scholarly journals RNA-Seq analysis of compatible and incompatible styles of Pyrus species at the beginning of pollination

2018 ◽  
Author(s):  
Yaqin Guan ◽  
Kun Li ◽  
Yongzhang Wang ◽  
Chunhui Ma
Keyword(s):  
High Throughput Sequencing ◽  
Early Stage ◽  
Enrichment Analysis ◽  
The Self ◽  
Pathway Enrichment Analysis ◽  
Self Incompatibility ◽  
Pollination System ◽  
Incompatible Pollination ◽  
Incompatibility Reaction ◽  
Calcium Ion Transport

AbstractIn Rosaceae, incompatible pollen can penetrate into the style during the gametophytic self-incompatibility response. It is therefore considered a stylar event rather than a stigmatic event. In this study, we explored the differences in gene expression between compatibility and incompatibility in the early stage of pollination. The self-compatible pear variety “Jinzhuili” is a naturally occurring bud mutant from “Yali”, a leading Chinese native cultivar exhibiting typical gametophytic self-incompatibility. We collected the styles of ‘Yali’ and ‘Jinzhuili’ at 0.5 and 2 h after self-pollination and then performed high-throughput sequencing. According to the pathway enrichment analysis of the differentially expressed genes, “plant-pathogen interaction” was the most represented pathway. Quantitative PCR was used to validate these differential genes. The expression levels of genes related to pollen growth and disease inhibition, such as LRR (LEUCINE-RICH REPEAT EXTENSIN), resistance, and defensin, differed significantly between compatible and incompatible pollination. Interestingly, at 0.5 h, most of these genes were upregulated in the compatible pollination system compared with the incompatible pollination system. Calcium ion transport, which requires ATPase, also demonstrated upregulated expression. In summary, the self-incompatibility reaction was initiated when the pollen came into contact with the stigma.

Two Different Prunus SFB Alleles Have the Same Function in the Self-incompatibility Reaction

2012 ◽  
Vol 31 (2) ◽  
pp. 425-434 ◽  
Author(s):  
C. Gu ◽  
J. Wu ◽  
Y.-H. Du ◽  
Y.-N. Yang ◽  
S.-L. Zhang
Keyword(s):  
The Self ◽  
Self Incompatibility ◽  
Incompatibility Reaction

scholarly journals Alterations in the Actin Cytoskeleton of Pollen Tubes Are Induced by the Self-Incompatibility Reaction in Papaver rhoeas

2000 ◽  
Vol 12 (7) ◽  
pp. 1239-1251 ◽  
Author(s):  
Anja Geitmann ◽  
Benjamin N. Snowman ◽  
Anne Mie C. Emons ◽  
Vernonica E. Franklin-Tong
Keyword(s):  
Actin Cytoskeleton ◽  
Pollen Tubes ◽  
The Self ◽  
Self Incompatibility ◽  
Papaver Rhoeas ◽  
Incompatibility Reaction

scholarly journals Identification of Potential Prognostic Competing Triplets in High-Grade Serous Ovarian Cancer

2021 ◽  
Vol 11 ◽  
Author(s):  
Jian Zhao ◽  
Xiaofeng Song ◽  
Tianyi Xu ◽  
Qichang Yang ◽  
Jingjing Liu ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
High Throughput Sequencing ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Sequencing Data ◽  
P53 Signaling ◽  
Oocyte Meiosis ◽  
The Difference ◽  
Division Cell ◽  
The Impact

Increasing lncRNA-associated competing triplets were found to play important roles in cancers. With the accumulation of high-throughput sequencing data in public databases, the size of available tumor samples is becoming larger and larger, which introduces new challenges to identify competing triplets. Here, we developed a novel method, called LncMiM, to detect the lncRNA–miRNA–mRNA competing triplets in ovarian cancer with tumor samples from the TCGA database. In LncMiM, non-linear correlation analysis is used to cover the problem of weak correlations between miRNA–target pairs, which is mainly due to the difference in the magnitude of the expression level. In addition, besides the miRNA, the impact of lncRNA and mRNA on the interactions in triplets is also considered to improve the identification sensitivity of LncMiM without reducing its accuracy. By using LncMiM, a total of 847 lncRNA-associated competing triplets were found. All the competing triplets form a miRNA–lncRNA pair centered regulatory network, in which ZFAS1, SNHG29, GAS5, AC112491.1, and AC099850.4 are the top five lncRNAs with most connections. The results of biological process and KEGG pathway enrichment analysis indicates that the competing triplets are mainly associated with cell division, cell proliferation, cell cycle, oocyte meiosis, oxidative phosphorylation, ribosome, and p53 signaling pathway. Through survival analysis, 107 potential prognostic biomarkers are found in the competing triplets, including FGD5-AS1, HCP5, HMGN4, TACC3, and so on. LncMiM is available at https://github.com/xiaofengsong/LncMiM.

