scholarly journals Identification of Genes Involved in the Responses of Tangor(C. reticulata×C. sinensis)to Drought Stress

2017 ◽  
Vol 2017 ◽  
pp. 1-15 ◽  
Author(s):  
Jin-Ping Xiao ◽  
Lan-Lan Zhang ◽  
Hui-Qin Zhang ◽  
Li-Xiang Miao
Keyword(s):  
Fragment Length Polymorphism ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Gene Products ◽  
Enzyme Expression ◽  
Altered Expression ◽  
Cellular Processes ◽  
Blast Search ◽  
Profile Changes ◽  
Stimuli Response

Drought is the major abiotic stress with adverse effects on citrus, decreasing the agronomical yield and influencing the fruit quality. In this study, cDNA-amplified fragment length polymorphism (cDNA-AFLP) technique was used to investigate the transcriptional profile changes and identify drought-responsive genes in “Amakusa” tangor(C. reticulata×C. sinensis), a hybrid citrus sensitive to water stress. The 255 out of 6,245 transcript-derived fragments (TDFs) displayed altered expression patterns including (A) induction, (B) repression, (C) upregulation, and (D) downregulation. With BLAST search, the gene products of differentially expressed fragments (DEFs) could be classified into several categories: cellular processes, transcription, transport, metabolism, stress/stimuli response, and developmental processes. Downregulated genes were highly represented by photosynthesis and basic metabolism, while upregulated ones were enriched in genes that were involved in transcription regulation, defense, energy, and transport. Present result also revealed some transient and up- and then downregulated genes such as aquaporin protein and photosystem enzyme. Expression patterns of 17 TDFs among 18 homologous to function-known genes were confirmed by qRT-PCR analysis. The present results revealed potential mechanism of drought tolerance in fruit crop and also provided candidate genes for future experiments in citrus.

scholarly journals Transcriptome analysis provides insights into the non-methylated lignin synthesis in Paphiopedilum armeniacum seed

2019 ◽  
Author(s):  
lin fang ◽  
Xin Xu ◽  
Ji Li ◽  
Feng Zheng ◽  
Mingzhi Li ◽  
...  
Keyword(s):  
Germination Rate ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Habitat Destruction ◽  
Seed Maturation ◽  
Pcr Analysis ◽  
Altered Expression ◽  
Lignin Synthesis ◽  
Phenylpropanoid Biosynthesis ◽  
Mature Seeds

Abstract Abstract Backgrounds Paphiopedilum is an important genus of orchid family (Orchidaceae) with high horticultural value. The wild populations are under the threat of extinction because of over collection and habitat destruction. Mature seeds of most Paphiopedilum species are difficult to germinate, which severely restricts the germplasm resources protection and commercial production. The germination inhibition factors are largely unknown. Results In this study, we found large amounts of non-methylated lignin were accumulated during seed maturation of Paphiopedilum armeniacum (P. armeniacum), which negatively correlates with the germination rate. We then further compared the transcriptome profiles of P. armeniacum seed at different development stages to explore molecular clues for the non-methylated lignin synthesis. KEGG enrichment analysis showed that a large number of genes associated with phenylpropanoid biosynthesis and phenylalanine metabolism as the seed maturation were differentially expressed. Several key genes in the lignin biosynthetic pathways displayed different expression patterns during the lignification process. PAL, 4CL, HCT and CSE were up-regulated to accelerate the C and H lignin accumulation. The expression of CCoAOMT, F5H and COMT were maintained at a low level or down-regulated to inhibit the conversion to the typical G and S lignin. Quantitative real-time RT-PCR analysis confirmed the altered expression levels of these genes among seeds and vegetative tissues. Conclusions This work demonstrated the plasticity of natural lignin polymer assembly in seed, and provided a better understanding of the molecular mechanism of seed-specific lignification process.

scholarly journals Transcriptome analysis provides insights into the non-methylated lignin synthesis in Paphiopedilum armeniacum seed

2020 ◽  
Author(s):  
Lin Fang ◽  
Xin Xu ◽  
Ji Li ◽  
Feng Zheng ◽  
Mingzhi Li ◽  
...  
Keyword(s):  
Germination Rate ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Habitat Destruction ◽  
Seed Maturation ◽  
Pcr Analysis ◽  
Altered Expression ◽  
Lignin Synthesis ◽  
Phenylpropanoid Biosynthesis ◽  
Mature Seeds

