scholarly journals Tobacco mosaic virus Induced Alterations in the Gene Expression Profile of Arabidopsis thaliana

2003 ◽  
Vol 16 (8) ◽  
pp. 681-688 ◽  
Author(s):  
Sheetal Golem ◽  
James N. Culver
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Tobacco Mosaic Virus ◽  
Mosaic Virus ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Infection Process ◽  
Cellular Processes ◽  
Genes Expression ◽  
Identify Gene Expression

In this study, mRNA profiles generated from cDNA microarrays were used to identify gene expression changes in Arabidopsis thaliana ecotype Shahdara infected with Tobacco mosaic virus (TMV). Shahdara is a susceptible TMV host, permitting rapid accumulations of virus in both inoculated and systemic tissues, accompanied by defined disease symptoms that include stunting, necrosis, and leaf curling. Gene expression profiles were monitored in whole tissues of inoculated leaves at four days postinoculation (dpi) and in systemically infected leaves at 14 dpi. Microarrays contained cDNAs representing between 8,000 and 10,000 Arabidopsis genes. Expression analysis identified 68 genes that displayed significant and consistent changes in expression levels, either up or down, in either TMV inoculated or systemically infected tissues, or both. Identified TMV-responsive genes encode a diverse array of functional proteins that include transcription factors, antioxidants, metabolic enzymes, and transporters. Thus, the TMV infection process has a significant impact on a wide array of cellular processes that likely reflect the biochemical and physiological changes involved in the development of this disease syndrome.

scholarly journals Identification and Validation of Novel Reference Genes in Acute Lymphoblastic Leukemia for Droplet Digital PCR

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 376 ◽  
Author(s):  
Vanessa Villegas-Ruíz ◽  
Karina Olmos-Valdez ◽  
Kattia Alejandra Castro-López ◽  
Victoria Estefanía Saucedo-Tepanecatl ◽  
Josselen Carina Ramírez-Chiquito ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Lymphoblastic Leukemia ◽  
Reference Genes ◽  
Expression Profiles ◽  
Lymphoblastic Leukemia ◽  
Gene Expression Profiles ◽  
Housekeeping Genes ◽  
Digital Pcr ◽  
Droplet Digital Pcr ◽  
Cellular Processes

Droplet digital PCR is the most robust method for absolute nucleic acid quantification. However, RNA is a very versatile molecule and its abundance is tissue-dependent. RNA quantification is dependent on a reference control to estimate the abundance. Additionally, in cancer, many cellular processes are deregulated which consequently affects the gene expression profiles. In this work, we performed microarray data mining of different childhood cancers and healthy controls. We selected four genes that showed no gene expression variations (PSMB6, PGGT1B, UBQLN2 and UQCR2) and four classical reference genes (ACTB, GAPDH, RPL4 and RPS18). Gene expression was validated in 40 acute lymphoblastic leukemia samples by means of droplet digital PCR. We observed that PSMB6, PGGT1B, UBQLN2 and UQCR2 were expressed ~100 times less than ACTB, GAPDH, RPL4 and RPS18. However, we observed excellent correlations among the new reference genes (p < 0.0001). We propose that PSMB6, PGGT1B, UBQLN2 and UQCR2 are housekeeping genes with low expression in childhood cancer.

scholarly journals Granulosa-Lutein Cell Sirtuin Gene Expression Profiles Differ between Normal Donors and Infertile Women

2019 ◽  
Vol 21 (1) ◽  
pp. 295
Author(s):  
Rebeca González-Fernández ◽  
Rita Martín-Ramírez ◽  
Deborah Rotoli ◽  
Jairo Hernández ◽  
Frederick Naftolin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Localization ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cellular Protein ◽  
Control Group ◽  
Poor Responders ◽  
Male Factor ◽  
Expression Levels ◽  
Genes Expression