scholarly journals Identification of Key Genes and Pathways in SARS-CoV-2 Infection using Bioinformatics Analysis

2020 ◽  
Author(s):  
Zhe Wang ◽  
Chenhao Jiang ◽  
Xuxuan Zhang ◽  
Yingna Zhang ◽  
Yan Ren ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Severe Pneumonia ◽  
Enrichment Analysis ◽  
Receptor Interaction ◽  
Pathway Enrichment Analysis ◽  
Airway Epithelial ◽  
Hub Genes ◽  
Bioinformatics Analyses ◽  
Human Airway

Abstract Background: Coronavirus disease 2019 (COVID-19) is a disease that causes fatal disorders including severe pneumonia. Our study aimed to utilize bioinformatics method to analyze the expression profiling by high throughput sequencing in human bronchial organoids/primary human airway epithelial infected with SARS-CoV-2 to identify the potentially crucial genes and pathways associated with COVID-19.Methods: We analyzed microarray datasets GSE153970 and GSE150819 derived from the GEO database. Firstly, the Differentially expressed genes （DEGs） in human bronchial organoids/primary human airway epithelial infected with SARS-CoV-2. Next, the DEGs were used for GO and KEGG pathway enrichment analysis. Then, the PPI network was constructed and Cytoscape was used to find the key genes.Results: Gene expression profiles of GSE153970 and GSE150819, in all 12 samples were analyzed. A total of 145 DEGs and 5 hub genes were identified in SARS-CoV-2. Meanwhile, we found that the 145 genes are associated with immune responses and the top 5 hub genes including CXCL8, CXCL1, CXCL2, CCL20, and CSF2 were mainly related to leukocyte migration, endoplasmic reticulum lumen, receptor ligand activity. In addition, the results also showed that the hub genes were associated with Cytokine−cytokine receptor interaction, IL−17 signaling pathway, and Rheumatoid arthritis in SARS-CoV-2 infection.Conclusion: The five crucial genes consisting of CXCL8, CXCL1, CXCL2, CCL20, and CSF2 were considered as hub genes of SARS-CoV-2, which may be used as diagnostic biomarkers or molecular targets for the treatment of SARS-CoV-2. It is evidenced that bioinformatics analyses in SARS-CoV-2 can be useful for understanding the underlying molecular mechanism and exploring effective therapeutic targets.

scholarly journals Multiple Regulatory Networks Are Activated during Cold Stress in Medicago sativa L.

2018 ◽  
Vol 19 (10) ◽  
pp. 3169 ◽  
Author(s):  
Qiang Zhou ◽  
Dong Luo ◽  
Xutian Chai ◽  
Yuguo Wu ◽  
Yanrong Wang ◽  
...  
Keyword(s):  
Cold Stress ◽  
Medicago Sativa ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Sequencing Platform ◽  
Medicago Sativa L ◽  
Perennial Legume

Cultivated alfalfa (Medicago sativa L.) is one of the most important perennial legume forages in the world, and it has considerable potential as a valuable forage crop for livestock. However, the molecular mechanisms underlying alfalfa responses to cold stress are largely unknown. In this study, the transcriptome changes in alfalfa under cold stress at 4 °C for 2, 6, 24, and 48 h (three replicates for each time point) were analyzed using the high-throughput sequencing platform, BGISEQ-500, resulting in the identification of 50,809 annotated unigenes and 5283 differentially expressed genes (DEGs). Metabolic pathway enrichment analysis demonstrated that the DEGs were involved in carbohydrate metabolism, photosynthesis, plant hormone signal transduction, and the biosynthesis of amino acids. Moreover, the physiological changes of glutathione and proline content, catalase, and peroxidase activity were in accordance with dynamic transcript profiles of the relevant genes. Additionally, some transcription factors might play important roles in the alfalfa response to cold stress, as determined by the expression pattern of the related genes during 48 h of cold stress treatment. These findings provide valuable information for identifying and characterizing important components in the cold signaling network in alfalfa and enhancing the understanding of the molecular mechanisms underlying alfalfa responses to cold stress.

