scholarly journals iTRAQ-Based Quantitative Proteome Revealed Metabolic Changes in Winter Turnip Rape (Brassica rapa L.) under Cold Stress

2018 ◽  
Vol 19 (11) ◽  
pp. 3346 ◽  
Author(s):  
Yaozhao Xu ◽  
Xiucun Zeng ◽  
Jian Wu ◽  
Fenqin Zhang ◽  
Caixia Li ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Cold Stress ◽  
Brassica Rapa ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Pentose Phosphate ◽  
Metabolic Process ◽  
Cellular Process ◽  
Turnip Rape

Winter turnip rape (Brassica rapa L.) is a large-scale winter-only oil crop cultivated in Northwest China. However, its cold-resistant molecular mechanism remains inadequate. Studying the cold adaptation mechanisms of winter turnip rape based on the proteomic technique of isobaric tags for relative and absolute quantification (iTRAQ) offers a solution to this problem. Under cold stress (−4 °C for eight hours), 51 and 94 differently accumulated proteins (DAPs) in Longyou 7 (cold-tolerant) and Tianyou 4 (cold-sensitive) were identified, respectively. These DAPs were classified into 38 gene ontology (GO) term categories, such as metabolic process, cellular process, catalytic activity, and binding. The 142 DAPs identified between the two cold-stressed cultivars were classified into 40 GO terms, including cellular process, metabolic process, cell, catalytic activity, and binding. Kyoto Encyclopedia of Genes and Genomes enrichment analysis indicated that the DAPs participated in 10 pathways. The abundance of most protein functions in ribosomes, carbon metabolism, photosynthesis, and energy metabolism including the citrate cycle, pentose phosphate pathway, and glyoxylate and dicarboxylate metabolism decreased, and the proteins that participate in photosynthesis–antenna and isoflavonoid biosynthesis increased in cold-stressed Longyou 7 compared with those in cold-stressed Tianyou 4. The expression pattern of genes encoding the 10 significant DAPs was consistent with the iTRAQ data. This study provides new information on the proteomic differences between the leaves of Longyou 7 and Tianyou 4 plants and explains the possible molecular mechanisms of cold-stress adaptation in B. rapa.

scholarly journals Identification of IL10RA by Weighted Correlation Network Analysis and in vitro Validation of Its Association With Prognosis of Metastatic Melanoma

2021 ◽  
Vol 8 ◽  
Author(s):  
Si Cheng ◽  
Zhe Li ◽  
Wenhao Zhang ◽  
Zhiqiang Sun ◽  
Zhigang Fan ◽  
...  
Keyword(s):  
Network Analysis ◽  
Metastatic Melanoma ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Migration And Invasion

Skin cutaneous melanoma (SKCM) is the major cause of death for skin cancer patients, its high metastasis often leads to poor prognosis of patients with malignant melanoma. However, the molecular mechanisms underlying metastatic melanoma remain to be elucidated. In this study we aim to identify and validate prognostic biomarkers associated with metastatic melanoma. We first construct a co-expression network using large-scale public gene expression profiles from GEO, from which candidate genes are screened out using weighted gene co-expression network analysis (WGCNA). A total of eight modules are established via the average linkage hierarchical clustering, and 111 hub genes are identified from the clinically significant modules. Next, two other datasets from GEO and TCGA are used for further screening of biomarker genes related to prognosis of metastatic melanoma, and identified 11 key genes via survival analysis. We find that IL10RA has the highest correlation with clinically important modules among all identified biomarker genes. Further in vitro biochemical experiments, including CCK8 assays, wound-healing assays and transwell assays, have verified that IL10RA can significantly inhibit the proliferation, migration and invasion of melanoma cells. Furthermore, gene set enrichment analysis shows that PI3K-AKT signaling pathway is significantly enriched in metastatic melanoma with highly expressed IL10RA, indicating that IL10RA mediates in metastatic melanoma via PI3K-AKT pathway.

