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Sequential light programs shape kale (Brassica napus) sproutappearance and alter metabolic and nutrient content 被引量:6
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作者 Sofia D Carvalho Kevin M Folta 《Horticulture Research》 SCIE 2014年第1期244-256,共13页
Different light wavelengths have specific effects on plant growth and development.Narrow-bandwidth light-emitting diode(LED)lighting may be used to directionally manipulate size,color and metabolites in high-value fru... Different light wavelengths have specific effects on plant growth and development.Narrow-bandwidth light-emitting diode(LED)lighting may be used to directionally manipulate size,color and metabolites in high-value fruits and vegetables.In this report,Red Russian kale(Brassica napus)seedlings were grown under specific light conditions and analyzed for photomorphogenic responses,pigment accumulation and nutraceutical content.The results showed that this genotype responds predictably to darkness,blue and red light,with suppression of hypocotyl elongation,development of pigments and changes in specific metabolites.However,these seedlings were relatively hypersensitive to far-red light,leading to uncharacteristically short hypocotyls and high pigment accumulation,even after growth under very low fluence rates(,1 mmol m^(-2) s^(-1)).General antioxidant levels and aliphatic glucosinolates are elevated by far-red light treatments.Sequential treatments of darkness,blue light,red light and far-red light were applied throughout sprout development to alter final product quality.These results indicate that sequential treatment with narrow-bandwidth light may be used to affect key economically important traits in high-value crops. 展开更多
关键词 treatment content NARROW
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Genome-wide identification and characterization of ACBP gene family in Populus reveal salinity alkali-responsive profiles 被引量:1
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作者 Yu Chang Xinru Xu +5 位作者 Hongxia Zheng Hao Xie Bo Li Sixue Chen Ying Li Shaojun Dai 《Journal of Forestry Research》 SCIE CAS CSCD 2023年第2期481-496,共16页
Acyl-CoA-binding proteins(ACBPs)are important for the transport of acyl groups for macro molecular biosynthesis involved in plant growth,development,and diverse stress(e.g.,cold,drought,salinity,and heavy metals)respo... Acyl-CoA-binding proteins(ACBPs)are important for the transport of acyl groups for macro molecular biosynthesis involved in plant growth,development,and diverse stress(e.g.,cold,drought,salinity,and heavy metals)responses.Here,we report the phylogeny and characteristics of the ACBP family in the woody plant Populus trichocarpa.Eight genes encoding ACBP proteins were identified,and they are distributed on eight chromosomes in P.trichocarpa.These PtACBP genes were divided into four subgroups according to gene structure,conserved motifs and phylogenetic relationship.Promoter analysis revealed that cis-elements were related to stress response,phytohormone response,and physical and reproductive growth regulation.Expression levels of PtACBP genes varied among different organs,with the highest expression in leaves and the lowest in stems.Quantitative real-time PCR(qRT-PCR)analysis showed that under salinity-alkali stresses(i.e.,200 mM NaCl,75 mM Na2CO3,and 100 mM NaHCO3),four(PtACBP1,PtACBP3,PtACBP4 and PtACBP8)of eight PtACBP genes were significantly induced in roots and leaves.These data provide a comprehensive analysis of the ACBPs family in P.trichocarpa,which could be useful for gene function analyses. 展开更多
关键词 Acyl-CoA-binding proteins(ACBPs) Gene structure Expression pattern Stress response Populus trichocarpa
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A survey of FLS2 genes from multiple citrus species identifies candidates for enhancing disease resistance to Xanthomonas citri ssp. citri. 被引量:4
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作者 Qingchun Shi Vicente J Febres +1 位作者 Jeffrey B Jones Gloria A Moore 《Horticulture Research》 SCIE 2016年第1期208-218,共11页
Pathogen-associated molecular patterns(PAMPs)-triggered immunity(PTI)is an important component of plant innate immunity.In a previous study,we showed that the PAMP flg22 from Xanthomonas citri ssp.citri(Xflg22),the ca... Pathogen-associated molecular patterns(PAMPs)-triggered immunity(PTI)is an important component of plant innate immunity.In a previous study,we showed that the PAMP flg22 from Xanthomonas citri ssp.citri(Xflg22),the causal agent of citrus canker,induced PTI in citrus,which correlated with the observed levels of canker resistance.Here,we identified and sequenced two bacterial flagellin/flg22 receptors(FLS2-1 and FLS2-2)from‘Duncan’grapefruit(Citrus paradisi,CpFLS2-1 and CpFLS2-2)and‘Sun Chu Sha’mandarin(C.reticulata,CrFLS2-1 and CrFLS2-2).We were able to isolate only one FLS2 from‘Nagami’kumquat(Fortunella margarita,FmFLS2-1)and gene flanking sequences suggest a rearrangement