scholarly journals Proteomic Analysis of Mycelial Exudates of Ustilaginoidea virens

Pathogens ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 364
Author(s):  
Haining Wang ◽  
Xiaohe Yang ◽  
Songhong Wei ◽  
Yan Wang
Keyword(s):  
Kegg Pathway ◽  
Shotgun Proteomics ◽  
Culture Conditions ◽  
Fungal Cell ◽  
Artificial Culture ◽  
Ustilaginoidea Virens ◽  
Protein Protein Interaction ◽  
Kegg Pathway Analysis ◽  
False Smut ◽  
Antioxidant Effects

Rice false smut (RFS) disease, which is caused by Ustilaginoidea virens, has been widespread all over the world in recent years, causing irreversible losses. Under artificial culture conditions, exudates will appear on colonies of U. virens during the growth of the hyphae. Exudation of droplets is a common feature in many fungi, but the functions of exudates are undetermined. As the executors of life functions, proteins can intuitively reflect the functions of exudates. Shotgun proteomics were used in this study. A total of 650 proteins were identified in the exudate of U. virens, and the raw data were made available via ProteomeXchange with the identifier PXD019861. There were 57 subcategories and 167 pathways annotated with Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, respectively. Through protein–protein interaction (PPI) network analysis, it was found that 20 proteins participated in the biosynthesis of secondary metabolites. Two separate PPI analyses were performed for carbon metabolism and microbial metabolism in diverse environments. After comparing and annotating the functions of proteins of the exudate, it was speculated that the exudate was involved in the construction and remodeling of the fungal cell wall. Pathogenicity, sporulation, and antioxidant effects might all be affected by the exudate.

scholarly journals Identification of Key Candidate Proteins and Pathways Associated with Temozolomide Resistance in Glioblastoma Based on Subcellular Proteomics and Bioinformatical Analysis

2018 ◽  
Vol 2018 ◽  
pp. 1-12 ◽  
Author(s):  
Guo-zhong Yi ◽  
Wei Xiang ◽  
Wen-yan Feng ◽  
Zi-yang Chen ◽  
Yao-min Li ◽  
...  
Keyword(s):  
Focal Adhesion ◽  
Kegg Pathway ◽  
Bioinformatic Analysis ◽  
Differentially Expressed Proteins ◽  
Ppi Network ◽  
Network Construction ◽  
Protein Protein Interaction ◽  
Kegg Pathway Analysis ◽  
Tcga Dataset ◽  
U87 Cells

TMZ resistance remains one of the main reasons why treatment of glioblastoma (GBM) fails. In order to investigate the underlying proteins and pathways associated with TMZ resistance, we conducted a cytoplasmic proteome research of U87 cells treated with TMZ for 1 week, followed by differentially expressed proteins (DEPs) screening, KEGG pathway analysis, protein–protein interaction (PPI) network construction, and validation of key candidate proteins in TCGA dataset. A total of 161 DEPs including 65 upregulated proteins and 96 downregulated proteins were identified. Upregulated DEPs were mainly related to regulation in actin cytoskeleton, focal adhesion, and phagosome and PI3K-AKT signaling pathways which were consistent with our previous studies. Further, the most significant module consisted of 28 downregulated proteins that were filtered from the PPI network, and 9 proteins (DHX9, HNRNPR, RPL3, HNRNPA3, SF1, DDX5, EIF5B, BTF3, and RPL8) among them were identified as the key candidate proteins, which were significantly associated with prognosis of GBM patients and mainly involved in ribosome and spliceosome pathway. Taking the above into consideration, we firstly identified candidate proteins and pathways associated with TMZ resistance in GBM using proteomics and bioinformatic analysis, and these proteins could be potential biomarkers for prevention or prediction of TMZ resistance in the future.

Transcriptional identification of differentially expressed genes during the prepupal–pupal transition in the oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae)

2021 ◽  
pp. 1-14
Author(s):  
Peirong Li ◽  
Xinru Li ◽  
Wei Wang ◽  
Xiaoling Tan ◽  
Xiaoqi Wang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Developmental Stages ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Mythimna Separata ◽  
Kegg Pathway Analysis ◽  
Oriental Armyworm ◽  
Lepidoptera Noctuidae