Sirtuins are a family of deacetylases that modify structural proteins, metabolic enzymes, and histones to change cellular protein localization and function. In mammals, there are seven sirtuins involved in processes like oxidative stress or metabolic homeostasis associated with aging, degeneration or cancer. We studied gene expression of sirtuins by qRT-PCR in human mural granulosa-lutein cells (hGL) from IVF patients in different infertility diagnostic groups and in oocyte donors (OD; control group). Study 1: sirtuins genes’ expression levels and correlations with age and IVF parameters in women with no ovarian factor. We found significantly higher expression levels of SIRT1, SIRT2 and SIRT5 in patients ≥40 years old than in OD and in women between 27 and 39 years old with tubal or male factor, and no ovarian factor (NOF). Only SIRT2, SIRT5 and SIRT7 expression correlated with age. Study 2: sirtuin genes’ expression in women poor responders (PR), endometriosis (EM) and polycystic ovarian syndrome. Compared to NOF controls, we found higher SIRT2 gene expression in all diagnostic groups while SIRT3, SIRT5, SIRT6 and SIRT7 expression were higher only in PR. Related to clinical parameters SIRT1, SIRT6 and SIRT7 correlate positively with FSH and LH doses administered in EM patients. The number of mature oocytes retrieved in PR is positively correlated with the expression levels of SIRT3, SIRT4 and SIRT5. These data suggest that cellular physiopathology in PR’s follicle may be associated with cumulative DNA damage, indicating that further studies are necessary.

scholarly journals Gene expression profiles induced by E6 from non-European HPV18 variants reveals a differential activation on cellular processes driving to carcinogenesis

Virology ◽  
2012 ◽  
Vol 432 (1) ◽  
pp. 81-90 ◽  
Author(s):  
Verónica Fragoso-Ontiveros ◽  
Rosa María Alvarez-García ◽  
Adriana Contreras-Paredes ◽  
Felipe Vaca-Paniagua ◽  
Luis Alonso Herrera ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Differential Activation ◽  
Cellular Processes

Changes in Gene Expression Profiles in Patients with 5q- Syndrome Caused by Lenalidomide Treatment

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 5023-5023
Author(s):  
Monika Belickova ◽  
Jaroslav Cermak ◽  
Jitka Vesela ◽  
Eliska Cechova ◽  
Zuzana Zemanova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Conflicts Of Interest ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Aurora A ◽  
Genes Expression ◽  
Marrow Stroma ◽  
Cell Niche

Abstract Abstract 5023 A direct effects of lenalidomide on gene expression in 5q- patients was studied using HumanRef-8 v2 Expression BeadChips (Illumina). Expression profiles of 6 patients (before treatment and at the time of the first erytroid response) and 6 healthy controls were investigated from CD14+ monocytes of peripheral blood. Differentially expressed genes were identified by Significance Analysis of Microarrays (SAM). Simultaneously, selected genes (TNF, JUN, IL1) were monitored in the course of treatment using Real-Time PCR with Taqman Gene Expression Assays. A comparison of gene expression levels before and during lenalidomide treatment revealed 97 differentially expressed genes (FC >2; p<0.05) related to following biological processes: immune response (16 genes), inflammatory response (11 genes), response to bacteria (8 genes), anti-apoptosis (7 genes), regulation of MAP kinase activity (5 genes), oxygen transport (4 genes), and regulation of cell proliferation (11 genes). An overexpression of a number of cytokines (e.g. TNF, IL8, IL1B, CCL3L, CXCL2, and TNFAIP3) was detected in patients before treatment, after lenalidomide administration expression of the majority of the up-regulated cytokine genes decreased to the control baseline level. Detected overproduction of the cytokines in 5q- syndrome may lead to an increased apoptosis of hematopoietic progenitor cells and together with excessive oxidative stress may contribute to the damage the hematopoietic niche. In the same manner, untreated patients showed suppressed expression of two genes (CXCR4, CRTAP) which play an important role in the stem cell niche. After treatment, we detected increased expression of these genes. Both the observations might explain favorable effects of lenalidomide on the bone marrow stroma defect seen in 5q- syndrome. On the other hand, a substantial increase of the ARPC1B gene (an activator and a substrate of Aurora A) expression was detected after lenalidomide treatment. Since overexpression of Aurora A leads to polyploidy and chromosomal instability, ARPC1B might play a role in the disease progression observed in some patients treated with lenalidomide. To conclude, described changes in genes expression may contribute to identification of the pathways affected by lenalidomide and to the explanation of some effects of this drug that have not been fully understood yet. Supported by grants NS/9634 MZCR, UHKT2005 00023736, MSM0021620808 and COST EUGESMA Disclosures: No relevant conflicts of interest to declare.

