUND:The dysfunction of type I interferon (IFN) signaling is an important mechanism of immune escape and metastasis in tumors. Increased NOS1 expression has been detected in melanoma, which correlated with dysfunctional IFN signaling and poor response to immunotherapy, but the specific mechanism has not been determined. In this study, we investigated the regulation of NOS1 on the interferon response and clarified the relevant molecular mechanisms. METHODS:After stable transfection of A375 cells with NOS1 expression plasmids, the transcription and expression of IFNα-stimulated genes (ISGs) were assessed using pISRE luciferase reporter gene analysis, RT-PCR, and western blotting, respectively. The effect of NOS1 on lung metastasis was assessed in melanoma mouse models. A biotin-switch assay was performed to detect the S-nitrosylation of HDAC2 by NOS1. ChIP-qPCR was conducted to measure the binding of HDAC2, H4K16ac, H4K5ac, H3ac, and RNA polymerase II in the promoters of ISGs after IFNα stimulation. This effect was further evaluated by altering the expression level of HDAC2 or by transfecting the HDAC2-C262A/C274A site mutant plasmids into cells. The coimmunoprecipitation assay was performed to detect the interaction of HDAC2 with STAT1 and STAT2. Loss-of-function and gain-of-function approaches were used to examine the effect of HDAC2-C262A/C274A on lung metastasis. Tumor infiltrating lymphocytes were analyzed by flow cytometry. RESULTS:HDAC2 is recruited to the promoter of ISGs and deacetylates H4K16 for the optimal expression of ISGs in response to IFNα treatment. Overexpression of NOS1 in melanoma cells decreases IFNα-responsiveness and induces the S-nitrosylation of HDAC2-C262/C274. This modification decreases the binding of HDAC2 with STAT1, thereby reducing the recruitment of HDAC2 to the ISG promoter and the deacetylation of H4K16. Moreover, expression of a mutant form of HDAC2, which cannot be nitrosylated, reverses the inhibition of ISG expression by NOS1 in vitro and decreases NOS1-induced lung metastasis and inhibition of tumor infiltrating lymphocytes in a melanoma mouse model. CONCLUSIONS:This study provides evidence that NOS1 induces dysfunctional IFN signaling to promote lung metastasis in melanoma, highlighting NOS1-induced S-nitrosylation of HDAC2 in the regulation of IFN signaling via histone modification.
- Published
- 2019
37. Identification and expression analysis of BURP domain-containing genes in jujube and their involvement in low temperature and drought response
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Wenzhu Wang, Zhong Zhang, and Xingang Li
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Ziziphus jujuba Mill ,BURP domain-containing protein ,Gene expression ,Abiotic stress ,Fruit development ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Plant-specific BURP domain-containing genes are involved in plant development and stress responses. However, the role of BURP family in jujube (Ziziphus jujuba Mill.) has not been investigated. Results In this study, 17 BURP genes belonging to four subfamilies were identified in jujube based on homology analysis, gene structures, and conserved motif confirmation. Gene duplication analysis indicated both tandem duplication and segmental duplication had contributed to ZjBURP expansion. The ZjBURPs were extensively expressed in flowers, young fruits, and jujube leaves. Transcriptomic data and qRT-PCR analysis further revealed that ZjBURPs also significantly influence fruit development, and most genes could be induced by low temperature, salinity, and drought stresses. Notably, several BURP genes significantly altered expression in response to low temperature (ZjPG1) and drought stresses (ZjBNM7, ZjBNM8, and ZjBNM9). Conclusions These results provided insights into the possible roles of ZjBURPs in jujube development and stress response. These findings would help selecting candidate ZjBURP genes for cold- and drought-tolerant jujube breeding.
