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Transcriptomic and proteomic analyses of far-red light effects in inducing shoot elongation in the presence or absence of paclobutrazol in Chinese pine

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Journal of Forestry Research 2022年第3期33卷 1033-1043页

作者： Yingtian Guo Shihui Niu yousry a.el-kassaby Wei Li National Engineering Laboratory for Forest Tree Breeding Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing100083People’s Republic of China Department of Forest and Conservation Sciences Faculty of ForestryUniversity of British Columbia2424 Main MallVancouverBCV6T 1Z4Canada

In angiosperms, low red (R)/far-red (FR) ratio light increases gibberellin (GA) levels. GA signaling in conifer seedlings requires FR to promote shoot elongation and reduce the inhibition of shoot elongation induced by paclobutrazol (PAC), yet the effects of far-red light in inducing shoot elongation in the presence or absence of PAC is poorly understood. In this study, transcriptomic and proteomic analyses was used to examine the molecular mechanism of FR regulation of shoot elongation in Chinese pine (Pinus tabuliformis Carr.) seedlings in the presence of PAC. Four treatments were compared: white light + water (WW), FR + water (RW), white light + PAC (WP), and FR + PAC (RP), and 1436 differentially expressed genes (DEGs) and 450 differentially expressed proteins (DEPs) were identified in RW_WW (RW contrast WW), and 1862 DEGs and 481 DEPs in RP_WP (RP contrast WP). Metabolic and signal transduction pathway analyses of DEGs and DEPs in RW_WW and RP_WP, indicated that the former required more energy than the latter. Moreover, gibberellic acid, auxin, and brassinolide are equally important in RW_WW and RP_WP for shoot elongation, except for the ethylene pathway. Amino acid metabolism and cell wall organization were significantly enriched in RW_WW and RP_WP, respectively. In summary, RW_WW and RP_WP had different effects in secondary metabolism, energy metabolism, amino acid metabolism, cell wall organization, and hormone response. These results provide an important theoretical and reference basis for studying the regulatory effect of low R/FR and PAC in conifer shoot elongation.

关键词： Low R/FR ratio Pinus tabuliformis Paclobutrazol Proteome Shoot elongation Transcriptome

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Integrative analysis of the metabolome and transcriptome reveals seed germination mechanism in Punica granatum L.

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Journal of Integrative Agriculture 2021年第1期20卷 132-146页

作者： FU Fang-fang PENG Ying-shu WANG Gui-bin yousry a.el-kassaby CAO Fu-liang Co-Innovation Center for Sustainable Forestry in Southern China Nanjing Forestry UniversityNanjing 210037P.R.China Department of Forest and Conservation Sciences Faculty of ForestryThe University of British ColumbiaVancouverB.C.V6T 1Z4Canada

We conducted an integrative system biology of metabolome and transcriptome profile analyses during pomegranate(Punica granatum L.) seed germination and utilized a weighted gene co-expression network analysis(WGCNA) to describe the functionality and complexity of the physiological and morphogenetic processes as well as gene expression and metabolic differences during seed germination stages. In total, 489 metabolites were detected, including 40 differentially accumulated metabolites. The transcriptomic analysis showed the expression of 6 984 genes changed significantly throughout the whole germination process. Using WGCNA, we identified modules related to the various seed germination stages and hub genes. In the initial imbibition stage(stage 1), the pivotal genes involved in RNA transduction and the glycolytic pathway were most active, while in the sprouting stage(stage 4), the pivotal genes were involved in multiple metabolic pathways. In terms of secondary metabolic pathways, we found flavonoid 4-reductase genes of anthocyanin biosynthesis pathway are most significantly affected during pomegranate seed germination, while the flavonol synthase gene was mainly involved in the regulation of isoflavonoid biosynthesis.

