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Gene expression profiles in early leaf of rice(Oryza sativa)and foxtail millet(Setaria italica)
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作者 Jing Sun Chen Deng +10 位作者 Xiuru Dai Haoshu Li Liying Zhang Jingke Wang Hang Zhao Yirong Yang NghiVan Phung Zhiguo Zhang Pinghua Li Xuehui Sun Tiegang Lu 《The Crop Journal》 SCIE CSCD 2024年第3期776-787,共12页
Plant anatomy is patterned early during leaf development which suggests studying the spatial–temporal transcriptomes of primordia will help identify critical regulative and functional genes.We successfully isolated t... Plant anatomy is patterned early during leaf development which suggests studying the spatial–temporal transcriptomes of primordia will help identify critical regulative and functional genes.We successfully isolated the leaf primordia tissues from the C3grass rice and the C4grass foxtail millet by laser capture microdissection(LCM)and studied the gene expression throughout leaf developmental stages.Our data analysis uncovered the conserved expression patterns of certain gene clusters both in rice and foxtail millet during leaf development.We revealed genes and transcription factors involved in vein formation,stomatal development,and suberin accumulation.We identified 79 candidate genes associated with functional regulation of C4anatomy formation.Screening phenotype of the candidate genes revealed that knock-out of a putative polar auxin transport related gene NAL1 resulted significantly reduced veinal space in rice leaf.Our present work provides a foundation for future analyses of genes with novel functions in grasses and their role in leaf development,in particular the role in leaves with a contrasting C3vs.C4biosynthetic pathway. 展开更多
关键词 RICE Foxtail millet Leaf development RNA-SEQ LCM
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Synthesis of betanin by expression of the core betalain biosynthetic pathway in carrot
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作者 Bo Wang Yahui Wang +2 位作者 Yuanjie Deng Quanhong Yao Aisheng Xiong 《Horticultural Plant Journal》 SCIE CAS CSCD 2024年第3期732-742,共11页
Betalain has received increased attention because of its high nutritional value and crucial physiological functions.Based on the elucidation of its core biosynthetic pathway,betalain can be produced in additional plan... Betalain has received increased attention because of its high nutritional value and crucial physiological functions.Based on the elucidation of its core biosynthetic pathway,betalain can be produced in additional plants by metabolic engineering.Synthesis of betalain in carrot(Daucus carota L.)can improve its nutritional quality and economic value by extracting betalain from the fleshy root,non-edible part,and processing residue of carrot.In this study,two different constructs,namely,pYB:mCD(AomelOS,BvCYP76AD1S,and BvDODA1S)and p YB:CDD(BvCYP76AD1S,BvDODA1S,and MjcDOPA5GTS),were introduced into carrot for betanin synthesis by Agrobacterium-mediated transformation.Betanin can be synthetized in both transgenic calli,and p YB:m CD-transgenic callus can be used to produce betacyanin by suspension culture.However,pYB:mCD-transgenic seedlings can synthetize betanin only by tyrosine feeding.The p YB:CDD-transgenic lines can synthetize betanin in whole plants.The betanin content in fleshy root of pYB:CDD-transgenic carrot was(63.4±9)μg·g^(-1)fresh weight according to quantitative analysis.These betanin-producing carrot plant materials can be used to synthesize betanin for industrial application or consumption as dietary sources. 展开更多
关键词 Daucus carota L. BETANIN Biosynthesis Metabolic engineering BIOFORTIFICATION
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Genetically modified pigs with CD163 point mutation are resistant to HP-PRRSV infection
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作者 Ying Liu Lin Yang +9 位作者 Hong-Yong Xiang Ming Niu Jia-Cheng Deng Xue-Yuan Li Wen-Jie Hao Hong-Sheng Ou-Yang Tong-Yu Liu Xiao-Chun Tang Da-Xin Pang Hong-Ming Yuan 《Zoological Research》 SCIE CSCD 2024年第4期833-844,共12页
Porcine reproductive and respiratory syndrome(PRRS)is a globally prevalent contagious disease caused by the positive-strand RNA PRRS virus(PRRSV),resulting in substantial economic losses in the swine industry.Modifyin... Porcine reproductive and respiratory syndrome(PRRS)is a globally prevalent contagious disease caused by the positive-strand RNA PRRS virus(PRRSV),resulting in substantial economic losses in the swine industry.Modifying the CD163 SRCR5 domain,either through deletion or substitution,can eff1ectively confer resistance to PRRSV infection in pigs.However,large fragment modifications in pigs inevitably raise concerns about potential adverse effects on growth performance.Reducing the impact of genetic modifications on normal physiological functions is a promising direction for developing PRRSV-resistant pigs.In the current study,we identified a specific functional amino acid in CD163 that influences PRRSV proliferation.Viral infection experiments conducted on Marc145 and PK-15CD163 cells illustrated that the mE535G or corresponding pE529G mutations markedly inhibited highly pathogenic PRRSV(HP-PRRSV)proliferation by preventing viral binding and entry.Furthermore,individual viral challenge tests revealed that pigs with the E529G mutation had viral loads two orders of magnitude lower than wild-type(WT)pigs,confirming effective resistance to HP-PRRSV.Examination of the physiological indicators and scavenger function of CD163 verified no significant differences between the WT and E529G pigs.These findings suggest that E529G pigs can be used for breeding PRRSV-resistant pigs,providing novel insights into controlling future PRRSV outbreaks. 展开更多
