Glucosinolate profile and Myrosinase gene expression are modulated upon Plasmodiophora brassicae infection in cabbage

2021 ◽  
Vol 48 (1) ◽  
pp. 103
Author(s):  
Md. Abdul Kayum ◽  
Ujjal Kumar Nath ◽  
Jong-In Park ◽  
Mohammad Rashed Hossain ◽  
Hoy-Taek Kim ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plasmodiophora Brassicae ◽  
Expression Patterns ◽  
Principal Component ◽  
Resistant Line ◽  
Clubroot Disease ◽  
Disease Symptoms ◽  
Susceptible Line ◽  
Glucosinolate Profile ◽  
In Silico Analyses

Clubroot is a devastating disease of Brassicaceae caused by the biotrophic protist Plasmodiophora brassicae. The progression of clubroot disease is modulated by the glucosinolate (GSL) profile of the host plant. GSL is hydrolysed by the enzyme myrosinase upon cell disruption and gives rise to metabolites like isothiocyanate, nitriles, thiocyanates, epithionitriles and oxazolidines. Some of these metabolites play important roles in the plant’s defence mechanism. We identified 13 Myrosinase (Myro) and 28 Myrosinase-Binding Protein-like (MBP) genes from Brassica oleracea L. using a comparative genomics approach and characterised them through in silico analyses. We compared the expression patterns of these genes in a clubroot-susceptible line and a resistant line following inoculation with P. brassicae. Two BolMyro and 12 BolMBP genes were highly expressed in the susceptible line, whereas only one BolMyro and five BolMBP genes were highly expressed in the resistant line. Principal component analysis confirmed that specific GSL profiles and gene expression were modulated due to pathogen infection. Plants with higher levels of neoglucobrassicin, glucobrassicin and methooxyglucobrassicin produced disease symptoms and formed galls, whereas, plants with higher levels of sinigrin, hydroxyglucobrassicin and progoitrin produced less symptoms with almost no galls. Our results provide insights into the roles of Myro and MBP genes in GSL hydrolysis during P. brassicae infection, which will help for developing clubroot resistant cabbage lines.

scholarly journals Comprehensive Comparison of Amnion Stromal Cells and Chorion Stromal Cells by RNA-Seq

2021 ◽  
Vol 22 (4) ◽  
pp. 1901
Author(s):  
Brielle Jones ◽  
Chaoyang Li ◽  
Min Sung Park ◽  
Anne Lerch ◽  
Vimal Jacob ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stromal Cells ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Principal Component ◽  
Differentially Expressed ◽  
Inflammatory Factor ◽  
Next Generation Sequencing Technology ◽  
Angiogenic Potential ◽  
Anti Inflammatory

Mesenchymal stromal cells derived from the fetal placenta, composed of an amnion membrane, chorion membrane, and umbilical cord, have emerged as promising sources for regenerative medicine. Here, we used next-generation sequencing technology to comprehensively compare amniotic stromal cells (ASCs) with chorionic stromal cells (CSCs) at the molecular and signaling levels. Principal component analysis showed a clear dichotomy of gene expression profiles between ASCs and CSCs. Unsupervised hierarchical clustering confirmed that the biological repeats of ASCs and CSCs were able to respectively group together. Supervised analysis identified differentially expressed genes, such as LMO3, HOXA11, and HOXA13, and differentially expressed isoforms, such as CXCL6 and HGF. Gene Ontology (GO) analysis showed that the GO terms of the extracellular matrix, angiogenesis, and cell adhesion were significantly enriched in CSCs. We further explored the factors associated with inflammation and angiogenesis using a multiplex assay. In comparison with ASCs, CSCs secreted higher levels of angiogenic factors, including angiogenin, VEGFA, HGF, and bFGF. The results of a tube formation assay proved that CSCs exhibited a strong angiogenic function. However, ASCs secreted two-fold more of an anti-inflammatory factor, TSG-6, than CSCs. In conclusion, our study demonstrated the differential gene expression patterns between ASCs and CSCs. CSCs have superior angiogenic potential, whereas ASCs exhibit increased anti-inflammatory properties.

scholarly journals Mining of Brassica-Specific Genes (BSGs) and Their Induction in Different Developmental Stages and under Plasmodiophora brassicae Stress in Brassica rapa

2018 ◽  
Vol 19 (7) ◽  
pp. 2064 ◽  
Author(s):  
Mingliang Jiang ◽  
Xiangshu Dong ◽  
Hong Lang ◽  
Wenxing Pang ◽  
Zongxiang Zhan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Rapa ◽  
Developmental Stages ◽  
Plasmodiophora Brassicae ◽  
Expression Patterns ◽  
Gc Content ◽  
Biological Information ◽  
Lower Percentage ◽  
Orphan Genes ◽  
Conserved Genes

