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

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 ◽  
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 Exosomal Aβ-Binding Proteins Identified by “In Silico” Analysis Represent Putative Blood-Derived Biomarker Candidates for Alzheimer´s Disease

2021 ◽  
Vol 22 (8) ◽  
pp. 3933
Author(s):  
Tânia Soares Martins ◽  
Rui Marçalo ◽  
Maria Ferreira ◽  
Margarida Vaz ◽  
Raquel M. Silva ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Expression Patterns ◽  
In Silico Analysis ◽  
Enrichment Analysis ◽  
Disease Diagnosis ◽  
Easy Access ◽  
Altered Expression ◽  
Disease Biomarkers ◽  
Go Enrichment

The potential of exosomes as biomarker resources for diagnostics and even for therapeutics has intensified research in the field, including in the context of Alzheimer´s disease (AD). The search for disease biomarkers in peripheral biofluids is advancing mainly due to the easy access it offers. In the study presented here, emphasis was given to the bioinformatic identification of putative exosomal candidates for AD. The exosomal proteomes of cerebrospinal fluid (CSF), serum and plasma, were obtained from three databases (ExoCarta, EVpedia and Vesiclepedia), and complemented with additional exosomal proteins already associated with AD but not found in the databases. The final biofluids’ proteomes were submitted to gene ontology (GO) enrichment analysis and the exosomal Aβ-binding proteins that can constitute putative candidates were identified. Among these candidates, gelsolin, a protein known to be involved in inhibiting Abeta fibril formation, was identified, and it was tested in human samples. The levels of this Aβ-binding protein, with anti-amyloidogenic properties, were assessed in serum-derived exosomes isolated from controls and individuals with dementia, including AD cases, and revealed altered expression patterns. Identification of potential peripheral biomarker candidates for AD may be useful, not only for early disease diagnosis but also in drug trials and to monitor disease progression, allowing for a timely therapeutic intervention, which will positively impact the patient’s quality of life.

scholarly journals Integrated Transcriptome and Metabolome Analysis Reveals Key Metabolites Involved in Camellia oleifera Defense against Anthracnose

2022 ◽  
Vol 23 (1) ◽  
pp. 536
Author(s):  
Chaochen Yang ◽  
Pengfei Wu ◽  
Xiaohua Yao ◽  
Yu Sheng ◽  
Chengcai Zhang ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Enrichment Analysis ◽  
Isoquinoline Alkaloid ◽  
Flavonoid Biosynthesis ◽  
Growth And Yield ◽  
Camellia Oleifera ◽  
Metabolome Analysis ◽  
Resistant Varieties ◽  
Phenylpropanoid Biosynthesis ◽  
Tyrosine Metabolism

Camellia oleifera (Ca. oleifera) is a woody tree species cultivated for the production of edible oil from its seed. The growth and yield of tea-oil trees are severely affected by anthracnose (caused by Colletotrichum gloeosporioides). In this study, the transcriptomic and metabolomic analyses were performed to detect the key transcripts and metabolites associated with differences in the susceptibility between anthracnose-resistant (ChangLin150) and susceptible (ChangLin102) varieties of Ca. oleifera. In total, 5001 differentially expressed genes (DEGs) were obtained, of which 479 DEGs were common between the susceptible and resistant varieties and further analyzed. KEGG enrichment analysis showed that these DEGs were significantly enriched in tyrosine metabolism, phenylpropanoid biosynthesis, flavonoid biosynthesis and isoquinoline alkaloid biosynthesis pathways. Furthermore, 68 differentially accumulated metabolites (DAMs) were detected, including flavonoids, such as epicatechin, phenethyl caffeate and procyanidin B2. Comparison of the DEGs and DAMs revealed that epicatechin, procyanidin B2 and arachidonic acid (peroxide free) are potentially important. The expression patterns of genes involved in flavonoid biosynthesis were confirmed by qRT-PCR. These results suggested that flavonoid biosynthesis might play an important role in the fight against anthracnose. This study provides valuable molecular information about the response of Ca. oleifera to Co. gloeosporioides infection and will aid the selection of resistant varieties using marker-assisted breeding.