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- 2022
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38. Correlation Analysis between Nutritional Evaluation and Gene Expression of Crassostrea hongkongensis in Different Fattening Sea Areas
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Xueyu YAN, Bozhong QIN, Weide HUANG, Jinxia PENG, Peng ZHU, Meijun JIANG, Bin ZHANG, Xuanji LI, Fangjie ZHONG, and Pinyuan WEI
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crassostrea hongkongensis ,different fattening sea areas ,nutritional evaluation ,gene expression ,correlation analysis ,Food processing and manufacture ,TP368-456 - Abstract
In the present study, the nutrient composition of Crassostrea hongkongensis from two oyster fattening areas in Qinzhou Bay, Guangxi was evaluated. And then the metabolism-related gene expression in the mantle, adductor muscle and gill tissues of C. hongkongensis was analyzed, and the correlation between nutrient composition and gene expression was discussed. The results showed that the contents of cholesterol, vitamin A, vitamin E, zinc and some amino acids including phenylalanine, histidine, glutamic acid and alanine of C. hongkongensis in Qinzhou Port fattening area were significantly higher than those in Dafeng River fattening area (P0.05). The heat map of Spearman correlation showed that the gene expression of P5CS, GP and SREBP were positively correlated with the contents of multiple nutrient composition and amino acids, in which the gene expression of GP was significantly positively correlated with energy, fat, cholesterol and vitamins (P
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- 2022
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39. Genome-wide characterization and identification of candidate ERF genes involved in various abiotic stress responses in sesame (Sesamum indicum L.)
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Ruqi Su, Senouwa Segla Koffi Dossou, Komivi Dossa, Rong Zhou, Aili Liu, Yanping Zhong, Sheng Fang, Xiurong Zhang, Ziming Wu, and Jun You
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ERF gene family ,Sesamum indicum ,Transcription factors ,Gene expression ,Abiotic stress ,Botany ,QK1-989 - Abstract
Abstract Background The adverse effects of climate change on crop production are constraining breeders to develop high-quality environmentally stable varieties. Hence, efforts are being made to identify key genes that could be targeted for enhancing crop tolerance to environmental stresses. ERF transcription factors play an important role in various abiotic stresses in plants. However, the roles of the ERF family in abiotic stresses tolerance are still largely unknown in sesame, the “queen” of oilseed crops. Results In total, 114 sesame ERF genes (SiERFs) were identified and characterized. 96.49% of the SiERFs were distributed unevenly on the 16 linkage groups of the sesame genome. The phylogenetic analysis with the Arabidopsis ERFs (AtERFs) subdivided SiERF subfamily proteins into 11 subgroups (Groups I to X; and VI-L). Genes in the same subgroup exhibited similar structure and conserved motifs. Evolutionary analysis showed that the expansion of ERF genes in sesame was mainly induced by whole-genome duplication events. Moreover, cis-acting elements analysis showed that SiERFs are mostly involved in environmental responses. Gene expression profiles analysis revealed that 59 and 26 SiERFs are highly stimulated under drought and waterlogging stress, respectively. In addition, qRT-PCR analyses indicated that most of SiERFs are also significantly up-regulated under osmotic, submerge, ABA, and ACC stresses. Among them, SiERF23 and SiERF54 were the most induced by both the abiotic stresses, suggesting their potential for targeted improvement of sesame response to multiple abiotic stresses. Conclusion This study provides a comprehensive understanding of the structure, classification, evolution, and abiotic stresses response of ERF genes in sesame. Moreover, it offers valuable gene resources for functional characterization towards enhancing sesame tolerance to multiple abiotic stresses.