scholarly journals iTRAQ-based quantitative proteome analysis insights into cold stress of Winter Rapeseed (Brassica rapa L.) grown in the field

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zaoxia Niu ◽  
Lijun Liu ◽  
Yuanyuan Pu ◽  
Li Ma ◽  
Junyan Wu ◽  
...  
Keyword(s):  
Cold Stress ◽  
Brassica Rapa ◽  
Molecular Mechanisms ◽  
Glutathione Transferase ◽  
Soluble Sugars ◽  
Freezing Stress ◽  
Transferase Activity ◽  
Oilseed Crop ◽  
Winter Rapeseed ◽  
Collar Diameter

AbstractWinter rapeseed (Brassica rapa L.) is a major oilseed crop in Northern China, where its production was severely affected by chilling and freezing stress. However, not much is known about the role of differentially accumulated proteins (DAPs) during the chilling and freezing stress. In this study, isobaric tag for relative and absolute quantification (iTRAQ) technology was performed to identify DAPs under freezing stress. To explore the molecular mechanisms of cold stress tolerance at the cellular and protein levels, the morphological and physiological differences in the shoot apical meristem (SAM) of two winter rapeseed varieties, Longyou 7 (cold-tolerant) and Lenox (cold-sensitive), were explored in field-grown plants. Compared to Lenox, Longyou 7 had a lower SAM height and higher collar diameter. The level of malondialdehyde (MDA) and indole-3-acetic acid (IAA) content was also decreased. Simultaneously, the soluble sugars (SS) content, superoxide dismutase (SOD) activity, peroxidase (POD) activity, soluble protein (SP) content, and collar diameter were increased in Longyou 7 as compared to Lenox. A total of 6330 proteins were identified. Among this, 98, 107, 183 and 111 DAPs were expressed in L7 CK/Le CK, L7 d/Le d, Le d/Le CK and L7 d/L7 CK, respectively. Quantitative real-time PCR (RT-qPCR) analysis of the coding genes for seventeen randomly selected DAPs was performed for validation. These DAPs were identified based on gene ontology enrichment analysis, which revealed that glutathione transferase activity, carbohydrate-binding, glutathione binding, metabolic process, and IAA response were closely associated with the cold stress response. In addition, some cold-induced proteins, such as glutathione S-transferase phi 2(GSTF2), might play an essential role during cold acclimation in the SAM of Brassica rapa. The present study provides valuable information on the involvement of DAPs during cold stress responses in Brassica rapa L, and hence could be used for breeding experiments.

scholarly journals iTRAQ-Based Comparative Proteomic Analysis of the Roots of TWO Winter Turnip Rapes (Brassica rapa L.) with Different Freezing-Tolerance

2018 ◽  
Vol 19 (12) ◽  
pp. 4077 ◽  
Author(s):  
Xiucun Zeng ◽  
Yaozhao Xu ◽  
Jinjin Jiang ◽  
Fenqin Zhang ◽  
Li Ma ◽  
...  
Keyword(s):  
Cold Acclimation ◽  
Linolenic Acid ◽  
Brassica Rapa ◽  
Freezing Tolerance ◽  
Stress Responses ◽  
Molecular Mechanisms ◽  
Carbon Fixation ◽  
Freezing Stress ◽  
Turnip Rape ◽  
Mannose Metabolism