event that resulted in the deletion of FLS2-2 from the genome.Phylogenetic analysis,gene structure and presence of critical amino acid domains all indicate we identified the true FLS2 genes in citrus.FLS2-2 was more transcriptionally responsive to Xflg22 than FLS2-1,with induced expression levels higher in canker-resistant citrus than in susceptible ones.Interestingly,‘Nagami’kumquat showed the highest FLS2-1 steady-state expression levels,although it was not induced by Xflg22.We selected FmFLS2-1,CrFLS2-2 and CpFLS2-2 to further evaluate their capacity to enhance bacterial resistance using Agrobacterium-mediated transient expression assays.Both FmFLS2-1 and CrFLS2-2,the two proteins from canker-resistant species,conferred stronger Xflg22 responses and reduced canker symptoms in leaves of the susceptible grapefruit genotype.These two citrus genes will be useful resources to enhance PTI and achieve resistance against canker and possibly other bacterial pathogens in susceptible citrus types. 展开更多
关键词 FLS2 CITRUS citri
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Inhibitors of glucose transport and glycolysis as novel anticancer therapeutics 被引量:1
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作者 Yanrong Qian Xuan Wang Xiaozhuo Chen 《World Journal of Translational Medicine》 2014年第2期37-57,共21页
Metabolic reprogramming and altered energetics have become an emerging hallmark of cancer and an active area of basic, translational, and clinical cancer research in the recent decade. Development of effective antican... Metabolic reprogramming and altered energetics have become an emerging hallmark of cancer and an active area of basic, translational, and clinical cancer research in the recent decade. Development of effective anticancer therapeutics may depend on improved understanding of the altered cancer metabolism compared to that of normal cells. Changes in glucose transport and glycolysis, which are drastically upregulated in most can-cers and termed the Warburg effect, are one of major focuses of this new research area. By taking advantage of the new knowledge and understanding of cancer's mechanisms, numerous therapeutic agents have been developed to target proteins and enzymes involved in glucose transport and metabolism, with promising results in cancer cells, animal tumor models and even clinical trials. It has also been hypothesized that targeting a pathway or a process, such as glucose transport or glucose metabolism, rather than a specific protein or enzyme in a signaling pathway may be more effective. This is based on the observation that cancer somehow can always bypass the inhibition of a target drug by switching to a redundant or compensatory pathway. In addition, cancer cells have higher dependence on glucose. This review will provide background information on glucose transport and metabolism in cancer, and summarize new therapeutic developments in basic and translational research in these areas, with a focus on glucose transporter inhibitors and glycolysis inhibitors. The daunting challenges facing both basic and clinical researchers of the field are also presented and discussed. 展开更多
关键词 Cancer metabolism WARBURG effect Glycolytic ENZYMES GLUCOSE transporters TRANSLATIONAL research
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Cytochrome P450 monooxygenase-mediated eicosanoid pathway:A potential mechanistic linkage between dietary fatty acid consumption and colon cancer risk
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作者 Weicang Wang Jianan Zhang Guodong Zhang 《Food Science and Human Wellness》 SCIE 2019年第4期337-343,共7页
Human consumption of linoleic acid(LA,18:2ω-6,abundant in vegetable oils)is very high.Animal experiments showed that excessive LA intake increased azoxymethane-induced colon tumorigenesis,however,the impact of excess... Human consumption of linoleic acid(LA,18:2ω-6,abundant in vegetable oils)is very high.Animal experiments showed that excessive LA intake increased azoxymethane-induced colon tumorigenesis,however,the impact of excessive LA on colon cancer in human is not conclusive,making it difficult to make dietary recommendations for optimal intake of LA.Understanding the molecular mechanisms of LA on colon tumorigenesis could help to clarify its health effect,and facilitate development of mechanismbased strategies for preventing colon cancer.Recent studies show that the previously unappreciated cytochrome P450 monooxygenase-mediated eicosanoid pathway is upregulated in colon cancer and plays critical roles in its pathogenesis,and could contribute to the effects of dietary LA,as well asω-3 fatty acids,on colon tumorigenesis.In this review,we will discuss recent studies about the roles of cytochrome P450 monooxygenases in fatty acid metabolism and its roles in colonic inflammation and colon cancer,and how this information could help us to clarify the health impacts of dietary fatty acids. 展开更多
关键词 Linoleic acid Polyunsaturated fatty acids ω-3 Fatty acids Colon cancer Colonic inflammation Cytochrome P450 EICOSANOIDS