Orphan genes, also called lineage-specific genes (LSGs), are important for responses to biotic and abiotic stresses, and are associated with lineage-specific structures and biological functions. To date, there have been no studies investigating gene number, gene features, or gene expression patterns of orphan genes in Brassica rapa. In this study, 1540 Brassica-specific genes (BSGs) and 1824 Cruciferae-specific genes (CSGs) were identified based on the genome of Brassica rapa. The genic features analysis indicated that BSGs and CSGs possessed a lower percentage of multi-exon genes, higher GC content, and shorter gene length than evolutionary-conserved genes (ECGs). In addition, five types of BSGs were obtained and 145 out of 529 real A subgenome-specific BSGs were verified by PCR in 51 species. In silico and semi-qPCR, gene expression analysis of BSGs suggested that BSGs are expressed in various tissue and can be induced by Plasmodiophora brassicae. Moreover, an A/C subgenome-specific BSG, BSGs1, was specifically expressed during the heading stage, indicating that the gene might be associated with leafy head formation. Our results provide valuable biological information for studying the molecular function of BSGs for Brassica-specific phenotypes and biotic stress in B. rapa.

scholarly journals Characterization of Five Molecular Markers for Pathotype Identification of the Clubroot Pathogen Plasmodiophora brassicae

2018 ◽  
Vol 108 (12) ◽  
pp. 1486-1492 ◽  
Author(s):  
Jing Zheng ◽  
Xuliang Wang ◽  
Qian Li ◽  
Shu Yuan ◽  
Shiqing Wei ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Plasmodiophora Brassicae ◽  
Expression Patterns ◽  
Chain Reaction ◽  
Clubroot Disease ◽  
Polymerase Chain ◽  
Differential Hosts ◽  
Reaction Cycles ◽  
Important Disease

Clubroot disease is an important disease on cruciferous crops caused by Plasmodiophora brassicae infections. The pathotypes have been classified based on the reactions of differential hosts. However, molecular markers of particular pathotypes for P. brassicae are limited. In this study, we found five genetic markers in association with different pathotypes. Different gene expression patterns among different pathotypes (P4, P7, P9, and P11) were assayed according to the transcriptome data. The assay indicated that molecular markers PBRA_007750 and PBRA_009348 could be used to distinguish P11 from P4, P7, and P9; PBRA_009348 and Novel342 could distinguish P9 from P4, P7, and P11; and PBRA_008439 and Novel342 could represent a kind of P4. Polymerase chain reaction cycles ranging from 25 to 30 were able to identify the predominant pathotype in general. Therefore, these molecular markers would be a valuable tool to identify and discriminate pathotypes in P. brassicae population.

Clinical phenotype and gene expression profile in Crohn's disease

2007 ◽  
Vol 292 (1) ◽  
pp. G298-G304 ◽  
Author(s):  
Claudio Csillag ◽  
Ole Haagen Nielsen ◽  
Rehannah Borup ◽  
Finn Cilius Nielsen ◽  
Jørgen Olsen
Keyword(s):  
Gene Expression ◽  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Intracellular Transport ◽  
Clinical Phenotype ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Principal Component ◽  
Gene Profiling ◽  
Gene Expression Patterns

The clinical course varies significantly among patients with Crohn's disease (CD). This study investigated whether gene expression profiles generated by DNA microarray technology might predict disease progression. Biopsies from the descending colon were obtained colonoscopically from 40 CD patients. Gene profiling analyses were performed using a Human Genome U133 Plus 2.0 GeneChip Array, and summarization into a single expression measure for each probe set was performed using the robust multiple array procedure. Principal component analysis demonstrated that three components explain two-thirds of the total variation. The most important parameters for the determination of the colonic gene expression patterns were the presence of disease (CD) and presence of inflammation. Superimposition of clinical phenotype data revealed a grouping of the samples from patients with stenosis toward negative values on the axis of the second principal component. The functional annotation analysis suggested that the expression of genes involved in intracellular transport and cytoskeletal organization might influence the development of stenosis. In conclusion, even though most variation in the colonic gene expression patterns is due to presence or absence of CD and inflammation status, the development of stenosis is a parameter that affects colonic gene expression to some extent.