关键词 PRRSV CD163 Point mutation E529G PIGS
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Genetic diversity of the S-type small subunit ribosomal RNA gene of Plasmodium knowlesi isolates from Sabah,Malaysian Borneo and Peninsular Malaysia
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作者 Eric Tzyy Jiann Chong Joveen Wan Fen Neoh +3 位作者 Tiek Ying Lau Kek Heng Chua Yvonne Ai-Lian Lim Ping-Chin Lee 《Asian Pacific Journal of Tropical Medicine》 SCIE CAS 2024年第2期84-90,共7页
Objective:To determine the genetic diversity of Plasmodium(P.)knowlesi isolates from Sabah,Malaysian Borneo and Peninsular Malaysia,targeting the S-type SSU rRNA gene and including aspects of natural selection and hap... Objective:To determine the genetic diversity of Plasmodium(P.)knowlesi isolates from Sabah,Malaysian Borneo and Peninsular Malaysia,targeting the S-type SSU rRNA gene and including aspects of natural selection and haplotype.Methods:Thirty-nine blood samples infected with P.knowlesi were collected in Sabah,Malaysian Borneo and Peninsular Malaysia.The S-type SSU rRNA gene was amplified using polymerase chain reaction,cloned into a vector,and sequenced.The natural selection and haplotype of the S-type SSU rRNA gene sequences were determined using DnaSP v6 and illustrated using NETWORK v10.This study's 39 S-type SSU rRNA sequences and eight sequences from the Genbank database were subjected to phylogenetic analysis using MEGA 11.Results:Overall,the phylogenetic analysis showed no evidence of a geographical cluster of P.knowlesi isolates from different areas in Malaysia based on the S-type SSU rRNA gene sequences.The S-type SSU rRNA gene sequences were relatively conserved and with a purifying effect.Haplotype sharing of the S-type SSU rRNA gene was observed between the P.knowlesi isolates in Sabah,Malaysian Borneo,but not between Sabah,Malaysian Borneo and Peninsular Malaysia.Conclusions:This study suggests that the S-type SSU rRNA gene of P.knowlesi isolates in Sabah,Malaysian Borneo,and Peninsular Malaysia has fewer polymorphic sites,representing the conservation of the gene.These features make the S-type SSU rRNA gene suitable for comparative studies,such as determining the evolutionary relationships and common ancestry among P.knowlesi species. 展开更多
关键词 Plasmodium knowlesi S-type small subunit ribosomal RNA Genetic diversity Natural selection HAPLOTYPE
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OsPPG encodes a pseudouridine-5'-phosphate glycosidase and regulates rice spikelet development
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作者 Rui Chen Dagang Tian +9 位作者 Yarong Lin Jiaqing Huang Qinqin Yang Yupei Li Huaqing Liu Shaohua Yang Jingyang Chen Shufen Zhou Feng Wang Shubiao Zhang 《The Crop Journal》 SCIE CSCD 2024年第3期698-708,共11页
Florets are the basic structural units of spikelets,and their morphogenesis determines the yield and quality of rice grains.However,whether and how pseudouridine-5’-phosphate glycosidase participates in rice spikelet... Florets are the basic structural units of spikelets,and their morphogenesis determines the yield and quality of rice grains.However,whether and how pseudouridine-5’-phosphate glycosidase participates in rice spikelet development remains an open question.In this study,we identified a novel gene,OsPPG,which encodes a peroxisome-localized pseudouridine-5’-phosphate glycosidase and regulates the development of rice spikelets.osppg mutants exhibited abnormal sterile lemma,lemma,palea,lodicule,stamens,and pistils;male sterility;shorter panicles;and reduced plant height.OsPPG was found to regulate several OsMADS genes,thereby affecting the morphogenesis of rice spikelets.Furthermore,metabolomics revealed that the OsPPG gene was involved in the decomposition of pseudouridine via the pyrimidine metabolism pathway and may affect the jasmonic acid signaling pathway.These results suggest that OsPPG is a key regulator of rice spikelet development. 展开更多
关键词 OsPPG Reproductive regulation Spikelet development RICE
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Development of a single transcript CRISPR/Cas9 toolkit for efficient genome editing in autotetraploid alfalfa
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作者 Haixia Zhao Siyi Zhao +12 位作者 Yingping Cao Xiping Jiang Lijuan Zhao Zhimeng Li Mengqi Wang Ruijuan Yang Chuanen Zhou Zhaoming Wang Feng Yuan Dongmei Ma Hao Lin Wenwen Liu Chunxiang Fu 《The Crop Journal》 SCIE CSCD 2024年第3期788-795,共8页