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Bringing CAM photosynthesis to the table:Paving the way for resilient and productive agricultural systems in a changing climate
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作者 Noe´Perron Matias Kirst Sixue Chen 《Plant Communications》 SCIE CSCD 2024年第3期17-30,共14页
Modern agricultural systems are directly threatened by global climate change and the resulting freshwater crisis.A considerable challenge in the coming years will be to develop crops that can cope with the conse-quenc... Modern agricultural systems are directly threatened by global climate change and the resulting freshwater crisis.A considerable challenge in the coming years will be to develop crops that can cope with the conse-quences of declining freshwater resources and changing temperatures.One approach to meeting this chal-lenge may lie in our understanding of plant photosynthetic adaptations and water use efciency.Plants from various taxa have evolved crassulacean acid metabolism(CAM),a water-conserving adaptation of photosynthetic carbon dioxidexation that enables plants to thrive under semi-arid or seasonally drought-prone conditions.Although past research on CAM has led to a better understanding of the inner workings of plant resilience and adaptation to stress,successful introduction of this pathway into C3 or C4 plants has not been reported.The recent revolution in molecular,systems,and synthetic biology,as well as innovations in high-throughput data generation and mining,creates new opportunities to uncover the minimum genetic tool kit required to introduce CAM traits into drought-sensitive crops.Here,we pro-pose four complementary research avenues to uncover this tool kit.First,genomes and computational methods should be used to improve understanding of the nature of variations that drive CAM evolution.Second,single-cell’omics technologies offer the possibility for in-depth characterization of the mecha-nisms that trigger environmentally controlled CAM induction.Third,the rapid increase in new’omics data enables a comprehensive,multimodal exploration of CAM.Finally,the expansion of functional geno-mics methods is paving the way for integration of CAM into farming systems. 展开更多
关键词 CAM photosynthesis single-cell genomics PHYLOGENETICS crop engineering synthetic biology stress resilience
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Redox proteomics of tomato in response to Pseudomonas syringae infection 被引量:7
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作者 Kelly Mayrink Balmant Jennifer Parker +3 位作者 Mi-Jeong Yoo Ning Zhu Craig Dufresne Sixue Chen 《Horticulture Research》 SCIE 2015年第1期103-114,共12页
Unlike mammals with adaptive immunity,plants rely on their innate immunity based on pattern-triggered immunity(PTI)and effector-triggered immunity(ETI)for pathogen defense.Reactive oxygen species,known to play crucial... Unlike mammals with adaptive immunity,plants rely on their innate immunity based on pattern-triggered immunity(PTI)and effector-triggered immunity(ETI)for pathogen defense.Reactive oxygen species,known to play crucial roles in PTI and ETI,can perturb cellular redox homeostasis and lead to changes of redox-sensitive proteins through modification of cysteine sulfhydryl groups.Although redox regulation of protein functions has emerged as an important mechanism in several biological processes,little is known about redox proteins and how they function in PTI and ETI.In this study,cysTMT proteomics technology was used to identify similarities and differences of protein redox modifications in tomato resistant(PtoR)and susceptible(prf3)genotypes in response to Pseudomonas syringae pv tomato(Pst)infection.In addition,the results of the redox changes were compared and corrected with the protein level changes.A total of 90 potential redox-regulated proteins were identified with functions in carbohydrate and energy metabolism,biosynthesis of cysteine,sucrose and brassinosteroid,cell wall biogenesis,polysaccharide/starch biosynthesis,cuticle development,lipid metabolism,proteolysis,tricarboxylic acid cycle,protein targeting to vacuole,and oxidation–reduction.This inventory of previously unknown protein redox switches in tomato pathogen defense lays a foundation for future research toward understanding the biological significance of protein redox modifications in plant defense responses. 展开更多
关键词 IMMUNITY METABOLISM MODIFICATION
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Identifying genomic regions controlling ratoon stunting disease resistance in sugarcane(Saccharum spp.) clonal F_(1) population 被引量:2
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作者 Qian You Sushma Sood +4 位作者 Ziliang Luo Hongbo Liu Md.Sariful Islam Muqing Zhang Jianping Wang 《The Crop Journal》 SCIE CSCD 2021年第5期1070-1078,共9页