The freezing tolerance of roots is crucial for winter turnip rape (Brassica rapa L.) survival in the winter in Northwest China. Cold acclimation (CA) can alleviate the root damage caused by freezing stress. To acknowledge the molecular mechanisms of freezing tolerance in winter turnip rape, two Brassica rapa genotypes, freezing stressed after the induction of cold acclimation, were used to compare the proteomic profiles of roots by isobaric tags for relative and absolute quantification (iTRAQ). Under freezing stress (−4 °C) for 8 h, 139 and 96 differentially abundant proteins (DAPs) were identified in the roots of “Longyou7” (freezing-tolerant) and “Tianyou4” (freezing-sensitive), respectively. Among these DAPs, 91 and 48 proteins were up- and down-accumulated in “Longyou7”, respectively, and 46 and 50 proteins were up- and down-accumulated in “Tianyou4”, respectively. Under freezing stress, 174 DAPs of two varieties were identified, including 9 proteins related to ribosome, 19 DAPs related to the biosynthesis of secondary metabolites (e.g., phenylpropanoid and the lignin pathway), and 22 down-accumulated DAPs enriched in oxidative phosphorylation, the pentose phosphate pathway, fructose and mannose metabolism, alpha-linolenic acid metabolism, carbon fixation in photosynthetic organisms, ascorbate and aldarate metabolism. The expressional pattern of the genes encoding the 15 significant DAPs were consistent with the iTRAQ data. This work indicates that protein biosynthesis, lignin synthesis, the reduction of energy consumption and a higher linolenic acid content contribute to the freezing tolerance of winter turnip rape. Functional analyses of these DAPs would be helpful in dissecting the molecular mechanisms of the stress responses in B. rapa.

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.

scholarly journals iTRAQ-Based Quantitative Proteome Analysis Insights into Cold Stress of Winter Turnip Rapa (Brassica rapa L.) Grown in the Field

2021 ◽  
Author(s):  
Zaoxia Niu ◽  
Lijun Liu ◽  
Yuanyuan Pu ◽  
Li Ma ◽  
Junyan Wu ◽  
...  
Keyword(s):  
Cold Stress ◽  
Brassica Rapa ◽  
Molecular Mechanisms ◽  
Glutathione Transferase ◽  
Function Analysis ◽  
Chilling Stress ◽  
Freezing Stress ◽  
Transferase Activity ◽  
Oilseed Crop ◽  
Collar Diameter

Abstract Winter Turnip rapa (Brassica rapa L.) is a major oilseed crop in Northern China, where its production was severely affected by chilling and freezing stress. Previous studies have demonstrated that differentially accumulated proteins (DAPs) were expressed in roots and leaves under control chilling stress. In this study, the isobaric tag for relative and absolute quantification (iTRAQ) technology was performed to identify DAPs under freezing stress. Two winter rapaseed varieties, Longyou 7 (cold-tolerant) and Lenox (cold-sensitive), were used to investigated morphological, physiological, cell and protein levels in the shoot apical meristem (SAM) of field-grown Brassica rapa to reveal the molecular mechanisms of cold stress tolerance. Compared to Lenox, Longyou 7 had a lower SAM of height, higher collar diameter. The level of malondialdehyde (MDA), SAM of height and IAA content were repressed. At the same time, compared to Lenox, the soluble sugars (SS) content, superoxide dismutase (SOD) activity, peroxidase(POD)activity, soluble protein (SP) content and collar diameter increased in Longyou 7. In total, we identified 6330 proteins, among this, 98 DAPs were expressed in L7 CK/Le CK, 107 DAPs were expressed in L7 d /Le d 183 DAPs were expressed in Le d /Le CK, 111 DAPs were expressed in L7 d /L7 CK. Quantitative real-time PCR (RT-qPCR) analysis of the coding genes for seventeen randomly selected DAPs were performed for validation. These DAPs were identified from the two winter rapa seed cultivars involved in the biological process, cellular component and molecular function analysis, which revealed glutathione transferase activity, carbohydrate-binding, and glutathione binding, glutathione metabolic process and response IAA were closely associated with the cold stress response. Some cold-induced proteins, such as glutathione S-transferase phi 2(GSTF2), might play essential roles cold acclimation in Brassica rapa of SAM. Our work will help to provide valuable information for responding to the cold stress in Brassica rapa L.

scholarly journals Transcriptome analysis of the Larimichthys polyactis under heat and cold stress