Alfalfa(Medicago sativa.L.)is a globally significant autotetraploid legume forage crop.However,despite its importance,establishing efficient gene editing systems for cultivated alfalfa remains a formidable challenge.I... Alfalfa(Medicago sativa.L.)is a globally significant autotetraploid legume forage crop.However,despite its importance,establishing efficient gene editing systems for cultivated alfalfa remains a formidable challenge.In this study,we pioneered the development of a highly effective ultrasonic-assisted leaf disc transformation system for Gongnong 1 alfalfa,a variety widely cultivated in Northeast China.Subsequently,we created a single transcript CRISPR/Cas9(CRISPR_2.0)toolkit,incorporating multiplex gRNAs,designed for gene editing in Gongnong 1.Both Cas9 and gRNA scaffolds were under the control of the Arabidopsis ubiquitin-10 promoter,a widely employed polymeraseⅡconstitutive promoter known for strong transgene expression in dicots.To assess the toolkit’s efficiency,we targeted PALM1,a gene associated with a recognizable multifoliate phenotype.Utilizing the CRISPR_2.0 toolkit,we directed PALM1 editing at two sites in the wild-type Gongnong 1.Results indicated a 35.1%occurrence of editing events all in target 2 alleles,while no mutations were detected at target 1 in the transgenic-positive lines.To explore more efficient sgRNAs,we developed a rapid,reliable screening system based on Agrobacterium rhizogenes-mediated hairy root transformation,incorporating the visible reporter MtLAP1.This screening system demonstrated that most purple visible hairy roots underwent gene editing.Notably,sgRNA3,with an 83.0%editing efficiency,was selected using the visible hairy root system.As anticipated,tetra-allelic homozygous palm1 mutations exhibited a clear multifoliate phenotype.These palm1 lines demonstrated an average crude protein yield increase of 21.5%compared to trifoliolate alfalfa.Our findings highlight the modified CRISPR_2.0 system as a highly efficient and robust gene editing tool for autotetraploid alfalfa. 展开更多
关键词 ALFALFA Gene editing CRISPR_2.0 toolkit Hairy root system Tetra-allelic homozygous mutants
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A simple and efficient CRISPR/Cas9 system permits ultra-multiplex genome editing in plants
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作者 Suting Wu Htin Kyaw +11 位作者 Zhijun Tong Yirong Yang Zhiwei Wang Liying Zhang Lihua Deng Zhiguo Zhang Bingguang Xiao William Paul Quick Tiegang Lu Guoying Xiao Guannan Qin Xue'an Cui 《The Crop Journal》 SCIE CSCD 2024年第2期569-582,共14页
The development and maturation of the CRISPR/Cas genome editing system provides a valuable tool for plant functional genomics and genetic improvement.Currently available genome-editing tools have a limited number of t... The development and maturation of the CRISPR/Cas genome editing system provides a valuable tool for plant functional genomics and genetic improvement.Currently available genome-editing tools have a limited number of targets,restricting their application in genetic research.In this study,we developed a novel CRISPR/Cas9 plant ultra-multiplex genome editing system consisting of two template vectors,eight donor vectors,four destination vectors,and one primer-design software package.By combining the advantages of Golden Gate cloning to assemble multiple repetitive fragments and Gateway recombination to assemble large fragments and by changing the structure of the amplicons used to assemble sg RNA expression cassettes,the plant ultra-multiplex genome editing system can assemble a single binary vector targeting more than 40 genomic loci.A rice knockout vector containing 49 sg RNA expression cassettes was assembled and a high co-editing efficiency was observed.This plant ultra-multiplex genome editing system advances synthetic biology and plant genetic engineering. 展开更多
关键词 CRISPR/Cas9 Multiplex genome editing Assembly system PLANT
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OsNPF3.1,a member of the NRT1/PTR family,increases nitrogen use efficiency and biomass production in rice 被引量:1
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作者 Xinghai Yang Baoxuan Nong +14 位作者 Can Chen Junrui Wang Xiuzhong Xia Zongqiong Zhang Yu Wei Yu Zeng Rui Feng Yanyan Wu Hui Guo Haifeng Yan Yuntao Liang Shuhui Liang Yong Yan Danting Li Guofu Deng 《The Crop Journal》 SCIE CSCD 2023年第1期108-118,共11页
The overuse of nitrogen(N)fertilizer in fields has increased production costs and raised environmental concerns.Increasing the N use efficiency(NUE)of rice varieties is crucial for sustainable agriculture.Here we repo... The overuse of nitrogen(N)fertilizer in fields has increased production costs and raised environmental concerns.Increasing the N use efficiency(NUE)of rice varieties is crucial for sustainable agriculture.Here we report the cloning and characterization of OsNPF3.1,a gene that controls rice NUE.An amino acid mutation in the OsNPF3.1 coding region caused different NUEs in wild and cultivated rice.OsNPF3.1,which is expressed mainly in the aerial parts of rice,also affects rice plant height,heading date,and thousand-grain weight.The OsNPF3.1 protein is located in the plasma membrane.When OsNPF3.1 was subjected to artificial selection,two naturally varying loci were associated with NUE,of which OsNPF3.1Chr6_8741040differed between indica and japonica rice.OsNPF3.1 can be used as a new target gene for breeding rice varieties with high NUE. 展开更多