The ratoon stunting disease (RSD) of sugarcane,caused by the bacterium Leifsonia xyli subsp.xyli,is one of the major concerns to sugarcane production and breeding programs worldwide.Due to no obvious external symptoms... The ratoon stunting disease (RSD) of sugarcane,caused by the bacterium Leifsonia xyli subsp.xyli,is one of the major concerns to sugarcane production and breeding programs worldwide.Due to no obvious external symptoms,RSD cannot be easily detected by the growers,hence has reduced the world’s sugarcane production significantly.This study aimed to identify quantitative trait loci (QTL) associated with RSD resistance and to assist in the development of linked molecular markers for marker-assisted breeding to minimize the reduction in sugarcane yield by the RSD infection.A set of 146 individuals derived from a self-crossing of CP80-1827 were evaluated for RSD resistance in a mechanically duplicated inoculated field trial from 2014 to 2017 using tissue blot immunoassay.Leveraging the genetic data and the four years phenotyping data of CP80-1827 selfing population,linkage map construction and QTL analysis were conducted based on clonal F_1 and F_2 mapping population types with GACD V.1.2 and Ici Mapping V.3.3,respectively.A total of 23 QTL associated with RSD resistance were identified,which explained 6%to13%of the phenotypic variation with the two types of software.A total of 82 disease resistance genes were identified by searching these 23 QTL regions on their corresponding regions on the Sorghum bicolor genome (44 genes),sugarcane R570 genome (20 genes),and S.spontaneum genome (18 genes),respectively.Compared with Ici Mapping V.3.3,GACD V.1.2 identified more major (6 vs.3) and stable QTL (2vs.0),and more disease resistance genes (51 vs.31),indicating GACD V.1.2 (clonal F_1 mapping type) is most likely to be more efficient than Ici Mapping (F_2 mapping type) for QTL analysis of a sefling population or clonal F_1 population in clonal species.The identified QTL controlling RSD resistance along with the associated SNP markers will assist sugarcane molecular breeding programs in combating this disease. 展开更多
关键词 Quantitative trait loci(QTL) GACD IciMapping SNP marker Sugarcaneratoon stunting disease
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Glioblastoma-derived tumor cells induce vasculogenic mimicry through Flk-1 protein activation 被引量:1
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作者 Francescone R Scully S +5 位作者 Bentley B Yan W Taylor SL Oh D Moral L Shao R 《中国神经肿瘤杂志》 2013年第3期193-193,共1页
Glioblastoma(GBM)is extremely aggressive and essentially incurable.Its malignancy is characterized by vigorous microvascular proliferations.Recent evidence has shown that tumor cells display the ability to drive blood... Glioblastoma(GBM)is extremely aggressive and essentially incurable.Its malignancy is characterized by vigorous microvascular proliferations.Recent evidence has shown that tumor cells display the ability to drive blood-perfused vasculogenic mimicry(VM),an alternative microvascular circulation independent of endothelial cell angiogenesis.However,molecular mechanisms underlying this vascular 展开更多
关键词 丝裂原活化蛋白激酶 肿瘤细胞 血管生成 胶质细胞 母细胞 拟态 诱导 VEGF
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Prot-Class: A bioinformatics tool for protein classification based on amino acid signatures
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作者 Jens Lichtenberg Brian D. Keppler +4 位作者 Thomas Conley Dazhang Gu Paul Burns Lonnie R. Welch Allan M. Showalter 《Natural Science》 2012年第12期1161-1164,共4页
Knowledge about characteristics shared across known members of a protein family enables their identification within the complete set of proteins in an organism. Shared features are usually expressed through motifs, wh... Knowledge about characteristics shared across known members of a protein family enables their identification within the complete set of proteins in an organism. Shared features are usually expressed through motifs, which can incorporate specific patterns and even amino acid (AA) biases. Based on a set of classification patterns and biases it can be determined which additional proteins may belong to a specific family and share its functionality. A bioinformatics tool (Prot-Class) was implemented to examine protein sequences and characterize them based upon user-defined AA composition percentages and user defined AA patterns. In addition the tool allows for the identification of repeated AA patterns, biased AA compositions within windows of user-defined length, and the characteristics of putative signal peptides and glycosylphosphatidylinositol (GPI) lipid anchors. ProtClass is general purpose and can be applied to analyze protein sequences from any organism. The Prot-Class source code is available through the GNU General Public License v3 and can be accessed via the Google Code Repository: http://code.google.com/p/prot-class/. 展开更多
关键词 BIOINFORMATICS PROTEIN Classification ARABIDOPSIS
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Structural basis for polyuridine tract recognition by SARS-CoV-2 Nsp15