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- 2022
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40. Screening and validation of reference genes for qPCR analysis in gonads and embryos of Takifugu bimaculatus
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Zhaowei Zhong, Lulu Ao, Liping Zhao, Zeyu Zhang, and Yonghua Jiang
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Reference gene screening ,qPCR ,Gene expression ,Takifugu bimaculatu ,Aquaculture. Fisheries. Angling ,SH1-691 - Abstract
Suitable reference genes are one of the necessary conditions for obtaining reliable results by real-time fluorescence quantitative PCR (qPCR). In this study, the expression of the 10 common candidate reference genes (18s rRNA, rps27, cnbp, rpl7, ube2, hsp-at, gapdh, β-actin, rpl13a, 1-ef1a) at different developmental stages of gonad and embryo of Takifugu bimaculatus were analyzed by qPCR. And the expression stability of these reference genes is analyzed by GeNorm, NormFinder and Bestkeeper softwares. The results showed that the expression stability of 1-ef1a was the highest (p
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- 2022
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41. Polysaccharide of Atractylodes macrocephala Koidz alleviate lipopolysaccharide-induced liver injury in goslings via the p53 and FOXO pathways
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Bingqi Zhang, Longsheng Hong, Jingfei Ke, Yueyun Zhong, Nan Cao, Wanyan Li, Danning Xu, Yunbo Tian, Yunmao Huang, Wenbin Chen, and Bingxin Li
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lipopolysaccharide ,polysaccharide of Atractylodes macrocephala Koidz ,gene expression ,liver ,gosling ,Animal culture ,SF1-1100 - Abstract
ABSTRACT: Lipopolysaccharide (LPS) can affect the immune system of geese by inducing liver injury. The polysaccharide of Atractylodes macrocephala Koidz (PAMK) have obvious immune-enhancing effects. Accordingly, this experiment investigated the effect of PAMK on LPS-induced liver injury in goslings. Two hundred 1-day-old goslings were randomly divided into the control group, LPS group, PAMK group, and PAMK+ LPS group, and the PAMK and PAMK+ LPS groups were fed the basal diet with 400 mg/kg PAMK, while the control and LPS groups were fed the basal diet. On D 21, 23, and 25 of the formal trial, the goslings in the LPS and PAMK+LPS groups were injected intraperitoneally with 2 mg/kg LPS, and goslings in the control and PAMK groups were injected intraperitoneally with the same amount of saline. Livers were collected on D 25. HE-stained sections showed that PAMK could effectively alleviate the LPS-induced indistinct hepatic cord structure, loss of cytoplasmic contents of hepatocytes, and dilatation of hepatic sinusoids. The biochemical parameters of liver tissues showed that PAMK could alleviate the LPS-induced upregulation of alanine aminotransferase and aspartate aminotransferase. To further investigate the mechanism of the mitigating effect of PAMK on LPS-induced injury, livers from the LPS and PAMK+LPS groups were selected for transcriptome sequencing. The sequencing results showed that there were 406 differentially expressed genes (DEGs) in the livers of LPS and PAMK+LPS goslings, of which 242 upregulated and 164 downregulated. The Kyoto Encyclopedia of Genes and Genome (KEGG) analysis showed that DEGs were significantly enriched in immune signal transduction, cell cycle, and cell metabolism. Besides, protein‒protein interaction analysis showed that 129 DEGs were associated with each other, including 7 DEGs enriched in the p53 and FOXO signaling pathway. In conclusion, PAMK may alleviate LPS-induced liver injury in gosling through the p53 and FOXO signaling pathway. These results provide a basis for further development of PAMK as an immunomodulator.
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- 2023
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42. Identification and expression analysis of BURP domain-containing genes in jujube and their involvement in low temperature and drought response
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Wang, Wenzhu, Zhang, Zhong, and Li, Xingang
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- 2022
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43. Proto Kranz-like leaf traits and cellular ionic regulation are associated with salinity tolerance in a halophytic wild rice
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Yong, Miing-Tiem, Solis, Celymar Angela, Amatoury, Samuel, Sellamuthu, Gothandapani, Rajakani, Raja, Mak, Michelle, Venkataraman, Gayatri, Shabala, Lana, Zhou, Meixue, Ghannoum, Oula, Holford, Paul, Huda, Samsul, Shabala, Sergey, and Chen, Zhong-Hua
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- 2022
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44. Genome-wide identification and expression analysis of magnesium transporter gene family in grape (Vitis vinifera)
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Ge, Mengqing, Zhong, Rong, Sadeghnezhad, Ehsan, Hakeem, Abdul, Xiao, Xin, Wang, Peipei, and Fang, Jinggui
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- 2022
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45. Genome-wide characterization and identification of candidate ERF genes involved in various abiotic stress responses in sesame (Sesamum indicum L.)