2019 ◽  
Author(s):  
Tianqi Chu ◽  
Feng Liu ◽  
Gaochan Qin ◽  
Wei Zhan ◽  
Mengjie Wang ◽  
...  
Keyword(s):  
Cold Stress ◽  
Temperature Stress ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Control Group ◽  
Pathway Enrichment Analysis ◽  
Larimichthys Polyactis ◽  
Small Yellow Croaker ◽  
Heat And Cold Stress ◽  
Temperature Group

AbstractThe small yellow croaker (Larimichthys polyactis) is an important marine economic fish that is widely distributed in the East Sea, Yellow Sea and Bohai of China. However, the wild populations of small yellow croaker are severely depleted, and there is currently a developing large-scale artificial propagation of this fish for aquaculture. However, the current variety of small yellow croaker that is cultivated is not capable to coping with large fluctuations in temperature. Therefore, it is important to understand the molecular mechanisms that are activated in response to temperature stress in the small yellow croaker. Here, we conducted transcriptomic analysis of the liver of small yellow croaker under heat and cold stress. A total of 270,844,888, 265,727,006 and 259,666,218 clean reads were generated from heat temperature group, low temperature group and control group, respectively, and comparing expression of genes in these transcriptomes,10,878 unigenes that were differential expressed were identified. Sixteen of the differentially expressed unigenes were validated by qRT-PCR. Pathway enrichment analysis identified that the ER pathway, immune signaling pathway and metabolic response pathway were affected by temperature stress. The results of this study provide a comprehensive overview of temperature stress-induced transcriptional patterns in liver tissues of the small yellow croaker. In addition, these results can guide future molecular studies of heat and cold stress response in this species for improving the stock used for aquaculture.

scholarly journals CENPE, PRC1, TTK, and PLK4 May Play Crucial Roles in the Osteosarcoma Progression

2020 ◽  
Vol 19 ◽  
pp. 153303382097327
Author(s):  
Fei Wang ◽  
Qiheng Zhao ◽  
Wenping Liu ◽  
Daliang Kong
Keyword(s):  
Chondroitin Sulfate ◽  
Molecular Mechanisms ◽  
Biological Process ◽  
Enrichment Analysis ◽  
Pentose Phosphate ◽  
Control Group ◽  
Ppi Network ◽  
Kegg Pathways ◽  
Smad Protein ◽  
Student’S T

Osteosarcoma (OS) is a cancerous tumor in a bone. We aimed to identify the critical genes involved in OS progression, and then try to elucidate the molecular mechanisms of this disease. The microarray data of GSE32395 was used for the present study. We analyzed differentially expressed genes (DEGs) in OS cells compared with control group by Student’s t-test. The significant enriched gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathways were analyzed for upregulated genes and downregulated genes, respectively. In addition, a protein-protein interaction (PPI) network was constructed. GO and KEGG enrichment analyses were conducted for genes in the PPI network. In total, 183 DEGs, including 100 upregulated DEGs and 83 downregulated DEGs were screened. The upregulated DEGs were significantly enriched in 2 KEGG pathways, such as “Glycosaminoglycan biosynthesis-chondroitin sulfate” and the downregulated DEGs were significantly enriched in 12 pathways, including “cell adhesion molecules,” “pentose phosphate pathway” and “allograft rejection.” GO enrichment analysis indicated that the upregulated DEGs were significantly involved in biological process, such as “multicellular organismal metabolic process” and “limb morphogenesis,” while the downregulated DEGs were significantly enriched in biological process, such as “Positive regulation of pathway-restricted SMAD protein phosphorylation.” The PPI network included 84 interactions and 51 nodes. The “glycosaminoglycan biosynthesis-chondroitin sulfate pathway,” “microtubule motor activityfunction,” and “regulation of mitosis process” were significantly enriched by genes in PPI network. In particular, CENPE, PRC1, TTK, and PLK4 had higher degrees in the PPI network. The interactions between TTK and PLK4 as well as CENPE and PRC1 may involve in the OS development. These 4 genes might be possible biomarkers for the treatment and diagnosis of OS.