Ischemic but not pharmacological preconditioning elicits a gene expression profile similar to unprotected myocardium

2004 ◽  
Vol 20 (1) ◽  
pp. 117-130 ◽  
Author(s):  
Rafaela da Silva ◽  
Eliana Lucchinetti ◽  
Thomas Pasch ◽  
Marcus C. Schaub ◽  
Michael Zaugg
Keyword(s):  
Gene Expression ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Ischemia Reperfusion ◽  
Expression Patterns ◽  
Principal Component ◽  
Gene Clusters ◽  
Stable Gene ◽  
Transcriptional Responses ◽  
Rat Hearts

Pharmacological (PPC) and ischemic preconditioning (IschPC) provide comparable protection against ischemia in the heart. However, the genomic phenotype may depend on the type of preconditioning. Isolated perfused rat hearts were used to evaluate transcriptional responses to PPC and IschPC in the presence (mediator/effector response) or absence (trigger response) of 40 min of test ischemia using oligonucleotide microarrays. IschPC was induced by 3 cycles of 5 min of ischemia, and PPC by 15 min of 2.1 vol% isoflurane. Unsupervised analysis methods were used to identify gene expression patterns. PPC and IschPC were accompanied by marked alterations in gene expression. PPC and IschPC shared only ∼25% of significantly up- and downregulated genes after triggering. The two types of preconditioning induced a more uniform genomic response after ischemia/reperfusion. Numerous genes separated preconditioned from unprotected ischemic hearts. Three stable gene clusters were identified in the trigger response to preconditioning, while eight stable clusters related to cytoprotection, inflammation, remodeling, and long interspersed nucleotide elements (LINEs) were delineated after prolonged ischemia. A single stable sample cluster emerged from cluster analysis for both IschPC and unprotected myocardium, indicating a close molecular relationship between these two treatments. Principal component analysis revealed differences between PPC vs. IschPC, and trigger vs. mediator/effector responses in transcripts predominantly related to biosynthesis and apoptosis. IschPC and PPC similarly but distinctly reprogram the genetic response to ischemic injury. IschPC elicits a postischemic gene expression profile closer to unprotected myocardium than PPC, which may be therefore more advantageous as therapeutic strategy in cardioprotection.

Gene expression profiling of cerebellar development with high-throughput functional analysis

2005 ◽  
Vol 22 (1) ◽  
pp. 8-13 ◽  
Author(s):  
Sakae Saito ◽  
Kimi Honma ◽  
Hiroko Kita-Matsuo ◽  
Takahiro Ochiya ◽  
Kikuya Kato
Keyword(s):  
Gene Expression ◽  
Neurite Outgrowth ◽  
High Throughput ◽  
Functional Data ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Principal Component ◽  
Data Matrix ◽  
Cerebellar Development ◽  
Gene Expression Patterns

We measured the expression levels of 450 genes during mouse postnatal cerebellar development by quantitative PCR using RNA purified from layers of the cerebellar cortex. Principal component analysis of the data matrix demonstrated that the first and second components corresponded to general levels of gene expression and gene expression patterns, respectively. We introduced 288 of the 450 genes into PC12 cells using a high-throughput transfection assay based on atelocollagen and determined the ability of each gene to promote neurite outgrowth or cell proliferation. Five genes induced neurite outgrowth, and seven genes enhanced proliferation. Evaluation of the functional data and gene expression patterns showed that none of these genes exhibited elevated expression at maturation, suggesting that genes characteristic of mature neurons are not likely to participate in neuronal development. These results demonstrate that functional data can facilitate interpretation of expression profiles and identification of new molecules that participate in biological processes.

scholarly journals Physiological Change Alters Endophytic Bacteria Community in Clubroot of Tumorous Stem Mustard Infected by Plasmodiophora Brassicae

2020 ◽  
Author(s):  
Diandong Wang ◽  
Tingting Sun ◽  
Songyu Zhao ◽  
Limei Pan ◽  
Hongfang Liu ◽  
...  
Keyword(s):  
Soluble Protein ◽  
Endophytic Bacteria ◽  
Redundancy Analysis ◽  
High Throughput Sequencing ◽  
Plasmodiophora Brassicae ◽  
Soluble Sugar ◽  
Principal Component ◽  
Dominant Group ◽  
Clubroot Disease ◽  
Weighted Principal Component