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.

scholarly journals Transcriptome differences between Cupriavidus necator NH9 grown with 3-chlorobenzoate and that grown with benzoate

2021 ◽  
Author(s):  
Ryota Moriuchi ◽  
Hideo Dohra ◽  
Yu Kanesaki ◽  
Naoto Ogawa
Keyword(s):  
Expression Patterns ◽  
Agar Plate ◽  
Enrichment Analysis ◽  
Cupriavidus Necator ◽  
Altered Expression ◽  
Solid Agar ◽  
Genes Encoding ◽  
Chemotaxis Proteins ◽  
Flagellar Proteins ◽  
Semi Solid

Abstract RNA-seq analysis of Cupriavidus necator NH9, a 3-chlorobenzoate degradative bacterium, cultured with 3-chlorobenzaote and benzoate, revealed strong induction of genes encoding enzymes in degradation pathways of the respective compound, including the genes to convert 3-chlorobenzaote and benzoate to chlorocatechol and catechol, respectively, and the genes of chlorocatechol ortho-cleavage pathway for conversion to central metabolites. The genes encoding transporters, components of the stress response, flagellar proteins, and chemotaxis proteins showed altered expression patterns between 3-chlorobenzoate and benzoate. Gene Ontology enrichment analysis revealed that chemotaxis related terms were significantly upregulated by benzoate compared with 3-chlorobenzoate. Consistent with this, in semi-solid agar plate assays, NH9 cells showed stronger chemotaxis to benzoate than to 3-chlorobenzoate. These results, combined with the absence of genes related to uptake/chemotaxis for 3-chlorobenzoate located closely to the degradation genes of 3-chlorobenzoate, suggested that NH9 has not fully adapted to the utilization of chlorinated benzoate, unlike benzoate, in nature.

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 Phenotypic Resemblance to Neuropsychiatric Disorder and Altered mRNA Profiles in Cortex and Hippocampus Underlying IL15Rα Knockout

2021 ◽  
Vol 14 ◽  
Author(s):  
Yi He ◽  
Yuxin Yu ◽  
Yanan Li ◽  
Weicheng Duan ◽  
Zuoli Sun ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Development ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Control Group ◽  
Rna Seq ◽  
Skeletal Muscle Development ◽  
Altered Expression ◽  
Y Maze

BackgroundPrevious studies of the functions of IL15Rα have been limited to immune activities and skeletal muscle development. Immunological factors have been identified as one of the multiple causes of psychosis, and neurological symptoms have been described in IL15Rα knockout (KO) mice. Seeking to explore possible mechanisms for this in the IL15Rα–/– mouse brain, we analyzed gene expression patterns in the cortex and hippocampus using the RNA-seq technique.MethodsIL15Rα KO mice were generated and littermate wildtype (WT) mice were used as a control group. A Y-maze was used to assess behavior differences between the two groups. The cortex and hippocampus of 3-month-old male mice were prepared and RNA-seq and transcriptome analysis were performed by gene set enrichment analysis (GSEA).ResultsCompared with the WT group, IL15Rα KO animals showed higher speed in the novel arm and more entrance frequency in the old arm in the Y-maze experiment. GSEA indicated that 18 pathways were downregulated and 13 pathways upregulated in both cortex and hippocampus from the GO, KEGG, and Hallmark gene sets. The downregulated pathways formed three clusters: respiratory chain and electron transport, regulation of steroid process, and skeletal muscle development.ConclusionIL15Rα KO mice exhibit altered expression of multiple pathways, which could affect many functions of the brain. Lipid biosynthesis and metabolism in the central nervous system (CNS) should be investigated to provide insights into the effect of IL15Rα on psychosis in this murine model.

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