关键词 RICE OsNPF3.1 Functional analysis Evolutionary analysis Natural variation
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Root Endophyte Shift and Key Genera Discovery in Rice under Barnyardgrass Stress
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作者 LI Shuyan YAN Qiling +3 位作者 WANG Jieyu JIANG Huidan LI Zuren PENG Qiong 《Rice science》 SCIE CSCD 2023年第2期160-170,I0040-I0048,共20页
Despite increasing knowledge of barnyardgrass(Echinochloa crus-galli) interference with rice, relatively little is known how endophytes improve the ability of rice against barnyardgrass stress. Here, we provided a det... Despite increasing knowledge of barnyardgrass(Echinochloa crus-galli) interference with rice, relatively little is known how endophytes improve the ability of rice against barnyardgrass stress. Here, we provided a detailed temporal characterization of rice root-associated microbiomes during co-cultivation with barnyardgrass and a comparison with the microbiomes of weed-free rice plants. Alpha diversity analysis indicated that barnyardgrass had the opposite effects on endophytic bacteria and fungi in rice roots, in terms of the community diversity, richness and coverage at the rice seedling stage. Principal coordinate analysis showed that barnyardgrass had only a minor effect on the community composition of endophytes in rice roots at the rice seedling stage, but showed a significant and maximum interference at the heading stage. Rice recruited many endophytes to resist biotic stress from barnyardgrass, especially for fungi. PICRUSt(phylogenetic investigation of communities by reconstruction of unobserved states) predictive analysis indicated that 23 metabolic pathways of bacteria were overrepresented in rice. In addition, the main trophic mode of fungi was pathotroph according to FUNGuild analysis. A positive correlation between bacteria and fungi in rice roots was found via network analysis. Anaeromyxobacter, Azospira and Pseudolabrys were the vital bacteria, Phaeosphaeria and Funneliformis were the dominant fungi in maintaining the stability of the ecological network. These results provided data and a theoretical basis for the in-depth understanding of what role endophytes play in rice resistance to barnyardgrass stress and will have implications on improving the resistance of rice against biotic stress using root microbiota. 展开更多
关键词 RICE Echinochloa crus-galli biotic stress endophytic bacterium endophytic fungus phylogenetic investigation of communities by reconstruction of unobserved states FUNGuild test
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Naringenin suppresses NLRP3 inflammasome activation via the mRNA-208a signaling pathway in isoproterenol-induced myocardial infarction
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作者 Ayman Eldourghamy Toka Hossam +2 位作者 Mohammed Abdalla Hussein Amal Abdel-Aziz Samir A.El-masry 《Asian Pacific Journal of Tropical Biomedicine》 SCIE CAS 2023年第10期443-450,共8页
Objective:To investigate the cardioprotective effect of naringenin against isoproterenol(ISO)-induced cardiotoxicity in rats.Methods:Rats were divided into five groups:the normal group,the ISO group(85 mg/kg b.w.);the... Objective:To investigate the cardioprotective effect of naringenin against isoproterenol(ISO)-induced cardiotoxicity in rats.Methods:Rats were divided into five groups:the normal group,the ISO group(85 mg/kg b.w.);the ISO+naringenin(50 mg/kg b.w.)group,the ISO+naringenin(100 mg/kg b.w.)group and the ISO+propranolol(10 mg/kg b.w.)group.Plasma creatine kinase-MB(CK-MB),cardiac troponin T,lactate dehydrogenase,brain natriuretic peptide(BNP),and IL-10,as well as cardiac transforming growth factor-β1(TGF-β1),vascular endothelial growth factor(VEGF)and malondialdehyde(MDA)were examined.In addition,NLRP3 and mRNA-208a expressions were evaluated by RT-PCR analysis.Histopathological examination was also performed to assess cardiac damages.Results:Naringenin treatment significantly decreased plasma lactate dehydrogenase,CK-MB,cardiac troponin T,BNP,and IL-10,as well as cardiac TGF-β1,VEGF,and MDA while increasing p-Akt and superoxide dismutase in ISO-administered rats.It also reduced NLRP3 and mRNA-208a gene expression levels.Furthermore,naringenin improved ISO-induced cardiac damage.Conclusions:Naringenin attenuates myocardial dysfunction in ISO-treated rats by decreasing oxidative stress and increasing cardiac endogenous antioxidant system,which may be modulated partly by improvement of NLRP3 and mRNA-208a gene expression. 展开更多
关键词 NARINGENIN ISOPROTERENOL Myocardial infarction Antioxidants NLRP3 mRNA-208a
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Characterization of transgenic wheat lines expressing maize ABP7 involved in kernel development