Abstract The oriental armyworm, Mythimna separata (Walker) is a serious pest of agriculture that does particular damage to Gramineae crops in Asia, Europe, and Oceania. Metamorphosis is a key developmental stage in insects, although the genes underlying the metamorphic transition in M. separata remain largely unknown. Here, we sequenced the transcriptomes of five stages; mature larvae (ML), wandering (W), and pupation (1, 5, and 10 days after pupation, designated P1, P5, and P10) to identify transition-associated genes. Four libraries were generated, with 22,884, 23,534, 26,643, and 33,238 differentially expressed genes (DEGs) for the ML-vs-W, W-vs-P1, P1-vs-P5, and P5-vs-P10, respectively. Gene ontology enrichment analysis of DEGs showed that genes regulating the biosynthesis of the membrane and integral components of the membrane, which includes the cuticular protein (CP), 20-hydroxyecdysone (20E), and juvenile hormone (JH) biosynthesis, were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that DEGs were enriched in the metabolic pathways. Of these DEGs, thirty CP, seventeen 20E, and seven JH genes were differentially expressed across the developmental stages. For transcriptome validation, ten CP, 20E, and JH-related genes were selected and verified by real-time PCR quantitative. Collectively, our results provided a basis for further studies of the molecular mechanism of metamorphosis in M. separata.

scholarly journals Identification of Key Candidate Genes Involved in the Progression of Idiopathic Pulmonary Fibrosis

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 1123
Author(s):  
Yu Cui ◽  
Jie Ji ◽  
Jiwei Hou ◽  
Yi Tan ◽  
Xiaodong Han
Keyword(s):  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Candidate Genes ◽  
Expression Profiles ◽  
Biological Processes ◽  
Protein Protein Interaction ◽  
Novel Treatments ◽  
Kegg Pathway Analysis ◽  
Cell Components ◽  
Upregulated Genes

Idiopathic pulmonary fibrosis (IPF) is a lethal, agnogenic interstitial lung disease with limited therapeutic options. To investigate vital genes involved in the development of IPF, we integrated and compared four expression profiles (GSE110147, GSE53845, GSE24206, and GSE10667), including 87 IPF samples and 40 normal samples. By reanalyzing these datasets, we managed to identify 62 upregulated genes and 20 downregulated genes in IPF samples compared with normal samples. Differentially expressed genes (DEGs) were analyzed by gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to illustrate relevant pathways of IPF, biological processes, molecular function, and cell components. The DEGs were then subjected to protein–protein interaction (PPI) for network analysis, serving to find 11 key candidate genes (ANXA3, STX11, THBS2, MMP1, MMP9, MMP7, MMP10, SPP1, COL1A1, ITGB8, IGF1). The result of RT-qPCR and immunohistochemical staining verified our finding as well. In summary, we identified 11 key candidate genes related to the process of IPF, which may contribute to novel treatments of IPF.

scholarly journals POS0399 TMT-BASED QUANTITATIVE PROTEOMICS ANALYSIS OF SYNOVIAL FLUID-DERIVED EXOSOMES IN RHEUMATOID ARTHRITIS, AXIAL SPONDYLOARTHRITIS, GOUT AND OSTEOARTHRITIS

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 428.3-429
Author(s):  
Y. Liu ◽  
Y. Huang ◽  
Q. Huang ◽  
Z. Huang ◽  
Z. Li ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Cluster Analysis ◽  
Synovial Fluid ◽  
Pathway Analysis ◽  
Quantitative Proteomics ◽  
Axial Spondyloarthritis ◽  
Kegg Pathway ◽  
Hierarchical Cluster ◽  
Kegg Pathway Analysis ◽  
Differential Proteins