关键词： seed germination stages weighted gene co-expression network analysis(WGCNA) metabolome transcriptome flavonoid pathway

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Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct f lower color

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Horticulture Research 2023年第1期10卷 193-206页

作者： Shuai Nie Shi-Wei Zhao Tian-Le Shi Wei Zhao Ren-Gang Zhang Xue-Chan Tian Jing-Fang Guo Xue-Mei Yan Yu-Tao Bao Zhi-Chao Li Lei Kong Hai-Yao Ma Zhao-Yang Chen Hui Liu yousry Ael-kassaby Ilga Porth Fu-Sheng Yang Jian-Feng Mao National Engineering Research Center of Tree Breeding and Ecological Restoration Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing 100083China Department of Ecology and Environmental Science UmeåPlant Science CentreUmeåUniversitySE-90187 UmeåSweden Department of Bioinformatics Ori(Shandong)Gene Science and Technology Co.Ltd.Weifang 261322China Department of Forest and Conservation Sciences Faculty of ForestryUniversity of British ColumbiaVancouverBCV6T 1Z4Canada Départment des Sciences du Bois et de la Forêt Facultéde Foresteriede Géographie et GéomatiqueUniversitéLavalQuébecQCG1V 0A6Canada State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China

The genus Rhododendron(Ericaceae),with more than 1000 species highly diverse in f lower color,is providing distinct ornamental values and a model system for f lower color ***,we investigated the divergence between two parental species with different f lower color widely used for azalea *** genome assembly was generated for the yellow-f lowered azalea,Rhododendron *** genomics found recent proliferation of long terminal repeat retrotransposons(LTR-RTs),especially Gypsy,has resulted in a 125 Mb(19%)genome size increase in species-specific regions,and a significant amount of dispersed gene duplicates(13402)and pseudogenes(17437).Metabolomic assessment revealed that yellow f lower coloration is attributed to the dynamic changes of carotenoids/f lavonols biosynthesis and chlorophyll ***-ordered gene co-expression networks(TO-GCNs)and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct f lower pigmentation.B3 and ERF TFs were found dominating the gene regulation of carotenoids/f lavonols characterized pigmentation in ***,while WRKY,ERF,WD40,C2H2,and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-f lowered R *** study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.

关键词： divergence yellow collective

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Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome

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Horticulture Research 2021年第1期8卷 2721-2735页

作者： Kai-Hua Jia Hui Liu Ren-Gang Zhang Jie Xu Shan-Shan Zhou Si-Qian Jiao Xue-Mei Yan Xue-Chan Tian Tian-Le Shi Hang Luo Zhi-Chao Li Yu-Tao Bao Shuai Nie Jing-Fang Guo Ilga Porth yousry Ael-kassaby Xiao-Ru Wang Charles Chen Yves Van de Peer Wei Zhao Jian-Feng Mao Beijing Advanced Innovation Center for Tree Breeding by Molecular Design National Engineering Laboratory for Tree BreedingKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing 100083China Ori(Shandong)Gene Science and Technology Co. LtdWeifang 261000 ShandongChina Department des Sciences du Bois et de la Foret Facultede Foresteriede Geographie et GeomatiqueUniversite LavalQuebec CityQC G1V 0A6Canada Department of Forest and Conservation Sciences Faculty of ForestryUniversity of British ColumbiaVancouverBC V6T 1Z4Canada Department of Ecology and Environmental Science UmeåPlant Science CentreUmeåUniversitySE-90187 UmeåSweden Department of Biochemistry and Molecular Biology 246 Noble Research CenterOklahoma State UniversityStillwaterOKUSA Department of Plant Biotechnology and Bioinformatics Ghent UniversityGhentBelgium VIB Center for Plant Systems Biology 9052 GhentBelgium Centre for Microbial Ecology and Genomics Department of BiochemistryGenetics and Microbiology GeneticsUniversity of PretoriaPrivate Bag X20Pretoria 0028South Africa College of Horticulture Academy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjing 210095China

Polyploidization plays a key role in plant evolution,but the forces driving the fate of homoeologs in polyploid genomes,i.e.,paralogs resulting from a whole-genome duplication(WGD)event,remain to be ***,we present a chromosome-scale genome assembly of tetraploid scarlet sage(Salvia splendens),one of the most diverse ornamental *** found evidence for three WGD events following an older WGD event shared by most eudicots(theγevent).A comprehensive,spatiotemporal,genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries,which could be associated with genomic rearrangements,transposable element proximity discrepancies,coding sequence variation,selection pressure,and transcription factor binding site *** observed differences between homoeologs may reflect the first step toward sub-and/or *** assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.