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作者 Fumiaki Ito Hanjing Yang +1 位作者 Z.Hong Zhou Xiaojiang S.Chen 《Protein & Cell》 SCIE CSCD 2024年第7期547-552,共6页
Dear Editor,Coronaviruses have evolved a wide array of tactics to evade host antiviral immunity.When host cells detect invading foreign nucleic acids including viral genome and viral replication intermediates,they act... Dear Editor,Coronaviruses have evolved a wide array of tactics to evade host antiviral immunity.When host cells detect invading foreign nucleic acids including viral genome and viral replication intermediates,they activate interferon(IFN)signaling via cytoplasmic pattern recognition receptors(Kang et al.,2002;Kato et al.,2006).Remarkable stealth activities exhibited by coronaviruses are facilitated by a series of non-structural proteins(Nsps),such as Nsp15(Deng and Baker,2018;Deng et al.,2019;Hackbart et al.,2020),which is a uridine-specific endoribonuclease that mediates evasion of host detection of viral double-stranded RNA(dsRNA)(Bhardwaj et al.,2004;Deng et al.,2017;Frazier et al.,2021;Ivanov et al.,2004).Nsp15 targets a polyuridine[poly(U)]tract on the coronavirus negative strand RNA(Hackbart et al.,2020).Nsp15 limits the abundance and length of poly(U)within the negative strand RNA 5ʹ-extension by trimming down the initially synthesized poly(U)lead sequence to the optimal length that can suppress dsRNA formation but still serves as a template for poly(A)tail of the positive strand genome of the coronaviruses(Hofmann and Brian,1991). 展开更多
关键词 P15 INTERFERON TEMPLATE
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IRX14 and IRX14-LIKE, Two Glycosyl Transferases Involved in Glucuronoxylan Biosynthesis and Drought Tolerance in Arabidopsis 被引量:10
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作者 Brian D. Keppler Allan M. Showalter 《Molecular Plant》 SCIE CAS CSCD 2010年第5期834-841,共8页
IRX14 and IRX14-LIKE (IRX14L) are two closely related glycosyl transferases in the glycosyl transferase 43 (GT43) family of Arabidopsis. A T-DNA insertion mutant for IRX14 results in comparatively minor changes, s... IRX14 and IRX14-LIKE (IRX14L) are two closely related glycosyl transferases in the glycosyl transferase 43 (GT43) family of Arabidopsis. A T-DNA insertion mutant for IRX14 results in comparatively minor changes, such as irregular xylem, while a mutation for IRX14L results in no changes. However, an irx14 and irx14L double mutant severely affects growth and development, with the dwarf plants failing to produce an inflorescence stem. Plants that are homozygous for IRX14 but heterozygous for IRX14L (irx14 irx14L(±)) exhibit an intermediate phenotype, including noticeably smaller leaves, stems, and underdeveloped siliques. Additionally, the T-DNA insertion mutant for IRX14 was found to result in a drought-tolerant phenotype. Carbohydrate analysis of total cell wall extracts revealed a reduction in xylose for the irx14 and irx14 irx14L(±) mutants, consistent with a defect in glucuronoxylan biosynthesis. Immunolocalization of xylan with the LM10 antibody revealed a loss of xylan in irx14 mutants and a further reduction in the irx14 irx14L(±) mutants. IRX14L likely functions redundantly with IRX14 in glucuronoxylan biosynthesis, with IRX14 having a more important role in the process. 展开更多
关键词 Abiotic/environmental stress cell walls genetics ARABIDOPSIS irregular xylem xylan.
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rhe Mitochondrion-Targeted PENTATRICOPEPTIDE REPEAT78 Protein Is Required for nad5 Mature mRNA Stability and Development in Maize 被引量:13
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作者 Ya-Feng Zhang Masaharu Suzuki +1 位作者 Feng Sun Bao-Cai Tan 《Molecular Plant》 SCIE CAS CSCD 2017年第10期1321-1333,共13页
Pentatricopepetide repeat (PPR) proteins are a large family of RNA-binding proteins involved in RNA meta- bolism in plant organelles. Although many PPR proteins have been functionally studied, few of them are identi... Pentatricopepetide repeat (PPR) proteins are a large family of RNA-binding proteins involved in RNA meta- bolism in plant organelles. Although many PPR proteins have been functionally studied, few of them are identified with a function in mitochondrial RNA stability. By using a reverse genetic approach, we characterized the role of the mitochondrion-targeted PPR78 protein in nad5 mature mRNA stability and maize (Zea mays) seed development. Loss of PPR78 function leads to a dramatic reduction in the steady-state level of mitochondrial nad5 mature mRNA, blocks the assembly of complex I in the electron transport chain, and causes an arrest in embryogenesis and endosperm development. Characterization of a second strong allele confirms the function of PPR78 in nad5 mRNA accumulation and maize seed development. The generation of mature nad5 requires the assembly of three distinct precursor RNAs via transsplicing reactions, and the accumulation ofnad5T1 precursor is reduced in the ppr78 mutants. However, it is the instability of mature nad5 rather than nad5T1 causing loss of the full-length nad5 transcript, and degradation of nad5 losing both translation start and stop codons is enriched in the mutant. Our data imply the assembly of mature nad5 mRNA precedes the protection of PPR78. 展开更多