Background:The pathogeneses of the joint diseases rheumatoid arthritis (RA), axial spondyloarthritis (axSpA), gout, and osteoarthritis (OA) are still not fully elucidated. Exosomes in synovial fluid (SF) has a critical role in the pathogenesis of arthritis. None of study has compared the proteomics of SF-derived exosomes in RA, axSpA, gout and OA.Objectives:To compare the proteomics of SF-derived exosomes in RA, axSpA, gout and OA based on tandem mass tags (TMT) labeled quantitative proteomics technique.Methods:SF-derived exosomes was isolated from RA, axSpA, gout and OA patients by the Exoquick kit combined ultracentrifugation method. TMT labeled quantitative proteomics technique was used to compare the proteomics of SF-derived exosomes. Volcano plot, hierarchical cluster, Gene Ontologies (GO), Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted.Results:A total of 1678 credible proteins were detected. With the cut off criteria of |log2 (fold-change)| ≥1.2 and p-value <0.05, 267 (140 up-regulated and 127 down-regulated)differential proteins were found in OA vs gout, 291 (179 and 112) in axSpA vs OA, 515 (109 and 406) in RA vs axSpA, 298 (191 and 107) in axSpA vs gout, 462 (160 and 302) in RA vs gout, 536 (170 and 366) in RA vs OA. GO analysis showed that the biological progress of differential proteins were mainly enriched in the “immune response”. Regarding the molecular function, the differential proteins mainly mediated “antigen binding”. GO analysis of the cellular components indicated that most proteins were annotated as “extracellular exosomes”. KEGG pathway analysis demonstrated differential proteins were significantly enriched in “complement and coagulation cascades”. The hierarchical cluster analysis of the differential proteins in the four groups showed that Lysozyme C and Keratin were more abundant in gout, Hemoglobin and Actin-related protein 2/3 complex subunit 3 in OA, Sodium/potassium-transporting ATPase subunit alpha-1 and Immunoglobulin heavy constant delta in axSpA, Pregnancy zone protein and Stromelysin-1 in RA.Conclusion:The protein profiles of SF-derived exosomes in RA, axSpA, gout and OA patients were different. The differential proteins were the potential biomarkers of RA, axSpA, gout and OA.References:[1]Cretu D, Diamandis E P, Chandran V. Delineating the synovial fluid proteome: recent advancements and ongoing challenges in biomarker research.[J]. Critical reviews in clinical laboratory sciences, 2013,50(2):51-63.[2]McArdle A J, Menikou S. What is proteomics?[J]. Archives of disease in childhood. Education and practice edition, 2020.Figure 1.The hierarchical cluster analysis of differential proteins in axSpA, OA, Gout and RA.Disclosure of Interests:None declared

scholarly journals A novel transcription factor UvCGBP1 regulates development and virulence of rice false smut fungus Ustilaginoidea virens

Virulence ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 1563-1579
Author(s):  
Xiaoyang Chen ◽  
Pingping Li ◽  
Hao Liu ◽  
Xiaolin Chen ◽  
Junbin Huang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Smut Fungus ◽  
Ustilaginoidea Virens ◽  
Rice False Smut ◽  
False Smut

scholarly journals Identification of Pathways and Key Genes in Venous Remodeling After Arteriovenous Fistula by Bioinformatics Analysis

2020 ◽  
Vol 11 ◽  
Author(s):  
Kong Jie ◽  
Wang Feng ◽  
Zhao Boxiang ◽  
Gong Maofeng ◽  
Zhang Jianbin ◽  
...  
Keyword(s):  
Arteriovenous Fistula ◽  
Pathway Analysis ◽  
Kegg Pathway ◽  
Function Analysis ◽  
Gene Set Enrichment Analysis ◽  
Control Group ◽  
Hub Genes ◽  
Molting Cycle ◽  
Kegg Pathway Analysis ◽  
First Choice

The arteriovenous fistula (AVF) is the first choice for vascular access for hemodialysis of renal failure patients. Venous remodeling after exposure to high fistula flow is important for AVF to mature but the mechanism underlying remodeling is still unknown. The objective of this study is to identify the molecular mechanisms that contribute to venous remodeling after AVF. To screen and identify the differentially expressed genes (DEGs) that may involve venous remodeling after AVF, we used bioinformatics to download the public microarray data (GSE39488) from the Gene Expression Omnibus (GEO) and screen for DEGs. We then performed gene ontology (GO) function analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and gene set enrichment analysis (GSEA) for the functional annotation of DEGs. The protein-protein interaction (PPI) network was constructed and the hub genes were carried out. Finally, we harvested 12 normal vein samples and 12 AVF vein samples which were used to confirm the expressions of the hub genes by immunohistochemistry. A total of 45 DEGs were detected, including 32 upregulated and 13 downregulated DEGs. The biological process (BP) of the GO analysis were enriched in the extrinsic apoptotic signaling pathway, cGMP-mediated pathway signaling, and molting cycle. The KEGG pathway analysis showed that the upregulated DEGs were enriched in glycosaminoglycan biosynthesis and purine metabolism, while the downregulated DEGs were mainly enriched in pathways of glycosaminoglycan biosynthesis, antifolate resistance, and ABC transporters. The GSEA analysis result showed that the top three involved pathways were oxidative phosphorylation, TNFA signaling via NF-K B, and the inflammatory response. The PPI was constructed and the hub genes found through the method of DMNC showed that INHBA and NR4A2 might play an important role in venous remodeling after AVF. The integrated optical density (DOI) examined by immunohistochemistry staining showed that the expression of both INHBA and NR4A2 increased in AVF compared to the control group. Our research contributes to the understanding of the molecular mechanism of venous remodeling after exposure to high fistula flow, which may be useful in treating AVF failure.