关键词： species evolution assembly

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Haplotype-resolved genome assembly and allele- specific gene expression in cultivated ginger

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Horticulture Research 2021年第1期8卷 2531-2545页

作者： Shi-Ping Cheng Kai-Hua Jia Hui Liu Ren-Gang Zhang Zhi-Chao Li Shan-Shan Zhou Tian-Le Shi Ai-Chu Ma Cong-Wen Yu Chan Gao Guang-Lei Cao Wei Zhao Shuai Nie Jing-Fang Guo Si-Qian Jiao Xue-Chan Tian Xue-Mei Yan Yu-Tao Bao Quan-Zheng Yun Xin-Zhu Wang Ilga Porth yousry Ael-kassaby Xiao-Ru Wang Zhen Li Yves Van de Peer Jian-Feng Mao Pingdingshan University Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody PlantPingdingshan 467000 HenanChina Beijing Advanced Innovation Center for Tree Breeding by Molecular Design National Engineering Laboratory for Tree BreedingKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing 100083China Ori(Shandong)Gene Science and Technology Co. LtdWeifang 261000 ShandongChina Pingdingshan Academy of Agricultural Sciences Pingdingshan 467000 HenanChina Department of Ecology and Environmental Science UPSCUmea UniversityUmeaSweden Departement des Sciences du Bois et de la Foret Facultede Foresteriede Geographie et GéomatiqueUniversite Laval QuebecQuebecQC G1V 0A6Canada Department of Forest and Conservation Sciences Faculty of ForestryUniversity of British ColumbiaVancouverBC V6T 1Z4Canada Department of Plant Biotechnology and Bioinformatics Ghent UniversityGhentBelgium VIB Center for Plant Systems Biology 9052 GhentBelgium Centre for Microbial Ecology and Genomics Department of BiochemistryGenetics and Microbiology GeneticsUniversity of PretoriaPrivate Bag X20Pretoria 0028South Africa College of Horticulture Academy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjing 210095China

Ginger(Zingiber officinale)is one of the most valued spice plants worldwide;it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural ***,we present a haplotype-resolved,chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 *** structural variation was identified between haplotypes,and two inversions larger than 15Mb on chromosome 4 may be associated with ginger *** performed a comprehensive,spatiotemporal,genome-wide analysis of allelic expression patterns,revealing that most alleles are coordina.ely *** alleles that exhibited the largest differences in expression showed closer proximity to transposable elements,greater coding sequence divergence,more relaxed selection pressure,and more transcription factor binding site *** also predicted the transcription factors potentially regulating 6-gingerol *** allele-aware assembly provides a powerful platform for future functional genomics,molecular breeding,and genome editing in ginger.

关键词： resolved closer breeding

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Improved genetic distance-based spatial deployment can effectively minimize inbreeding in seed orchard

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Forest Ecosystems 2020年第1期7卷 117-124,126,125,127页

作者： Boning Yang Haihong Sun Jiandong Qi Shihui Niu yousry Ael-kassaby Wei Li Beijing Advanced Innovation Center for Tree Breeding by Molecular Design National Engineering Laboratory for Forest Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing 100083China Liaoning Research Institute of Sandy Land Control and Utilization Xihe DistrictFuxin City 123000Liaoning ProvinceChina College of Information Science and Technology Beijing Forestry UniversityBeijing 100083China Department of Forest and Conservation Sciences Faculty of ForestryThe University of British Columbia2424 Main MallVancouverBritish Columbia V6T 1Z4Canada

Background:Inbreeding in seed orchards is expected to increase with the advancement of breeding cycles,which results in the delivery of crops with suboptimal genetic gain,reduced genetic diversity,and lower seed ***,a genetic distance-dependent method for clonal spatial deployment in seed orchards was developed and demonstrated,which reduced the inbreeding *** method’s main evaluation parameter of inbreeding is the genetic distance among individuals and the deployment method used an improved adaptive parallel genetic algorithm(IAPGA)based on Python *** inbreeding-prone Chinese Mongolian pine breeding population material originating from a single natural population,the proposed method was compared to a traditional orchard design and a distance-based design;na.ely,complete randomized block(RCB)and optimum neighborhood(ONA)designs,***:With the advancement of selective breeding cycles,group separation among orchard related individuals is expected to *** on the genetic distance among individuals,the IAPGA design was superior in significantly reducing the inbreeding level as compared to the two existing designs,confirming its suitability to advanced-generation orchards where relatedness among parents is *** the 1st,2nd,and mixed generations clonal deployment schemes,the IAPGA design produced lower inbreeding with 87.22%,81.49%,and 87.23%of RCB,and 92.78%,91.30%,and 91.67%of ONA designs,***:The IAPGA clonal deployment proposed in this study has the obvious advantage of controlling inbreeding,and it is expected to be used in clonal deployment in seed orchards on a *** studies are needed to focus on the actual states of pollen dispersal and mating in seed orchards,and more assumptions should be taken into account for the optimized deployment method.