scholarly journals Identification of potential core genes in hepatoblastoma via bioinformatics analysis

2020 ◽  
Author(s):  
Basavaraj Vastrad ◽  
Chanabasayya Vastrad ◽  
Iranna Kotturshetti
Keyword(s):  
Gene Ontology ◽  
Regulatory Network ◽  
Target Gene ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Metabolic Process ◽  
Chromosome Organization ◽  
Hub Genes ◽  
Go Enrichment ◽  
Go Enrichment Analysis

AbstractHepatoblastoma is the childhood liver cancer. Profound efforts have been made to illuminate the pathology, but the molecular mechanisms of hepatoblastoma are still not well understood. To identify the candidate genes in the carcinogenesis and progression of hepatoblastoma, microarray dataset GSE131329 was downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified, and pathway and Gene Ontology (GO) enrichment analysis were performed. The protein-protein interaction network (PPI), module analysis, target gene - miRNA regulatory network and target gene - TF regulatory network were constructed and analyzed. A total of 996 DEGs were identified, consisting of 499 up regulated genes and 497 down regulated genes. The pathway and Gene Ontology (GO) enrichment analysis of the DEGs include proline biosynthesis, superpathway of tryptophan utilization, chromosome organization and organic acid metabolic process. Twenty-four hub genes were identified and biological process analysis revealed that these genes were mainly enriched in cell cycle, chromosome organization, lipid metabolic process and oxidation-reduction process. Validation of hub genes showed that TP53, PLK1, AURKA, CDK1, ANLN, ESR1, FGB, ACAT1, GOT1 and ALAS1 may be involved in the carcinogenesis, invasion or recurrence of hepatoblastoma. In conclusion, DEGs and hub genes identified in the present study help us understand the molecular mechanisms underlying the carcinogenesis and progression of hepatoblastoma, and provide candidate targets for diagnosis and treatment of hepatoblastoma.

scholarly journals Genetics of Behçet's Disease: Functional Genetic Analysis and Estimating Disease Heritability

2021 ◽  
Vol 8 ◽  
Author(s):  
Lourdes Ortiz-Fernández ◽  
Amr H. Sawalha
Keyword(s):  
Behçet’S Disease ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Behcet’S Disease ◽  
Behçet's Disease ◽  
Enrichment Analysis ◽  
Genetic Component ◽  
Pathway Enrichment Analysis ◽  
Inflammatory Disorder ◽  
Behcet's Disease

Behçet's disease is a chronic multisystemic inflammatory disorder characterized by recurrent oral and genital ulcers. Although its etiology remains unclear, it is thought that both genetic and environmental factors contribute to the onset and progression of Behçet's disease. Here, we provide an updated view of the genetic landscape and architecture of Behçet's disease. Large-scale genetic studies performed to date revealed 21 genetic susceptibility loci associated with the disease at a GWAS level of significance (p-value = 5 × 10−8). We performed epigenetic pattern enrichment analysis in Behçet's disease associated loci, providing new insights into the molecular mechanisms underlying its pathophysiology. Our data suggest the crucial involvement of several immune cell types, including natural killer cells, monocytes, and B cells in the pathogenesis of the disease. Pathway enrichment analysis identified important biological processes involved. Using large-scale genetic data available from ~200 immune-related loci (Immunochip), we estimate Behçet's disease heritability to be at least 16%. We further used the same approach to estimate the heritability explained by the known Behçet's disease-associated loci, suggesting that they explain ~ 60% of the genetic component underlying Behçet's disease. These results indicate a significant role of non-genetic factors in causing Behçet's disease and that additional genetic variation influencing the risk of Behçet's disease remains to be identified. Finally, we calculated a cumulative genetic risk score across populations reinforcing the link between geographic variations in disease prevalence with its genetic component.

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