Transcriptomic Analysis and Gene Expression Patterns of Nicotiana benthamiana in Response to Low Root-Zone Temperatures and Ultraviolet Radiation
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ABSTRACT: We explored the effects of low temperature (LT) and UV exposure (LT or UV alone and combined) on changes in transcription of N. benthamiana plants. Agilent One-Color Gene Expression Microarray analysis was conducted using an Agilent Tobacco 4 × 44 K format N. tabacum Array.
Project description:This study aimed to evaluate the effects of UV-B wavelength regions (< 300 nm) in canola plants (Brassica napus L.). Agilent One-Color Gene Expression Microarray analysis was conducted using an Agilent-022520 Brassica napus 4x44K Array.
Project description:The aim of this study was to evaluate short-duration (24 h) UV-B irradiation (3, 5, 7 W m-2) as a preharvest abiotic stressor in canola plants. Agilent One-Color Gene Expression Microarray analysis was conducted using an Agilent-022520 Brassica napus 4x44K Array.
Project description:To explore possible interactive effects of UV-radiation, temperature and growth conditions, cultivated and field sporophytes of Saccharina latissima were exposed for 24h to UV-radiation at three different temperatures (2,7 & 12°C). Gene expression profiles under UV-radiation at different temperatures were assessed through microarray hybridizations, afterwards comparisons of gene expression profiles in field and culture sporophytes were carried out.
Project description:Two maize genotypes exhibiting differential tolerance towards LT including the temperate grown Gurez local and its tropical counterpart GM6 were dissected for analysing and characterizing the functions of differentially regulated proteins (DRPs) in response to LT stress.
Project description:Tocopherols (vitamin E) are lipid-soluble antioxidants produced by all plants and algae, and many cyanobacteria, yet their functions in these photosynthetic organisms are still not fully understood. We have previously reported that the vitamin E deficient 2 (vte2) mutant of Arabidopsis thaliana is sensitive to low temperature (LT) due to impaired transfer cell wall (TCW) development and photoassimilate export, associated with massive callose deposition in transfer cells of the phloem. To further understand the roles of tocopherols in LT induced TCW development we compared the global transcript profiles of vte2 and wild type leaves during LT treatment. Tocopherol deficiency had no significant impact on global gene expression in permissive conditions, but significantly affected expression of 77 genes after 48 hours of LT treatment. In vte2 relative to wild type, genes associated with solute transport were repressed, while those involved in various pathogen responses and cell wall modifications, such as GLUCAN SYNTHASE LIKE genes (GSL4 and GSL11), were induced. The vte2 LT experiment comprised 18 chips in a factorial design. vte2 and Col plants were grown under permisive conditions for four weeks, Three independent biological replicates were conducted for Col and vte2 at each of the three time points during LT treatment. 0h represent when they are physiologically and biochemically indistinguishable, and at two time points of LT treatment (48 h, 120 h) selected based on our previous timecourse study of the physiological and biochemical changes of vte2 and Col during LT treatment (Maeda et al., 2006). After 48 h of LT, vascular callose deposition is strongly induced and photoassimilate export capacity is significantly lower in vte2 compared to Col, though the visible whole plant phenotypes and soluble sugar accumulation between the two genotypes do not differ (Maeda et al., 2006). The 120 h LT timepoint represents a relatively late response of vte2 when soluble sugars are significantly higher and callose deposition is even more extensive and wide spread in vte2 (Maeda et al., 2006). Thus the 48 h time point should allow identification of early responses to tocopherol deficiency that are distinct from later, pleiotropic responses resulting from the strongly elevated sugar levels in vte2 after 120 h of LT. The 0 h time point represents the absence of LT treatment (see method) and serves as a critical treatment control. 7°C. Three biological replicated the 9 to 11th oldest rosetta leaves from three independent plants were harvested together into a tube filled with liquid nitrogen one hour into the light cycle after 48 and 120 hours of LT-treatment or without LT-treatment (referred to as 0 hour LT treatment).