关键词： Seed orchard Deployment Inbreeding Genetic distance Clone SSR

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Synthesis and spectroscopic characterization of novel 2-amino-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidine and pyrimido[1,2-α]pyrimidine derivatives

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Chinese Chemical Letters 2015年第6期26卷 690-694页

作者： Mohamed S.a.el-Gaby Jehan A.Micky Nadia M.Saleh yousry A.Ammar Heba S.A.Mohamed Chemistry Department Faculty of ScienceAl-Azhar University at Assiut Chemistry Department Faculty of Science (Girl’s)Al-Azhar University Chemistry Department Faculty of ScienceAl-Azhar University Photochemistry Department National Research CenterEl-DokkiGizaEgypt

2-Aminocyclopenta[d]pyrimidines 3a-c were achieved via a one-pot, three-component reactions of cyclopentanone 1, aromatic aldehyde and guanidine hydrochloride （1：2：1 molar ratio）. Also, cyclization of 2,5-bis-（arylmethylidene）cyclopentanones 2 with guanidine hydrochloride （1：1 molar ratio） in methanol in the presence of sodium methoxide afforded cyclopenta-[d]pyrimidines 3. Compound 3c has been shown to be a useful building block for the synthesis of some novel pyrimido[ 1,2-a]pyrimidines 5, 7 and 12. The structures of the newly synthesized compounds were confirmed on the basis of analytical and spectral data,

关键词： Multicomponent reaction Cyclopenta[d]pyrimidine Pyrimido[1 2-a]pyrimidine Cyclopentanone

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Decreased apoptosis in advanced-stage/high-grade hepatocellular carcinoma complicating chronic hepatitis C is mediated through the downregulation of p21 ras

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Chinese Journal of Cancer Research 2013年第3期25卷 281-288页

作者： Nahed Baddour Ebtehal Farrag Ahmed Zeid Essam Bedewy yousry Taher Departments of Pathology Alexandria Egypt Departments of Hepatobiliary Unit Internal MedicineAlexandria Egypt Departments of Tropical Medicine of the Alexandria Faculty of Medicine Alexandria Egypt

Objective and background： Although p21 ras has been reported to be upregulated in hepatocellular carcinoma complicating chronic hepatitis C type I, p21 ras has a different role in advanced stages, as it has been found to be downregulated. The goal of this study was to investigate the status of p21 ras in early-stage/low-grade and late-stage/high-grade hepatocellular carcinoma and its possible link to apoptosis. Material and methods： Thirty-five cases each of chronic HCV hepatitis type 4 （group I） and cirrhosis with hepatocellular carcinoma （HCC） complicating chronic HCV hepatitis （groups Ⅱ and Ⅲ） were immunohistochemically evaluated using a p21 ras polyclonal antibody. The apoptotic index was determined in histologic sections using the terminal deoxynncleotidyl transferase-mediated d-UTP biotin nick end la.eling （TUNel） assay. Results： Significant differences （P=0.001） were detected in p21 ras protein expression between the three groups. A near 2-fold increase in p21 ras staining was observed in the cirrhotic cases compared to the hepatitis cases, and p21 ras expression was decreased in the HCC group, p21 ras expression correlated with stage （r=0.64, P--0.001） and grade （r=-0.65, P=0.001） in the HCC group and grade in the HCV group （r=0.44, P=0.008）. Both p21 ras expression and TUNel-LI were significantly lower in large HCCs compared to small HCCs （P=0.01 each）. The TUNel values were negatively correlated with stage in the HCC group （r=-0.85, P=0.001）. The TUNel values were also negatively correlated with grade in both the HCV and HCC groups （r=0.89, P=0.001 and r=0.53, P=0.001, respectively）. The p21 ras scores were significantly correlated with the TUNel-LI values in the HCC group （r=0.63, P=0.001） and HCV group （r=0.88, P=0.001）. Conclusions： p21 ras acts as an initiator in HCC complicating type 4 chronic HCV and is downregulated with HCC progression, which most likely promotes tumor cell survival because it facilitates the downregulation of apoptosis with tumor