Abstract Background: Endophytic bacteria are considered as symbionts living within plants and are influenced by abiotic and biotic environmemts. Here, we reveal how endophytic bacteria in tumorous stem mustard (Brassica juncea var. tumida) are affected by clubroot disease using 16S rRNA high-throughput sequencing.Results: The results showed that Proteobacteria was the dominant group in both healthy roots and clubroots, but their abundance differed. At the genus level, Pseudomonas was dominant in clubroots, whereas Rhodanobacter was the dominant in healthy roots. Hierarchical clustering, UniFrac-weighted principal component analysis (PCA), non-metric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM) indicated significant differences between the endophytic bacteria communities in healthy roots and clubroots. The physiologcial properties including soluble sugar, soluble protein, methanol, POD and SOD significantly differed between healthy roots and clubroots. The distance-based redundancy analysis (db-RDA) and two-factor correlation network showed that soluble sugar, soluble protein and methanol were strongly related to the endophytic bacteria community in clubroots, wheares POD and SOD correlated with the endophytic bacteria community in healthy roots.Conclusions: Our results illustrate that physiologcial change caused by P. brassicae infection may alter the endophytic bacteria community in clubroots of tumorous stem mustard.

scholarly journals A Novel Target (Oxidation Resistant 2) in Arabidopsis thaliana to Reduce Clubroot Disease Symptoms via the Salicylic Acid Pathway without Growth Penalties

Horticulturae ◽  
2021 ◽  
Vol 8 (1) ◽  
pp. 9
Author(s):  
Regina Mencia ◽  
Elina Welchen ◽  
Susann Auer ◽  
Jutta Ludwig-Müller
Keyword(s):  
Arabidopsis Thaliana ◽  
Salicylic Acid ◽  
Plant Growth ◽  
Plasmodiophora Brassicae ◽  
Gene Encoding ◽  
Clubroot Disease ◽  
Disease Symptoms ◽  
Oxidation Resistant ◽  
Acid Pathway ◽  
Novel Target

The clubroot disease (Plasmodiophora brassicae) is one of the most damaging diseases worldwide among brassica crops. Its control often relies on resistant cultivars, since the manipulation of the disease hormones, such as salicylic acid (SA) alters plant growth negatively. Alternatively, the SA pathway can be increased by the addition of beneficial microorganisms for biocontrol. However, this potential has not been exhaustively used. In this study, a recently characterized protein Oxidation Resistant 2 (OXR2) from Arabidopsis thaliana is shown to increase the constitutive pathway of SA defense without decreasing plant growth. Plants overexpressing AtOXR2 (OXR2-OE) show strongly reduced clubroot symptoms with improved plant growth performance, in comparison to wild type plants during the course of infection. Consequently, oxr2 mutants are more susceptible to clubroot disease. P. brassicae itself was reduced in these galls as determined by quantitative real-time PCR. Furthermore, we provide evidence for the transcriptional downregulation of the gene encoding a SA-methyltransferase from the pathogen in OXR2-OE plants that could contribute to the phenotype.

scholarly journals Analysis of Gene Expression Profiles to study Malaria Vaccine Dose Efficacy & Immune Response Modulation.

2021 ◽  
Author(s):  
Supantha Dey ◽  
Harpreet Kaur ◽  
Elia Brodsky ◽  
Mohit Mazumder
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Vaccine Dose ◽  
Principal Component ◽  
Enrichment Analysis ◽  
Distinct Pattern ◽  
Response Modulation

Malaria is a life-threatening disease, and Africa is still one of the most affected endemic regions despite years of policy to limit infection and transmission rates. Further, studies into the variable efficacy of the vaccine are needed to provide a better understanding of protective immunity. Thus, the current study is designed to delineate the effect of the different vaccination doses on the transcriptional profiles of subjects to determine its efficacy and understand the molecular mechanisms underlying the protection this vaccine provides. Here, we used gene expression profiles of pre and post-vaccination patients after various doses of RTS,S based on 275 and 583 samples collected from the GEO datasets. At first, exploratory data analysis based Principal component analysis (PCA) shown the distinct pattern of different doses. Subsequently, differential gene expression analysis using edgeR revealed the significantly (FDR <0.005) 158 down-regulated and 61 upregulated genes between control vs. Controlled Human Malaria Infection (CHMI) samples. Further, enrichment analysis of significant genes using Annotation and GAGE tools delineate the involvement of CCL8, CXCL10, CXCL11, XCR1, CSF3, IFNB1, IFNE, IL12B, IL22, IL6, IL27, etc., genes which found to be upregulated after earlier doses but downregulated after the 3rd dose in cytokine-chemokine pathways. Notably, we identified 13 cytokine genes whose expression significantly varied during three doses. Eventually, these findings give insight into the dual role of cytokine responses in malaria pathogenesis and variations in their expression patterns after various doses of vaccination involved in protection.

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