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作者 Zaid CHACHAR Siffat Ullah KHAN +3 位作者 ZHANG Xu-huan LENG Peng-fei ZONG Na ZHAO Jun 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2023年第2期389-399,共11页
Wheat is one of the major food crops in the world.Functional validation of the genes in increasing the grain yield of wheat by genetic engineering is essential for feeding the ever-growing global population.This study... Wheat is one of the major food crops in the world.Functional validation of the genes in increasing the grain yield of wheat by genetic engineering is essential for feeding the ever-growing global population.This study investigated the role of ABP7,a bHLH transcription factor from maize involved in kernel development,in regulating grain yield-related traits in transgenic wheat.Molecular characterization showed that transgenic lines HB123 and HB287 contained multicopy integration of ABP7 in the genome with higher transgene expression.At the same time,QB205 was a transgenic event of single copy insertion with no significant difference in ABP7 expression compared to wild-type(WT) plants.Phenotyping under field conditions showed that ABP7 over-expressing transgenic lines HB123 and HB287 exhibited improved grain yield-related traits(e.g.,grain number per spike,grain weight per spike,thousand-grain weight,grain length,and grain width) and increased grain yield per plot,compared to WT plants,whereas line QB205 did not.In addition,total chlorophyll,chlorophyll a,chlorophyll b,and total soluble sugars were largely increased in the flag leaves of both HB123and HB287 transgenic lines compared to the WT.These results strongly suggest that ABP7 positively regulates yieldrelated traits and plot grain yield in transgenic wheat.Consequently,ABP7 can be utilized in wheat breeding for grain yield improvement. 展开更多
关键词 transgenic wheat ABP7 kernel development grain weight grain width
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BEAR1, a bHLH transcription factor, controls seedling growth by regulating gibberellins biosynthesis in rice
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作者 Yantong Teng Maohong Cai +3 位作者 Qinyu Xie Qinglong Liu Haiwen Zhang Tao Chen 《The Crop Journal》 SCIE CSCD 2023年第3期744-755,共12页
The genetic pathways of rice seedling growth have a major impact on seedling emergence from soil and development.In this study,we identified a new bHLH transcription factor,BEAR1,from rice RNAi mutant library.Both the... The genetic pathways of rice seedling growth have a major impact on seedling emergence from soil and development.In this study,we identified a new bHLH transcription factor,BEAR1,from rice RNAi mutant library.Both the BEAR1-RNAi and bear1 CRISPR mutants had accelerated seedling growth.Histological section of leaves showed accelerated development of lacuna and vascular bundles in bear1 mutant.GUS staining revealed that BEAR1 was highly expressed in coleoptiles and leaves at seedling stage.Expression analysis of gibberellin(GA)biosynthesis and metabolic genes and content determination of active GAs indicated that the expression of GA biosynthesis genes,especially OsKS4 and OsCPS2,were upregulated and the GAs content were significantly increased in bear1,which correlated with the seedling phenotype of bear1 mutant.Molecular and biochemical assays revealed that BEAR1 directly binds to the promoter of OsKS4,thereby repressing its expression.Haplotypes analysis showed clear differentiation in indica and japonica rice varieties,and a strong correlation with seedling height.These findings provide novel insights into the regulation of seedling growth in rice. 展开更多
关键词 RICE BEAR1 Seedling growth GIBBERELLINS OsKS4
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Integrated genomic and transcriptomic analysis reveals genes associated with plant height of foxtail millet
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作者 Mengyuan Zhu Qiang He +14 位作者 Mingjie Lyu Tiantian Shi Qian Gao Hui Zhi Huan Wang Guanqing Jia Sha Tang Xiliu Cheng Rui Wanga Andi Xu Haigang Wang Zhijun Qiao Jun Liu Xianmin Diao Ying Gao 《The Crop Journal》 SCIE CSCD 2023年第2期593-604,共12页
Foxtail millet(Setaria italica)is an important C4 model crop;however,due to its high-density planting and high stature,lodging at the filling stage resulted in a serious reduction in yield and quality.Therefore,it is ... Foxtail millet(Setaria italica)is an important C4 model crop;however,due to its high-density planting and high stature,lodging at the filling stage resulted in a serious reduction in yield and quality.Therefore,it is imperative to identify and deploy the genes controlling foxtail millet plant height.In this study,we used a semi-dwarf line 263A and an elite high-stalk breeding variety,Chuang 29 to construct an F2 population to identify dwarf genes.We performed transcriptome analysis(RNA-seq)using internode tissues sampled at three jointing stages of 263A and Chuang 29,as well as bulk segregant analysis(BSA)on their F2 population.A total of 8918 differentially expressed genes(DEGs)were obtained from RNA-seq analysis,and GO analysis showed that DEGs were enriched in functions such as‘‘gibberellin metabolic process”and‘‘oxidoreductase