关键词 PPR nad5 mitochondrial RNA stability complex I seed development MAIZE
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Proteomics and Metabolomics of Arabidopsis Responses to Perturbation of Glucosinolate Biosynthesis 被引量:3
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作者 Ya-zhou Chen Qiu-Ying Pang +4 位作者 Yan He Ning Zhu Isabel Branstrom Xiu-Feng Yan Sixue Chen 《Molecular Plant》 SCIE CAS CSCD 2012年第5期1138-1150,共13页
To understand plant molecular networks of glucosinolate metabolism, perturbation of aliphatic glucosinolate biosynthesis was established using inducible RNA interference (RNAi) in Arabidopsis. Two RNAi lines were ch... To understand plant molecular networks of glucosinolate metabolism, perturbation of aliphatic glucosinolate biosynthesis was established using inducible RNA interference (RNAi) in Arabidopsis. Two RNAi lines were chosen for examining global protein and metabolite changes using complementary proteomics and metabolomics approaches. Pro- teins involved in metabolism including photosynthesis and hormone metabolism, protein binding, energy, stress, and defense showed marked responses to glucosinolate perturbation. In parallel, metabolomics revealed major changes in the levels of amino acids, carbohydrates, peptides, and hormones. The metabolomics data were correlated with the pro- teomics results and revealed intimate molecular connections between cellular pathways/processes and glucosinolate me- tabolism. This study has provided an unprecedented view of the molecular networks of glucosinolate metabolism and laid a foundation towards rationale glucosinolate engineering for enhanced defense and quality. 展开更多
关键词 Arabidopsis thaliana RNAi glucosinolate perturbation PROTEOMICS metabolomics molecular networks.
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G-Quadruplex(G4) Motifs in the Maize(Zea mays L.) Genome Are Enriched at Specific Locations in Thousands of Genes Coupled to Energy Status,Hypoxia,Low Sugar,and Nutrient Deprivation 被引量:2
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作者 Carson M.Andorf Mykhailo Kopylov +4 位作者 Drena Dobbs Karen E.Koch M.Elizabeth Stroupe Carolyn J.Lawrence Hank W.Bass 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2014年第12期627-647,共21页
The G-quadruplex (G4) elements comprise a class of nucleic acid structures formed by stacking of guanine base quartets in a quadruple helix. This (34 DNA can form within or across single-stranded DNA molecules and ... The G-quadruplex (G4) elements comprise a class of nucleic acid structures formed by stacking of guanine base quartets in a quadruple helix. This (34 DNA can form within or across single-stranded DNA molecules and is mutually exclusive with duplex B-form DNA. The reversibility and structural diversity of G4s make them highly versatile genetic structures, as demonstrated by their roles in various functions including telomere metabolism, genome maintenance, immunoglobulin gene diversification, transcription, and translation. Sequence motifs capable of forming G4 DNA are typically located in telomere repeat DNA and other non-telomeric genomic loci. To investigate their potential roles in a large-genome model plant species, we computationaily identified 149,988 non-telomeric G4 motifs in maize (Zea mays L., B73 AGPv2), 29% of which were in non-repetitive genomic regions. G4 motif hotspots exhibited non-random enrichment in genes at two locations on the antisense strand, one in the 5~ UTR and the other at the 5~ end of the first intron. Several genic G4 motifs were shown to adopt sequence-specific and potassium-dependent G4 DNA structures in vitro. The G4 motifs were prevalent in key regulatory genes associated with hypoxia (group VII ERFs), oxidative stress (D J-1/GATasel), and energy status (AMPK/ SnRK) pathways. They also showed statistical enrichment for genes in metabolic pathways that function in glycolysis, sugar degradation, inositol metabolism, and base excision repair. Collectively, the maize G4 motifs may represent conditional regulatory elements that can aid in energy status gene responses. Such a network of elements could provide a mechanistic basis for linking energy status signals to gene regulation in maize, a model genetic system and major world crop species for feed, food, and fuel. 展开更多
关键词 MAIZE G-QUADRUPLEX G4 HYPOXIA Sucrose synthase
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Na_(2)CO_(3)-responsive Photosynthetic and ROS Scavenging Mechanisms in Chloroplasts of Alkaligrass Revealed by Phosphoproteomics
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作者 Jinwei Suo Heng Zhang +19 位作者 Qi Zhao Nan Zhang Yongxue Zhang Ying Li Baohua Song Juanjuan Yu Jianguo Cao Tai Wang Ji Luo Lihai Guo Jun Ma Xumin Zhang Yimin She Lianwei Peng Weimin Ma Siyi Guo Yuchen Miao Sixue Chen Zhi Qin Shaojun Dai 《Genomics, Proteomics & Bioinformatics》 SCIE CAS CSCD 2020年第3期271-288,共18页