Abstract Backgrounds: Paphiopedilum is an important genus of orchid family (Orchidaceae) with high horticultural value. The wild populations are under the threat of extinction because of over collection and habitat destruction. Mature seeds of most Paphiopedilum species are difficult to germinate, which severely restricts the germplasm resources protection and commercial production. The germination inhibition factors are largely unknown.Results: In this study, we found large amounts of non-methylated lignin were accumulated during seed maturation of Paphiopedilum armeniacum (P. armeniacum), which negatively correlates with the germination rate. We then further compared the transcriptome profiles of P. armeniacum seed at different development stages to explore molecular clues for the non-methylated lignin synthesis. KEGG enrichment analysis showed that a large number of genes associated with phenylpropanoid biosynthesis and phenylalanine metabolism as the seed maturation were differentially expressed. Several key genes in the lignin biosynthetic pathways displayed different expression patterns during the lignification process. PAL, 4CL, HCT and CSE were up-regulated to accelerate the C and H lignin accumulation. The expression of CCoAOMT, F5H and COMT were maintained at a low level or down-regulated to inhibit the conversion to the typical G and S lignin. Quantitative real-time RT-PCR analysis confirmed the altered expression levels of these genes among seeds and vegetative tissues. Conclusions: This work demonstrated the plasticity of natural lignin polymer assembly in seed, and provided a better understanding of the molecular mechanism of seed-specific lignification process.

scholarly journals Transcriptome analysis provides insights into the non-methylated lignin synthesis in Paphiopedilum armeniacum seed

2020 ◽  
Author(s):  
lin fang ◽  
Xin Xu ◽  
Ji Li ◽  
Feng Zheng ◽  
Mingzhi Li ◽  
...  
Keyword(s):  
Germination Rate ◽  
Expression Patterns ◽  
Germplasm Conservation ◽  
Enrichment Analysis ◽  
Habitat Destruction ◽  
Seed Maturation ◽  
Pcr Analysis ◽  
Altered Expression ◽  
Lignin Synthesis ◽  
Phenylpropanoid Biosynthesis

Abstract Backgrounds: Paphiopedilum is an important genus of the orchid family Orchidaceae and has high horticultural value. The wild populations are under threat of extinction because of overcollection and habitat destruction. Mature seeds of most Paphiopedilum species are difficult to germinate, which severely restricts their germplasm conservation and commercial production. The factors inhibiting germination are largely unknown.Results: In this study, large amounts of non-methylated lignin accumulated during seed maturation of Paphiopedilum armeniacum (P. armeniacum), which negatively correlates with the germination rate. The transcriptome profiles of P. armeniacum seed at different development stages were compared to explore the molecular clues for non-methylated lignin synthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that a large number of genes associated with phenylpropanoid biosynthesis and phenylalanine metabolism during seed maturation were differentially expressed. Several key genes in the lignin biosynthetic pathway displayed different expression patterns during the lignification process. PAL, 4CL, HCT, and CSE upregulation was associated with C and H lignin accumulation. The expression of CCoAOMT, F5H, and COMT were maintained at a low level or down-regulated to inhibit the conversion to the typical G and S lignin. Quantitative real-time RT-PCR analysis confirmed the altered expression levels of these genes in seeds and vegetative tissues. Conclusions: This work demonstrated the plasticity of natural lignin polymer assembly in seed and provided a better understanding of the molecular mechanism of seed-specific lignification process.

scholarly journals Transcriptome analysis provides insights into the non-methylated lignin synthesis in Paphiopedilum armeniacum seed

2020 ◽  
Author(s):  
lin fang ◽  
Xin Xu ◽  
Ji Li ◽  
Feng Zheng ◽  
Mingzhi Li ◽  
...  
Keyword(s):  
Germination Rate ◽  
Expression Patterns ◽  
Germplasm Conservation ◽  
Enrichment Analysis ◽  
Habitat Destruction ◽  
Seed Maturation ◽  
Pcr Analysis ◽  
Altered Expression ◽  
Lignin Synthesis ◽  
Phenylpropanoid Biosynthesis

Abstract Backgrounds: Paphiopedilum is an important genus of the orchid family Orchidaceae and has high horticultural value. The wild populations are under threat of extinction because of overcollection and habitat destruction. Mature seeds of most Paphiopedilum species are difficult to germinate, which severely restricts their germplasm conservation and commercial production. The factors inhibiting germination are largely unknown.Results: In this study, large amounts of non-methylated lignin accumulated during seed maturation of Paphiopedilum armeniacum (P. armeniacum), which negatively correlates with the germination rate. The transcriptome profiles of P. armeniacum seed at different development stages were compared to explore the molecular clues for non-methylated lignin synthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that a large number of genes associated with phenylpropanoid biosynthesis and phenylalanine metabolism during seed maturation were differentially expressed. Several key genes in the lignin biosynthetic pathway displayed different expression patterns during the lignification process. PAL, 4CL, HCT, and CSE upregulation was associated with C and H lignin accumulation. The expression of CCoAOMT, F5H, and COMT were maintained at a low level or down-regulated to inhibit the conversion to the typical G and S lignin. Quantitative real-time RT-PCR analysis confirmed the altered expression levels of these genes in seeds and vegetative tissues. Conclusions: This work demonstrated the plasticity of natural lignin polymer assembly in seed and provided a better understanding of the molecular mechanism of seed-specific lignification process.