activity”,which have previously been shown to be associated with plant height.A total 593 mutated genes were screened by BSA-seq method.One hundred and seventy-six out of the 593 mutated genes showed differential expression levels between the two parental lines,and seven genes not only showed differential expression in two or three internode tissues but also showed high genomic variation in coding regions,which indicated they play a crucial role in plant height determination.Among them,we found a gibberellin biosynthesis related GA20 oxidase gene(Seita.5G404900),which had a single-base at the third exon,leading to the frameshift mutation at 263A.Cleaved amplified polymorphic sequence assay and association analysis proved the single-base in Seita.5G404900 co-segregated with dwarf phenotype in two independent F2 populations planted in entirely different environments.Taken together,the candidate genes identified in this study will help to elucidate the genetic basis of foxtail millet plant height,and the molecular marker will be useful for marker-assisted dwarf breeding. 展开更多
关键词 Foxtail millet Plant height Transcriptome analysis Bulk segregant analysis Functional markers Association analysis
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Genetic Diversity and Population Structure Analysis of Barley Landraces from Shanghai Region Using Genotyping-by-Sequencing
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作者 Luli Li Nigel G.Halford +5 位作者 Huihui Wang Yingjie Zong Zhenzhu Guo Ruiju Lu Chenghong Liu Zhiwei Chen 《Phyton-International Journal of Experimental Botany》 SCIE 2023年第4期1275-1287,共13页
Barley(Hordeum vulgare L.)is an important economic crop for food,feed and industrial raw materials.In the present research,112 barley landraces from the Shanghai region were genotyped using genotyping-by-sequencing(GB... Barley(Hordeum vulgare L.)is an important economic crop for food,feed and industrial raw materials.In the present research,112 barley landraces from the Shanghai region were genotyped using genotyping-by-sequencing(GBS),and the genetic diversity and population structure were analyzed.The results showed that 210,268 Single Nucleotide Polymorphisms(SNPs)were present in total,and the average poly-morphism information content(PIC)was 0.1642.Genetic diversity and population structure analyses suggested that these barley landraces were differentiated and could be divided into three sub-groups,with morphological traits of row-type and adherence of the hulls the main distinguishing factors between groups.Genotypes with similar or duplicated names were also investigated according to their genetic backgrounds and seed appearances.This study provided valuable information on barley landraces from the Shanghai region,and showed that all these barley landraces should be protected and used for future breeding programs. 展开更多
关键词 Hordeum vulgare L cluster analysis population structure SNP markers
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Optimal Deep Transfer Learning Based Colorectal Cancer Detection and Classification Model
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作者 Mahmoud Ragab Maged Mostafa Mahmoud +2 位作者 Amer H.Asseri Hani Choudhry Haitham A.Yacoub 《Computers, Materials & Continua》 SCIE EI 2023年第2期3279-3295,共17页
Colorectal carcinoma(CRC)is one such dispersed cancer globally and also prominent one in causing cancer-based death.Conventionally,pathologists execute CRC diagnosis through visible scrutinizing under the microscope t... Colorectal carcinoma(CRC)is one such dispersed cancer globally and also prominent one in causing cancer-based death.Conventionally,pathologists execute CRC diagnosis through visible scrutinizing under the microscope the resected tissue samples,stained and fixed through Haematoxylin and Eosin(H&E).The advancement of graphical processing systems has resulted in high potentiality for deep learning(DL)techniques in interpretating visual anatomy from high resolution medical images.This study develops a slime mould algorithm with deep transfer learning enabled colorectal cancer detection and classification(SMADTL-CCDC)algorithm.The presented SMADTL-CCDC technique intends to appropriately recognize the occurrence of colorectal cancer.To accomplish this,the SMADTLCCDC model initially undergoes pre-processing to improve the input image quality.In addition,a dense-EfficientNet technique was employed to extract feature vectors from the pre-processed images.Moreover,SMA with Discrete Hopfield neural network(DHNN)method was applied for the recognition and classification of colorectal cancer.The utilization of SMA assists in appropriately selecting the parameters involved in the DHNN approach.A wide range of experiments was implemented on benchmark datasets to assess the classification performance.A comprehensive comparative study highlighted the better performance of the SMADTL-CDC model over the recent approaches. 展开更多
关键词 Colorectal cancer deep transfer learning slime mould algorithm hyperparameter optimization biomedical imaging