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Su, Ruqi, Dossou, Senouwa Segla Koffi, Dossa, Komivi, Zhou, Rong, Liu, Aili, Zhong, Yanping, Fang, Sheng, Zhang, Xiurong, Wu, Ziming, and You, Jun
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- 2022
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46. Genome-wide annotation of protein-coding genes in pig
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Karlsson, Max, Sjöstedt, Evelina, Oksvold, Per, Sivertsson, Åsa, Huang, Jinrong, Álvez, María Bueno, Arif, Muhammad, Li, Xiangyu, Lin, Lin, Yu, Jiaying, Ma, Tao, Xu, Fengping, Han, Peng, Jiang, Hui, Mardinoglu, Adil, Zhang, Cheng, von Feilitzen, Kalle, Xu, Xun, Wang, Jian, Yang, Huanming, Bolund, Lars, Zhong, Wen, Fagerberg, Linn, Lindskog, Cecilia, Pontén, Fredrik, Mulder, Jan, Luo, Yonglun, and Uhlen, Mathias
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- 2022
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47. Effects of Zinc Oxide Nanoparticles on Growth, Development, and Flavonoid Synthesis in Ginkgo biloba
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Qingjie Wang, Shiyuan Xu, Lei Zhong, Xiya Zhao, and Li Wang
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Ginkgo biloba ,ZnO-NPs ,mineral elements ,gene expression ,GbF3H gene ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Ginkgo biloba is a highly valuable medicinal plant known for its rich secondary metabolites, including flavonoids. Zinc oxide nanoparticles (ZnO-NPs) can be used as nanofertilizers and nano-growth regulators to promote plant growth and development. However, little is known about the effects of ZnO-NPs on flavonoids in G. biloba. In this study, G. biloba was treated with different concentrations of ZnO-NPs (25, 50, 100 mg/L), and it was found that 25 mg/L of ZnO-NPs enhanced G. biloba fresh weight, dry weight, zinc content, and flavonoids, while 50 and 100 mg/L had an inhibitory effect on plant growth. Furthermore, quantitative reverse transcription (qRT)-PCR revealed that the increased total flavonoids and flavonols were mainly due to the promotion of the expression of flavonol structural genes such as GbF3H, GbF3′H, and GbFLS. Additionally, when the GbF3H gene was overexpressed in tobacco and G. biloba calli, an increase in total flavonoid content was observed. These findings indicate that 25 mg/L of ZnO-NPs play a crucial role in G. biloba growth and the accumulation of flavonoids, which can potentially promote the yield and quality of G. biloba in production.
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- 2023
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48. miR-124 and VAMP3 Act Antagonistically in Human Neuroblastoma
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Xiaoxiao Zhang, Chengyong Yang, Zhen Meng, Huanhuan Zhong, Xutian Hou, Fenfen Wang, Yiping Lu, Jingjing Guo, and Yan Zeng
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miR-124 ,VAMP3 ,neuroblastoma ,apoptosis ,gene expression ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Neuroblastoma (NB) is the most common extracranial solid tumor that affects developing nerve cells in the fetus, infants, and children. miR-124 is a microRNA (miRNA) enriched in neuronal tissues, and VAMP3 (vesicle-associated membrane protein 3) has been reported to be an miR-124 target, although the relationship between NB and miR-124 or VAMP3 is unknown. Our current work identified that miR-124 levels are high in NB cases and that elevated miR-124 correlates with worse NB outcomes. Conversely, depressed VAMP3 correlates with worse NB outcomes. To investigate the mechanisms by which miR-124 and VAMP3 regulate NB, we altered miR-124 or VAMP3 expression in human NB cells and observed that increased miR-124 and reduced VAMP3 stimulated cell proliferation and suppressed apoptosis, while increased VAMP3 had the opposite effects. Genome-wide mRNA expression analyses identified gene and pathway changes which might explain the NB cell phenotypes. Together, our studies suggest that miR-124 and VAMP3 could be potential new markers of NB and targets of NB treatments.