scholarly journals Host Response to the Attenuated Poxvirus Vector NYVAC: Upregulation of Apoptotic Genes and NF-κB-Responsive Genes in Infected HeLa Cells

2006 ◽  
Vol 80 (2) ◽  
pp. 985-998 ◽  
Author(s):  
Susana Guerra ◽  
Luis A. López-Fernández ◽  
Alberto Pascual-Montano ◽  
José Luis Nájera ◽  
Angel Zaballos ◽  
...  
Keyword(s):  
Hela Cells ◽  
Host Response ◽  
Target Genes ◽  
Interleukin 1 ◽  
Expression Patterns ◽  
Gene Activation ◽  
Gene Clusters ◽  
Current Phase ◽  
Pcr Analysis ◽  
Altered Expression

ABSTRACT NYVAC has been engineered as a safe, attenuated vaccinia virus (VV) vector for use in vaccination against a broad spectrum of pathogens and tumors. Due to the interest in NYVAC-based vectors as vaccines and current phase I/II clinical trials with this vector, there is a need to analyze the human host response to NYVAC infection. Using high-density cDNA microarrays, we found 368 differentially regulated genes after NYVAC infection of HeLa cells. Clustering of the regulated genes identified six discrete gene clusters with altered expression patterns. Clusters 1 to 3 represented 47.5% of the regulated genes, with three patterns of gene activation kinetics, whereas clusters 4 to 6 showed distinct repression kinetics. Quantitative real-time reverse transcription-PCR analysis of selected genes validated the array data. Upregulated transcripts correlated with genes implicated in immune responses, including those encoding interleukin-1 receptor 2 (IL-1R2), IL-6, ISG-15, CD-80, and TNFSF7. NYVAC upregulated several intermediates of apoptotic cascades, including caspase-9, correlating with its ability to induce apoptosis. NYVAC infection also stimulated the expression of NF-κB1 and NF-κB2 as well as that of NF-κB target genes. Expression of the VV host range K1L gene during NYVAC infection prevented NF-κB activation, but not the induction of apoptosis. This study is the first overall analysis of the transcriptional response of human cells to NYVAC infection and provides a framework for future functional studies to evaluate this vector and its derivatives as human vaccines.

Dysregulation of HOX as a Potential Therapeutic Target in Breast Cancer

2020 ◽  
Vol 27 ◽  
Author(s):  
Ji-Yeon Lee ◽  
Myoung Hee Kim
Keyword(s):  
Breast Cancer ◽  
Hox Genes ◽  
Therapeutic Potential ◽  
Expression Patterns ◽  
Genome Structure ◽  
Control Cell ◽  
Three Dimensional ◽  
Cellular Processes ◽  
Hox Protein

: HOX genes belong to the highly conserved homeobox superfamily, responsible for the regulation of various cellular processes that control cell homeostasis, from embryogenesis to carcinogenesis. The abnormal expression of HOX genes is observed in various cancers, including breast cancer; they act as oncogenes or as suppressors of cancer, according to context. In this review, we analyze HOX gene expression patterns in breast cancer and examine their relationship, based on the three-dimensional genome structure of the HOX locus. The presence of non-coding RNAs, embedded within the HOX cluster, and the role of these molecules in breast cancer have been reviewed. We further evaluate the characteristic activity of HOX protein in breast cancer and its therapeutic potential.

scholarly journals Ras, TrkB, and ShcA Protein Expression Patterns in Pediatric Brain Tumors

2021 ◽  
Vol 10 (10) ◽  
pp. 2219
Author(s):  
Monika Prill ◽  
Agnieszka Karkucinska-Wieckowska ◽  
Magdalena Lebiedzinska-Arciszewska ◽  
Giampaolo Morciano ◽  
Agata Charzynska ◽  
...  
Keyword(s):  
Brain Tumors ◽  
Expression Patterns ◽  
Pediatric Brain Tumors ◽  
Astrocytic Tumors ◽  
Embryonal Tumors ◽  
Altered Expression ◽  
Malignancy Grade ◽  
Oligodendroglial Tumors ◽  
Different Types ◽  
Pediatric Brain