Alkali-salinity exerts severe osmotic,ionic,and high-p H stresses to plants.To understand the alkali-salinity responsive mechanisms underlying photosynthetic modulation and reactive oxygen species(ROS)homeostasis,phys... Alkali-salinity exerts severe osmotic,ionic,and high-p H stresses to plants.To understand the alkali-salinity responsive mechanisms underlying photosynthetic modulation and reactive oxygen species(ROS)homeostasis,physiological and diverse quantitative proteomics analyses of alkaligrass(Puccinellia tenuiflora)under Na_(2)CO_(3)stress were conducted.In addition,Western blot,real-time PCR,and transgenic techniques were applied to validate the proteomic results and test the functions of the Na_(2)CO_(3)-responsive proteins.A total of 104 and 102 Na_(2)CO_(3)-responsive proteins were identified in leaves and chloroplasts,respectively.In addition,84 Na_(2)CO_(3)-responsive phosphoproteins were identified,including 56 new phosphorylation sites in 56 phosphoproteins from chloroplasts,which are crucial for the regulation of photosynthesis,ion transport,signal transduction,and energy homeostasis.A full-length Pt FBA encoding an alkaligrass chloroplastic fructosebisphosphate aldolase(FBA)was overexpressed in wild-type cells of cyanobacterium Synechocystis sp.Strain PCC 6803,leading to enhanced Na_(2)CO_(3)tolerance.All these results indicate that thermal dissipation,state transition,cyclic electron transport,photorespiration,repair of photosystem(PS)Ⅱ,PSI activity,and ROS homeostasis were altered in response to Na_(2)CO_(3)stress,which help to improve our understanding of the Na_(2)CO_(3)-responsive mechanisms in halophytes. 展开更多
关键词 CHLOROPLASTS Na_(2)CO_(3)stress ROS scavenging PHOSPHOPROTEOMICS Puccinellia tenuiflora
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Advances in quantitative proteomics 被引量:1
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作者 Yuguang WANG Haiying LI Sixue CHEN 《Frontiers in Biology》 CSCD 2010年第3期195-203,共9页
Large-scale protein quantification has become a major proteomics application in many areas of biological and medical research.During the past years,different techniques have been developed,including gel-based such as ... Large-scale protein quantification has become a major proteomics application in many areas of biological and medical research.During the past years,different techniques have been developed,including gel-based such as differential in-gel electrophoresis(DIGE)and liquid chromatography-based such as isotope labeling and labelfree quantification.These quantitative proteomics tools hold significant promise for biomarker discovery,diagnostic and therapeutic applications.They are also important for research in functional genomics and systems biology towards basic understanding of molecular networks and pathway interactions.In this review,we summarize current technologies in quantitative proteomics and discuss recent applications of the technologies. 展开更多
关键词 two dimensional gel liquid chromatographymass spectrometry(LC-MS) stable isotope quantification APPLICATION
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Fern spore germination in response to environmental factors 被引量:1
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作者 Jinwei Suo Sixue Chen +2 位作者 Qi Zhao Lei Shi Shaojun Dai 《Frontiers in Biology》 CAS CSCD 2015年第4期358-376,共19页
Fern spore germination gives rise to the rhizoid and protonemal cell through asymmetric cell division, and then develops into a gametophyte. Spore germination is also a representative single-cell model for the investi... Fern spore germination gives rise to the rhizoid and protonemal cell through asymmetric cell division, and then develops into a gametophyte. Spore germination is also a representative single-cell model for the investigation of nuclear polar movement, asymmetrical cell division, polarity establishment and rhizoid tip-growth. These processes are affected by various environmental factors, such as light, gravity, phytohormones, metal ions, and temperature. Here, we present a catalog of spore germination in response to different environmental factors. They are as follows: (1) Representative modes of light affecting spore germination from different fern species include red light-stimulated and far red light-inhibited spore germination, far red light-uninhibited spore germination, blue light-inhibited spore germination, and spore germination in the dark. The optimal light intensity and illumination time for spore germination are different among various fern species. Light response upon spore germination is initiated from the cell mitosis that regulated by phytochromes (PHYs) and cryptochromes (CRYs). AcPHY2, AcCRY3 and/or AcCRY4 are hypothesized to be involved in spore germination; (2) Gravity and calcium are crucial to early nuclear movement and polarity establishment of spores; (3) Gibberellin and antheridiogen can initiate and promote spore germination in many species, but abscisic acid, jasmonic acid, and ethylene pose only minor effects; (4) Spores can obtain the maximal germination rate in their favorable growth medium. Moreover, metal ions, pH, and spore density in the culture medium also affect spore germination; (5) Most fern spores germinate at 25℃, and an optimal CO2 concentration is necessary for spore germination of certain fern plants. These provide valuable information for understanding fern spore germination in response to environmental factors. 展开更多