scholarly journals Quantitative Proteomics Analysis Reveals the Function of the Putative Ester Cyclase UvEC1 in the Pathogenicity of the Rice False Smut Fungus Ustilaginoidea virens

2021 ◽  
Vol 22 (8) ◽  
pp. 4069
Author(s):  
Xiaoyang Chen ◽  
Zhangxin Pei ◽  
Pingping Li ◽  
Xiabing Li ◽  
Yuhang Duan ◽  
...  
Keyword(s):  
Quantitative Proteomics ◽  
Fungal Pathogens ◽  
Protein Localization ◽  
Proteomics Data ◽  
Ustilaginoidea Virens ◽  
Rice False Smut ◽  
Oxidative Stresses ◽  
Tandem Mass Tag ◽  
Cyclase Domain ◽  
False Smut

Rice false smut is a fungal disease distributed worldwide and caused by Ustilaginoidea virens. In this study, we identified a putative ester cyclase (named as UvEC1) as being significantly upregulated during U. virens infection. UvEC1 contained a SnoaL-like polyketide cyclase domain, but the functions of ketone cyclases such as SnoaL in plant fungal pathogens remain unclear. Deletion of UvEC1 caused defects in vegetative growth and conidiation. UvEC1 was also required for response to hyperosmotic and oxidative stresses and for maintenance of cell wall integrity. Importantly, ΔUvEC1 mutants exhibited reduced virulence. We performed a tandem mass tag (TMT)-based quantitative proteomic analysis to identify differentially accumulating proteins (DAPs) between the ΔUvEC1-1 mutant and the wild-type isolate HWD-2. Proteomics data revealed that UvEC1 has a variety of effects on metabolism, protein localization, catalytic activity, binding, toxin biosynthesis and the spliceosome. Taken together, our findings suggest that UvEC1 is critical for the development and virulence of U. virens.

The role of Ustilaginoidea virens sclerotia in increasing incidence of rice false smut disease in the subtropical zone in China

2017 ◽  
Vol 150 (3) ◽  
pp. 669-677 ◽  
Author(s):  
Mingli Yong ◽  
Qide Deng ◽  
Linlin Fan ◽  
Jiankun Miao ◽  
Chaohui Lai ◽  
...  
Keyword(s):  
Ustilaginoidea Virens ◽  
Subtropical Zone ◽  
Rice False Smut ◽  
False Smut

scholarly journals Transcriptomic inspection revealed a possible pathway regulating the formation of the high-quality brush hair in Chinese Haimen goat ( Capra hircus )

2018 ◽  
Vol 5 (1) ◽  
pp. 170907 ◽  
Author(s):  
Dejun Ji ◽  
Bo Yang ◽  
Yongjun Li ◽  
Miaoying Cai ◽  
Wei Zhang ◽  
...  
Keyword(s):  
Biological Process ◽  
Kegg Pathway ◽  
Cellular Component ◽  
Biological Information ◽  
Capra Hircus ◽  
Molecular Function ◽  
High Quality ◽  
Type Iii ◽  
Kegg Pathways ◽  
Kegg Pathway Analysis

The high-quality brush hair, or Type III brush hair, is coarse hair but with a tip and little medulla, which uniquely grows in the cervical carina of Chinese Haimen goat ( Capra hircus ). To unveil the mechanism of the formation of Type III brush hair in Haimen goats, transcriptomic RNAseq technology was used for screening of differentially expressed genes (DEGs) in the skin samples of the Type III and the non-Type III hair goats, and these DEGs were analysed by KEGG pathway analysis. The results showed that a total of 295 DEGs were obtained, mainly from three main functional types: cellular component, molecular function and biological process. These DEGs were mainly enriched in three KEGG pathways, such as protein processing in endoplasmic reticulum, MAPK, and complement and coagulation cascades. These DEGs gave hints to a possible mechanism, under which heat stress possibly initiated the formation. The study provided some useful biological information, which could give a new view about the roles of certain factors in hair growth and give hints on the mechanism of the formation of the Type III brush hair in Chinese Haimen goat.

scholarly journals Novel Fungicides for the Management of False Smut Disease of Rice Caused by Ustilaginoidea virens

2017 ◽  
Vol 6 (11) ◽  
pp. 2664-2669 ◽  
Author(s):  
K.M. Muniraju ◽  
D. Pramesh ◽  
S.B. Mallesh ◽  
K. Mallikarjun ◽  
G.S. Guruprasad
Keyword(s):  
Ustilaginoidea Virens ◽  
False Smut
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