Numerous papers have reported altered expression patterns of Ras and/or ShcA proteins in different types of cancers. Their level can be potentially associated with oncogenic processes. We analyzed samples of pediatric brain tumors reflecting different groups such as choroid plexus tumors, diffuse astrocytic and oligodendroglial tumors, embryonal tumors, ependymal tumors, and other astrocytic tumors as well as tumor malignancy grade, in order to characterize the expression profile of Ras, TrkB, and three isoforms of ShcA, namely, p66Shc, p52Shc, and p46Shc proteins. The main aim of our study was to evaluate the potential correlation between the type of pediatric brain tumors, tumor malignancy grade, and the expression patterns of the investigated proteins.

scholarly journals Betulinic Acid Affects the Energy-Related Proteomic Profiling in Pancreatic Ductal Adenocarcinoma Cells

Molecules ◽  
2021 ◽  
Vol 26 (9) ◽  
pp. 2482
Author(s):  
Ching-Feng Chiu ◽  
Hsin-Yi Chang ◽  
Chun-Yine Huang ◽  
Chen-Zou Mau ◽  
Tzu-Ting Kuo ◽  
...  
Keyword(s):  
Pancreatic Ductal Adenocarcinoma ◽  
Betulinic Acid ◽  
Expression Patterns ◽  
Apolipoprotein A1 ◽  
Ductal Adenocarcinoma ◽  
Therapeutic Window ◽  
Pdac Cell ◽  
Cell Growth And Migration ◽  
Altered Expression ◽  
Clinical Prognosis

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease with a 5-year survival rate of <8%. Therefore, finding new treatment strategies against PDAC cells is an imperative issue. Betulinic acid (BA), a plant-derived natural compound, has shown great potential to combat cancer owing to its versatile physiological functions. In this study, we observed the impacts of BA on the cell viability and migratory ability of PDAC cell lines, and screened differentially expressed proteins (DEPs) by an LC-MS/MS-based proteomics analysis. Our results showed that BA significantly inhibited the viability and migratory ability of PDAC cells under a relatively low dosage without affecting normal pancreatic cells. Moreover, a functional analysis revealed that BA-induced downregulation of protein clusters that participate in mitochondrial complex 1 activity and oxidative phosphorylation, which was related to decreased expressions of RNA polymerase mitochondrial (POLRMT) and translational activator of cytochrome c oxidase (TACO1), suggesting that the influence on mitochondrial function explains the effect of BA on PDAC cell growth and migration. In addition, BA also dramatically increased Apolipoprotein A1 (APOA1) expression and decreased NLR family CARD domain-containing protein 4 (NLRC4) expression, which may be involved in the dampening of PDAC migration. Notably, altered expression patterns of APOA1 and NLRC4 indicated a favorable clinical prognosis of PDAC. Based on these findings, we identified potential proteins and pathways regulated by BA from a proteomics perspective, which provides a therapeutic window for PDAC.

scholarly journals Transformation and functional verification of Cry5Aa in cotton

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shihao Zhao ◽  
Feng Wang ◽  
Qiuping Zhang ◽  
Jiayi Zou ◽  
Zhangshu Xie ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Insect Resistance ◽  
Expression Patterns ◽  
Instar Larva ◽  
Cotton Bollworm ◽  
Pcr Analysis ◽  
Functional Verification ◽  
Study Results ◽  
Significant Difference ◽  
Transgenic Strains

AbstractMost of the cotton bollworm-resistant genes applied in cotton are more than 20 years and they all belong to Cry1Ab/c family, but the insect-resistant effects of Cry5Aa on cotton were rarely reported. The possible risk of resistance is increasing. The study synthesized a novel bollworm-resistant gene Cry5Aa artificially based on preferences of cotton codon. The new gene was transferred to cotton through the method of pollen tube pathway. The transgenic strains were identified by kanamycin test in field and laboratory PCR analysis. Meanwhile, an insect resistance test was conducted by artificial bollworm feeding with transgenic leaves and GK19 was used as a control in this study. Results showed that rate of positive transgenic strains with kanamycin resistance in the first generation (T1), the second generation (T2) and the third generation (T3) respectively were 7.76%, 73.1% and 95.5%. However, PCR analysis showed that the positive strain rate in T1, T2 and T3 were 2.35%, 55.8% and 94.5%, respectively. The resistant assay of cotton bollworm showed that the mortality rate of the second, third and fourth instar larva feed by the transgenic cotton leaves, were 85.42%, 73.35% and 62.79%, respectively. There was a significant difference between transgenic plant of Cry5Aa and GK19 in insect resistance. Finally, we also conducted the further analysis of gene expression patterns, gene flow and the effect on non-target pest in the study. The results showed that Cry5Aa gene had less environmental impact, and Cry5Aa has been transferred successfully and expressed stably in cotton. Therefore, the novel bollworm resistance gene can partially replace the current insect-resistance gene of Lepidoptera insects.

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