Alterations in the Actin Cytoskeleton of Pollen Tubes Are Induced by the Self-Incompatibility Reaction in Papaver rhoeas

2000 ◽  
Vol 12 (7) ◽  
pp. 1239 ◽  
Author(s):  
Anja Geitmann ◽  
Benjamin N. Snowman ◽  
Anne Mie C. Emons ◽  
Vernonica E. Franklin-Tong
Keyword(s):  
Actin Cytoskeleton ◽  
Pollen Tubes ◽  
The Self ◽  
Self Incompatibility ◽  
Papaver Rhoeas ◽  
Incompatibility Reaction

scholarly journals Different Immune Responses of the Lymphoid Organ in Shrimp at Early Challenge Stage of Vibrio parahaemolyticus and WSSV

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2160
Author(s):  
Fuxuan Wang ◽  
Shihao Li ◽  
Fuhua Li
Keyword(s):  
Immune Responses ◽  
Vibrio Parahaemolyticus ◽  
Early Stage ◽  
Enrichment Analysis ◽  
Lymphoid Organ ◽  
Receptor Interaction ◽  
Pathway Enrichment Analysis ◽  
Immune Functions ◽  
Humoral Immune ◽  
Humoral Immune Responses

The lymphoid organ is an essential part of the immune system involved in cellular and humoral immune responses in shrimp. However, its roles in the immune responses against different pathogens are still largely unclear. In the present study, transcriptomic analysis was applied to compare the differentially expressed genes (DEGs) in the lymphoid organ of shrimp after Vibrio or WSSV challenge. In total, 2127 DEGs were screened in the lymphoid organ of shrimp at 6 h post Vibrio parahaemolyticus injection, and 1569 DEGs were obtained at the same time after WSSV challenge. KEGG pathway enrichment analysis of these DEGs revealed that two significantly enriched pathways including “neuroactive ligand–receptor interaction” and “protein digestion and absorption” were responsive to both pathogens. In contrast, “lysosome” was the significantly enriched pathway only in Vibrio challenge whereas carbohydrate metabolism related pathways were the significantly enriched pathways only in WSSV challenge. Further analysis on immune-related DEGs showed that Vibrio challenge induced broad immune responses in the lymphoid organ including activation of several pattern recognition receptors, the proPO activating system, phagocytosis related genes, and immune effectors. In contrast, the immune responses seemed to be inhibited after WSSV infection. The data suggest that the shrimp lymphoid organ plays different functions in response to the infection of distinct pathogens at the early stage, which provides new insights into the immune functions of lymphoid organ in shrimp.

scholarly journals Identification of Blood Based biomarker for Huntington's disease using in-silico gene expression analysis

2021 ◽  
Author(s):  
Souvik Chakraborty
Keyword(s):  
Gene Expression ◽  
Neurodegenerative Disorder ◽  
Early Stage ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Signs And Symptoms ◽  
Pathway Enrichment Analysis ◽  
Hub Genes ◽  
Phenotypic Characters ◽  
Potential Biomarker

Huntingtons disease (HD) is an autosomal dominant neurodegenerative disorder with profound phenotypic characters. HD is at present incurable and there are several trials going on to find a cure. HD is caused when there is a mutation in the Huntingtin gene which is found to be associated with axonal transport. Diagnosis is based on the signs and symptoms of the patients but by that time the psychomotor problems have already reached the level from where reversing the disease is impossible. Blood based biomarkers can be used for the diagnosis of the disease at an early stage. In this study several gene expression study data were analyzed and there were 329 Differentially Expressed Genes (DEGs) in all the three chosen datasets. Protein protein interaction network was created using STRING and CytoHubba plug-in was used to identify top ten hub genes which are CXCL8, PSMC6, UBE2D1, UBE2D1, CD27, UBE2D3, SF3B1, CASP3, EIF4E, BIRC2 and PTEN. Online software Enrichr was used for Gene Ontology and KEGG pathway enrichment analysis to find out the biological process, molecular function, cellular component and the pathways that were enriched in HD. This study finds out that those genes which were present in all the three datasets namely FNDC3A, BCLAF1 and ALCAM were not the hub genes. So further studies are required for identifying a potential biomarker of HD.

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