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- 2023
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49. Effects of Fermented Cottonseed Meal Substitution for Fish Meal on Intestinal Enzymatic Activity, Inflammatory and Physical-Barrier-Related Gene Expression, and Intestinal Microflora of Juvenile Golden Pompano (Trachinotus ovatus)
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Zhanzhan Wang, Shuling Liao, Jun Wang, Yun Wang, Zhong Huang, Wei Yu, Xiaolin Huang, Heizhao Lin, Maoyan Luo, Zhenyan Cheng, and Chuanpeng Zhou
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fermented cottonseed meal ,substitution ,intestinal enzymatic activity ,gene expression ,intestinal microflora ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
The present study was conducted to investigate the effects of dietary fermented cottonseed meal (FCSM) substitution for fish meal on intestinal enzymatic activity, inflammatory and physical-barrier-related gene expression, and intestinal microflora of juvenile golden pompano. The 375 golden pompanos were divided into 15 groups of 25 fish each, with three replicates for each experimental group. The fish were fed five experimental diets (0 (FM), 12.5% (CSM12.5), 25% (CSM25), 50% (CSM50), and 100% (CSM100) substitution levels) for 8 weeks. The fish were reared and fed the experimental diets under a natural-day light cycle. Compared with the control group, the activities of AMY (amylase) enzymes in the CSM12.5 group and all other groups were elevated (p < 0.05). The CSM25 group exhibited a considerable up-regulation of IL-10 (Interleukin-10) expression relative to the FM group (p < 0.05). With an increase in dietary FM substitution with FCSM from 0 to 25%, the relative expressions of NF-κB (Nuclear factor kappa-B), IL-1β (Interleukin-1 beta), and IL-8 (Interleukin-8) were down-regulated. In this study, the relative expressions of ZO-1 (zonula occluden-1) and Occludin were up-regulated, and those of Claudin-3 and Claudin-15 significantly up-regulated, when the FCSM substitution ratio was 25%. The results of high-throughput sequencing of the intestinal microflora showed that ACE indices the lowest in the CSM25 group, which was significantly different from those in the CSM100 group (p < 0.05). The CSM50 group had the highest Shannon and Simpson indices and the highest community diversity. In addition, replacing a high percentage of fish meal with FCSM can negatively affect the intestinal flora of fish. In this study, the 25% substitution ratio improved nutrient absorption, reduced intestinal inflammation, improved intestinal physical barrier damage, did not affect intestinal microecology, and had no adverse effects on fish. However, substitution of a high proportion of FM with FCSM negatively affects the intestinal microflora and nutrient absorption capacity of fish.
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- 2023
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50. Genome-Wide Analysis of WUSCHEL-Related Homeobox Gene Family in Sacred Lotus (Nelumbo nucifera)
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Gui-Zhen Chen, Jie Huang, Zhi-Cong Lin, Fei Wang, Song-Min Yang, Xiao Jiang, Sagheer Ahmad, Yu-Zhen Zhou, Siren Lan, Zhong-Jian Liu, and Dong-Hui Peng
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NnWOXs ,transcription factor ,Nelumbo nucifera ,protein subcellular localization ,gene expression ,gene network ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
WUSCHEL-related homeobox (WOX) is a plant-specific transcription factor (TF), which plays an essential role in the regulation of plant growth, development, and abiotic stress responses. However, little information is available on the specific roles of WOX TFs in sacred lotus (Nelumbo nucifera), which is a perennial aquatic plant with important edible, ornamental, and medicinal values. We identified 15 WOX TFs distributing on six chromosomes in the genome of N. nucifera. A total of 72 WOX genes from five species were divided into three clades and nine subclades based on the phylogenetic tree. NnWOXs in the same subclades had similar gene structures and conserved motifs. Cis-acting element analysis of the promoter regions of NnWOXs found many elements enriched in hormone induction, stress responses, and light responses, indicating their roles in growth and development. The Ka/Ks analysis showed that the WOX gene family had been intensely purified and selected in N. nucifera. The expression pattern analysis suggested that NnWOXs were involved in organ development and differentiation of N. nucifera. Furthermore, the protein–protein interaction analysis showed that NnWOXs might participate in the growth, development, and metabolic regulation of N. nucifera. Taken together, these findings laid a foundation for further analysis of NnWOX functions.
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- 2023
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