scholarly journals Spatial Analysis of Arabidopsis thaliana Gene Expression in Response to Turnip mosaic virus Infection

2007 ◽  
Vol 20 (4) ◽  
pp. 358-370 ◽  
Author(s):  
Chunling Yang ◽  
Rong Guo ◽  
Fei Jie ◽  
Dan Nettleton ◽  
Jiqing Peng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Spatial Analysis ◽  
Mosaic Virus ◽  
Expression Profiles ◽  
Turnip Mosaic Virus ◽  
Infected Leaf ◽  
Altered Expression ◽  
Virus Accumulation ◽  
Mrna Transcripts

Virus-infected leaf tissues comprise a heterogeneous mixture of cells at different stages of infection. The spatial and temporal relationships between sites of virus accumulation and the accompanying host responses, such as altered host gene expression, are not well defined. To address this issue, we utilized Turnip mosaic virus (TuMV) tagged with the green fluorescent protein to guide the dissection of infection foci into four distinct zones. The abundance of Arabidopsis thaliana mRNA transcripts in each of the four zones then was assayed using the Arabidopsis ATH1 GeneChip oligonucleotide microarray (Affymetrix). mRNA transcripts with significantly altered expression profiles were determined across gradients of virus accumulation spanning groups of cells in and around foci at different stages of infection. The extent to which TuMV-responsive genes were up- or downregulated primarily correlated with the amount of virus accumulation regardless of gene function. The spatial analysis also allowed new suites of coordinately regulated genes to be identified that are associated with chloroplast functions (decreased), sulfate assimilation (decreased), cell wall extensibility (decreased), and protein synthesis and turnover (induced). The functions of these downregulated genes are consistent with viral symptoms, such as chlorosis and stunted growth, providing new insight into mechanisms of pathogenesis.

Liver and colon DNA oxidative damage and gene expression profiles of rats fed Arabidopsis thaliana mutant seeds containing contrasted flavonoids

2008 ◽  
Vol 46 (4) ◽  
pp. 1213-1220 ◽  
Author(s):  
Cristina Luceri ◽  
Lisa Giovannelli ◽  
Vanessa Pitozzi ◽  
Simona Toti ◽  
Cinzia Castagnini ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Oxidative Damage ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Dna Oxidative Damage

scholarly journals Gene expression stasis and plasticity following migration into a foreign environment

2017 ◽  
Author(s):  
Brian K. Lohman ◽  
William E. Stutz ◽  
Daniel I. Bolnick
Keyword(s):  
Gene Expression ◽  
Phenotypic Plasticity ◽  
Expression Profile ◽  
Gasterosteus Aculeatus ◽  
Expression Profiles ◽  
Survival Rates ◽  
Gene Expression Profiles ◽  
Genes Expression ◽  
The Impact ◽  
Fish Performance

AbstractSelection against migrants is key to maintaining genetic differences between populations linked by dispersal. Yet, migrants are not just passively weeded out by selection. Migrants may mitigate fitness costs by proactively choosing among available habitats, or by phenotypic plasticity. We previously reported that a reciprocal transplant of lake and stream stickleback (Gasterosteus aculeatus) found little support for divergent selection. We revisit that experiment to test whether phenotypic plasticity in gene expression may have helped migrants adjust to unfamiliar habitats. We measured gene expression profiles in stickleback via TagSeq and tested whether migrants between lake and stream habitats exhibited a plastic response to their new environment that allowed them to converge on the expression profile of adapted natives. We report extensive gene expression differences between genetically divergent lake and stream stickleback, despite gene flow. But for many genes, expression was highly plastic. Fish transplanted into the adjoining habitat partially converged on the expression profile typical of their new habitat. This suggests that expression plasticity may soften the impact of migration. Nonetheless, lake and stream fish differed in survival rates and parasite infection rates in our study, implying that expression plasticity is not fast or extensive enough to fully homogenize fish performance.

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