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Focusing on individualized nutrition within the algorithmic diet: an in-depth look at recent advances in nutritional science, microbial diversity studies, and human health
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作者 Reyed M Reyed 《Food and Health》 2023年第1期22-50,共29页
A healthy balanced diet and a healthy lifestyle are very closely linked.Whichever the biological link is,it is overwhelming to understand.Modifications in how food is served,divided up,and supervised,such as the intro... A healthy balanced diet and a healthy lifestyle are very closely linked.Whichever the biological link is,it is overwhelming to understand.Modifications in how food is served,divided up,and supervised,such as the introduction of nutritional hygiene standards,food handling practices,and the entry of macro and micronutrients,have had a big impact on human health in the last few decades.Growing evidence indicates that our gut microbiota may affect our health in ways that are at least in part influenced by our diet and the ingredients used in the preparation of our food and drinks,as well as other factors.As a new problem,this one is getting a lot of attention,but it would be hard to figure out how the gut microbiota and nutrition molecules work together and how they work in certain situations.Genetic analysis,metagenomic characterization,configuration analysis of foodstuffs,and the shift to digital health information have provided massive amounts of data that might be useful in tackling this problem.Machine learning and deep learning methods will be employed extensively as part of this research in order to blend complicated data frames and extract crucial information that will be capable of exposing and grasping the incredibly delicate links that prevail between diet,gut microbiome,and overall wellbeing.Nutrition,well-being,and gut microorganisms are a few subjects covered in this field.It takes into account not only databases and high-speed technology,but also virtual machine problem-solving skills,intangible assets,and laws.This is how it works:Computer vision,data mining,and analytics are all discussed extensively in this study piece.We also point out limitations in existing methodologies and new situations that discovered in the context of current scientific knowledge in the decades to come.We also provide background on"bioinformatics"algorithms;recent developments may seem to herald a revolution in clinical research,pushing traditional techniques to the sidelines.Furthermore,their true potential rests in their ability to work in conjunction with,rather than as a substitute for,traditional research hypotheses and procedures.When new metadata propositions are made by focusing on easily understandable frameworks,they will always need to be rigorously validated and brought into question.Because of the huge datasets available,assumption analysis may be used to complement rather than a substitute for more conventional concept-driven scientific investigation.It is only by employing all of us that we will all increase the quality of evidence-based practice. 展开更多
关键词 nutritional databank nutritional human gut microbiota MICROBIOME big data algorithms public health dietary programming application
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High-throughput discovery of plastid genes causing albino phenotypes in ornamental chimeric plants
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作者 Hyun-Seung Park Jae-Hyeon Jeon +15 位作者 Woohyeon Cho Yeonjeong Lee Jee Young Park Jiseok Kim Young Sang Park Hyun Jo Koo Jung Hwa Kang Taek Joo Lee Sang Hoon Kim Jin-Baek Kim Hae-Yun Kwon Suk-Hwan Kim Nam-Chon Paek Geupil Jang Jeong-Yong Suh Tae-Jin Yang 《Horticulture Research》 SCIE CSCD 2023年第1期249-259,共11页
Chimeric plants composed of green and albino tissues have great ornamental value.To unveil the functional genes responsible for albino phenotypes in chimeric plants,we inspected the complete plastid genomes(plastomes)... Chimeric plants composed of green and albino tissues have great ornamental value.To unveil the functional genes responsible for albino phenotypes in chimeric plants,we inspected the complete plastid genomes(plastomes)in green and albino leaf tissues from 23 ornamental chimeric plants belonging to 20 species,including monocots,dicots,and gymnosperms.In nine chimeric plants,plastomes were identical between green and albino tissues.Meanwhile,another 14 chimeric plants were heteroplasmic,showing a mutation between green and albino tissues.We identified 14 different point mutations in eight functional plastid genes related to plastid-encoded RNA polymerase(rpo)or photosystems which caused albinism in the chimeric plants.Among them,12 were deleterious mutations in the target genes,in which early termination appeared due to small deletion-mediated frameshift or single nucleotide substitution.Another was single nucleotide substitution in an intron of the ycf3 and the other was a missense mutation in coding region of the rpoC2 gene.We inspected chlorophyll structure,protein functional model of the rpoC2,and expression levels of the related genes in green and albino tissues of Reynoutria japonica.A single amino acid change,histidine-to-proline substitution,in the rpoC2 protein may destabilize the peripheral helix of plastid-encoded RNA polymerase,impairing the biosynthesis of the photosynthesis system in the albino tissue of R.japonica chimera plant. 展开更多