关键词： p21 ras terminal deoxynucleotidyl transferase-mediated d-UTP biotin nick end la.eling (TUNel) apoptosis HCV type 4 hepatocellular carcinoma

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North-South Asymmetry of the Interplanetary Magnetic Field Magnitude and the Geomagnetic Indices

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International Journal of Astronomy and Astrophysics 2016年第1期6卷 14-22页

作者： Mohammed Ali el-Borie Ali Abdel-Moniem Abdel-Halim Shady yousry el-Monier Physics Department Faculty of Science Alexandria University Alexandria Egypt Arab Academy for Science & Technology and Maritime Transport Alexandria Egypt

Data of the daily interplanetary magnetic field (IMF), and the geomagnetic indices (aa, Ap, Kp, and DST) have been used to examine the asymmetry between the solar field north and south of the heliospheric current sheet, over the period (1975-2013). It important to note that during the positive polarity epochs: (T) refers to Toward the South of the heliospheric current sheet (Southern Hemisphere), and (A) refers to Away from North of the heliospheric current sheet (Northern Hemisphere). While, during the negative polarity epochs the opposite will be happened. The present study finds no clear indication of the presence of north-south asymmetry in the field magnitude, and also there is no magnetic solar cycle dependence that is evident. During the considered period, the north-south asymmetry for the considered parameters reaches maximum values around the declining phase or near to the minimum of the solar cycle. The geomagnetic indices have a clear asymmetry during the positive solar magnetic polarity period (qA > 0) and have a northern dominance during cycles (22 & 23) and southern dominance during cycles (21 & 24). From the power spectrum density, the considered parameters showed significant peaks which appeared in the north-south asymmetry but the 10.7 yr solar cycle was absent. In addition, the main periodicity of the asymmetry may be 5.2, 4.0 and 3.3 years that exist in the parameters with higher confidence levels. Finally, one can conclude that the asymmetry of the interplanetary parameters and the geomagnetic indices may provide multiple causes for producing the observed asymmetric modulations of cosmic rays.

关键词： Geomagnetic Indices Interplanetary Magnetic Field North-South Asymmetry Solar Activity Distribution

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Annexin A2 as a biomarker for hepatocellular carcinoma in Egyptian patients

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World Journal of Hepatology 2017年第9期9卷 469-476页

作者： Mohamed K Shaker Hanzada I Abdel Fattah Ghada S Sabbour Iman F Montasser Sara M Abdelhakam Eman el Hadidy Rehab yousry Ahmed K el Dorry Department of Tropical Medicine Faculty of MedicineAin Shams University Department of Clinical Pathology Faculty of MedicineAin Shams University Department of Radiodiagnosis and Inter-ventional Radiology Faculty of MedicineAin Shams University

AIM To investigate the clinical utility of serum annexin A2(ANXA2) as a diagnostic marker for early hepatocellular carcinoma(HCC).METHODS This study was performed in HCC Clinic of Ain Shams University Hospitals, Cairo, Egypt and included: Group 1: Fifty patients with early stage HCC(Barcelona Clinic Liver Cancer stage A); Group 2: Twenty five patients with chronic liver disease; and Control Group: Fifteen healthy, age-and sex-matched subjects who were seronegative for viral hepatitis markers. The followinglaboratory investigations were done: Viral hepatitis markers [hepatitis B surface antigen and hepatitis C virus(HCV) antibodies], HCV RNA in HCV antibody-positive patients, serum alpha fetoprotein(AFP), and serum ANXA2 *** In this study, 88% of HCC patients(n = 44) were HCVpositive, while HBV infection represented only 8% of all HCC patients(n = 4); and two patients were negative for both viral markers. A highly significant difference was found between patients with HCC and chronic liver disease as well as controls with regard to serum ANXA2 levels(130, IQR 15-240; 15, IQR 15-17; and 17, IQR 15-30 ng/m L, respectively). The area under the curve of ANXA2 was 0.865; the cut-off value was established to be 18 ng/mL with a diagnostic sensitivity of 74% and a specificity of 88%, while the sensitivity and specificity of AFP at the cut-off value of 200 ng/dL were 20% and 100%, *** Serum ANXA2 may serve as a biomarker for the early detection of HCC.

关键词： Hepatocellular carcinoma Hepatitis C virus Annexin A2 Alpha-fetoprotein Tumor markers

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