关键词 FEM SPORE GERMINATION environmental factors
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Proteomics characteristics of rice leaves in response to environmental factors
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作者 Sining KANG Sixue CHEN Shaojun DAI 《Frontiers in Biology》 CSCD 2010年第3期246-254,共9页
Rice is an important food crop worldwide.Its productivity has been influenced by various abiotic and biotic factors including temperature,drought,salt,microbe,ozone,hormone and glyphosate.The responses of plants to st... Rice is an important food crop worldwide.Its productivity has been influenced by various abiotic and biotic factors including temperature,drought,salt,microbe,ozone,hormone and glyphosate.The responses of plants to stress are regulated by multiple signaling pathways,and the mechanisms of leaf growth and development in response to stress remain unclear to date.Recently,proteomics studies have provided new evidence for better understanding the mechanisms.The proteins in response to different stress conditions are mainly involved in photosynthesis,signal transduction,transcription,protein synthesis and destination,defense response,cytoskeleton,energy,cell wall and other metabolism.In addition,some stress type-specific proteins have been identified,such as small heat shock proteins under temperature stress,S-like RNase homolog and actin depolymerizing factor under drought stress,ascorbate peroxidase and lipid peroxidation under salt stress,probenazole-inducible protein and rice pathogenesis-related proteins under blast fungus.Many of the proteins including ribulose-1,5-bisphosphate carboxylase/oxygenase(RuBisCO),molecular chaperones,antioxidases and S-adenosylmethionine synthetase play very important roles in leaves.This paper reviews the proteomic characterization of rice leaves in response to various environmental factors. 展开更多
关键词 RICE LEAF PROTEOMICS environmental factor
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Stimulation of in vitro bone formation by canine prostate cancer
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作者 Shiyu Yuan Noriko Kantake +2 位作者 Daniel E.Hellmann Said M.Elshafae Thomas J.Rosol 《Journal of Cancer Metastasis and Treatment》 2021年第1期511-523,共13页
Aim:Patients with prostate cancer frequently develop osteoblastic bone metastases.Canine models are important because dogs are the only mammal to develop spontaneous prostate cancer with osteoblastic bone metastases s... Aim:Patients with prostate cancer frequently develop osteoblastic bone metastases.Canine models are important because dogs are the only mammal to develop spontaneous prostate cancer with osteoblastic bone metastases similar to men.The mechanism by which prostate cancer induces bone formation is unclear;however,it depends on the complex interaction between prostate cancer cells and bone microenvironment.This study investigated the effects of three canine prostate cancer cell lines(Ace-1,LuMa,and Probasco)on bone formation and resorption in vitro.Methods:Mouse calvaria were treated with conditioned medium(CM)from cell lines.Calvaria were evaluated by histology,fluorescent calcein uptake at sites of bone mineralization,medium calcium assay,and alkaline phosphatase activity.The expression of bone-related genes was measured using quantitative reverse transcription PCR.Results:A novel calcein uptake assay was developed to measure bone formation and mineralization in vitro.Ace-1 CM induced predominantly bone resorption in calvaria,while Probasco CM induced marked bone formation,mineralization,and healing of calvaria defects.The expression of osteoblast-related genes in calvaria showed that Probasco CM stimulated the maturation and differentiation of osteoblasts and inhibited osteoclastogenesis.Both bone modeling and remodeling were involved in Probasco CM-induced bone formation and mineralization by inhibiting remodeling with zoledronic acid.Inhibition of WNT activity by DKK-1 decreased the osteoblastic activity of Probasco cells.Conclusion:Probasco cells induced bone formation and mineralization in vitro that depended on the WNT signaling pathway.Probasco cells will serve as a valuable model for studying the mechanisms of osteoblastic bone metastasis in prostate cancer. 展开更多
关键词 Bone CANINE DOG METASTASIS OSTEOBLAST prostate cancer zoledronic acid DKK-1
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