关键词 plast substitution ORNAMENTAL
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Barrett食管诊治共识(修订版2011年6月重庆) 被引量:46
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作者 房殿春 林三仁 +11 位作者 于中麟 袁耀宗 陈旻湖 白文元 黄勤 陈晓欣 张军 李延青 周丽雅 柯美云 方秀才 蓝宇 《胃肠病学》 2011年第8期485-486,共2页
为规范我国Barrett食管(BE)的诊断和治疗,中华医学会消化病学分会于2011年6月4日在重庆召开了"全国第二届Barrett食管专题学术研讨会",就BE有关问题进行了广泛的讨论,并对2005年制定的"Barrett食管诊治共识(草案)"作了修订和补... 为规范我国Barrett食管(BE)的诊断和治疗,中华医学会消化病学分会于2011年6月4日在重庆召开了"全国第二届Barrett食管专题学术研讨会",就BE有关问题进行了广泛的讨论,并对2005年制定的"Barrett食管诊治共识(草案)"作了修订和补充,达成以下共识。 展开更多
关键词 BARRETT食管 重庆 修订 诊治 专题学术研讨会 中华医学会 消化病 5年制
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Expression of hepatitis B virus genes in early embryonic cells originated from hamster ova and human spermatozoa transfected with the complete viral genome 被引量:62
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作者 Bahy Ahmed Ali Tian-Hua Huang +1 位作者 Halima-Hassan Salem Qing-Dong Xie 《Asian Journal of Andrology》 SCIE CAS CSCD 2006年第3期273-279,共7页
Aim: To detect the expression of hepatitis B virus (HBV) genes (HB S and C genes) in early embryonic cells after introducing motile human sperm carrying HBV DNA into zona-free hamster oocytes via the in vitro fer... Aim: To detect the expression of hepatitis B virus (HBV) genes (HB S and C genes) in early embryonic cells after introducing motile human sperm carrying HBV DNA into zona-free hamster oocytes via the in vitro fertilization (IVF) technique. Methods: Human sperm-mediated HBV genes were delivered into zona-free hamster oocytes by the IVF method. Polymerase chain reaction (PCR) was used to detect HB S and pre-Core/Core (pre-C/C) coding genes both in one- and two-cell embryos. Reverse transcription-PCR (RT-PCR) analysis was used to study the expression of the two genes. Fluorescence in situ hybridization (FISH) analysis using the full-length HBV DNA as the hybridization probe was performed to confirm the integration of viral DNA in the host embryonic genome. Results: Both HB S and pre-C/C coding genes are present and transcribed in one- and two-cell embryos originated from hamster ova IVF with human spermatozoa carrying HBV DNA sequences. Conclusion: Sperm-mediated HBV genes are able to replicate and express themselves in early embryonic cells. These results provide direct evidence that HBV DNA could transmit vertically to the next generation via the male germ line. 展开更多
关键词 hepatitis B virus gene expression hamster ovary human spermatozoa in vitro fertilization
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In vitro total phenolics,flavonoids contents and antioxidant activity of essential oil,various organic extracts from the leaves of tropical medicinal plant Tetrastigma from Sabah 被引量:11
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作者 M Amzad Hossain Muhammad Dawood Shah +1 位作者 Charles Gnanaraj Muhammad Iqbal 《Asian Pacific Journal of Tropical Medicine》 SCIE CAS 2011年第9期717-721,共5页
Objective:To detect the in vitro total phenolics,flavonoids contents and antioxidant activity of essential oil,various organic extracts from the leaves of tropical medicinal plant Tetrastigma from Sabah.Methods:The dr... Objective:To detect the in vitro total phenolics,flavonoids contents and antioxidant activity of essential oil,various organic extracts from the leaves of tropical medicinal plant Tetrastigma from Sabah.Methods:The dry powder leaves of Tetrastigma were extracted with different organic solvent such as hexane.ethyl acetate,chloroform,butanol and aqueous methanol.The total phenolic and total flavonoids contents of the essential oil and various organic extracts such as hexane,ethyl acetate,chloroform,butanol and aqueous ethanol were determined by Folin-Ciocalteu method and the assayed antioxidant activity was determined in vitro models such as antioxidant capacity by radical scavenging activity usingα,α-diphenyl-β-picrylhydrazyl (DPPH) method.Results:The total phenolic contents of the essential oil and different extracts as gallic acid equivalents were found to be highest in methanol extract(386.22 mg/g) followed by ethyl acetate(190.89 mg/g).chloroform(175.89 mg/g).hexane(173.44 mg/g).and Imtanol extract (131.72 mg/g) and the phenolic contents not detected in essential oil.The antioxidant capacity of the essential oil and different extracts as ascorbic acid standard was in the order of methanol extract】ethyl acetate extract】chloroform】butanol】hexane extract also the antioxidant activity was not detected in essential oil.Conclusions:The findings show that the extent of antioxidant activity of the essential oil and all extracts are in accordance with the amount of phenolics present in that extract.Leaves of Tetrastigma being rich in phenolics may provide a good source of antioxidant. 展开更多
关键词 Total phenolics FLAVONOIDS Antioxidant aotivity Essential oil EXTRACTS Tetrastigma
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