Project description:UV radiation is a ubiquitous component of solar radiation that affects plant growth and development. Analysis of natural variation in response to UV radiation revealed significant differences among natural accessions of Arabidopsis thaliana. However, the genetic basis of this is to a large extent unknown. Here, we analyzed the response of Arabidopsis accessions to UV radiation stress by performing RNA-sequencing of three UV sensitive and three UV resistant accessions. The genome-wide transcriptional analysis revealed a large number of genes significantly up- or down-regulated only in sensitive or only in resistant accessions, respectively. Mutant analysis of few selected candidate genes suggested by the RNA-sequencing results indicate a connection between UV radiation stress and plant-pathogen-like defense responses. Examination of transcriptional changes in response to UV treatment in Arabidopsis natural accessions
Project description:In the present study we have used a new custom made Affymetrix GrapeGen GeneChip to investigate gene expression responses of grapevine cultivar Malbec to one dose of biologically effective UV-B radiation (4.75 kJ m-2 d-1), administered at two different intensities (16 h, to 8.25 µW cm-2 or 4 h, to 33 µW cm2 UV-B).
Project description:Comparison of mRNA expression profiles of LT-HSCs with or without mutations in JAK2 and Ezh2 by RNA sequencing. LT-HSC mRNA was extracted from six different transgenic mice (SclCre, SclCre;Ezh2+/-, SclCre;Ezh2-/-, SclCre; JAK2V617F, SclCre; JAK2V617F;Ezh2+/-, SclCre; JAK2V617F;Ezh2-/-) 10 weeks after tamoxifen injection. Our study represents the first detailed analysis of mRNA expression profile of LT-HSC with or without mutations in JAK2 and Ezh2 , with biologic replicates, generated by RNA-seq technology. Our results revealed that mRNA expression profile of LT-HSC with different genotype showed specific gene expression patterns, which allows to do biological comprehensive and quantitative analysis for hematopoiesis. LT-HSCs mRNA profiles six different transgenic mice (SclCre, SclCre;Ezh2+/-, SclCre;Ezh2-/-, SclCre; JAK2V617F, SclCre; JAK2V617F;Ezh2+/-, SclCre; JAK2V617F;Ezh2-/-) were generated by deep sequencing.
Project description:The small genome of polyomaviruses encodes a limited number of proteins that are highly dependent on interactions with host cell proteins for efficient viral replication. The SV40 large T antigen (LT) contains several discrete functional domains that contribute to the viral life cycle, including the DNA binding and helicase domains. In addition, the LT the C-terminal region is required for lytic infection in certain restrictive cell types. To understand how LT affects the host cell to facilitate viral replication, we expressed full-length or functional domains of LT in cells and identified interacting cellular proteins and performed expression profiling. LT perturbed the expression of p53 target genes and subsets of cell-cycle dependent genes regulated by the DREAM and the B-Myb-MuvB complexes. To examine transcriptome perturbations directly in human cells, we generated expression constructs of each LT fragment. Full length and truncated LT containing N-terminal HA and FLAG epitope tags were expressed from the pMSCV retroviral vector and introduced into U-2 OS cells. Total RNA was isolated from three biological replicate U-2 OS stable cell lines and gene expression was assayed on Affymetrix Human Gene U133 Plus 2.0 arrays.
Project description:UV radiation (UV) alters secondary metabolism in the skin of Vitis vinifera L. berries, which may affect on the final composition of both, grapes and wines. We compared berry skin transcriptome and phenolic composition between Tempranillo berries grown in the presence or absence of solar UV in a mid-altitude Tempranillo vineyard. By analysing two different ripening degrees, expression of 121 genes was significantly altered. Functional enrichment identified that, principally, secondary metabolism-related transcripts were induced by UV, including VvFLS1, VvGT5 and VvGT6 flavonol biosynthetic genes induction. Concurrently, flavonol accumulation was the most evident impact of UV on the berry skin phenolic composition. Monoterpenoid biosynthetic transcripts were also up-regulated by UV, whereas induction of stilbenoid biosynthetic transcripts and stilbenes accumulation was probably induced by the joint action of UV and other condition under the UV-blocking filter, likely higher temperature. Among regulatory genes, VvMYBF1, VvMYB24 and three bHLH transcription factors were up-regulated by UV. Homologs to Arabidopsis UVR8-dependent UV-B-induced genes were also induced, including VvHY5-1, VvHY5-2 and VvRUP UV-B signalling genes. This suggests that the UV-B-specific signalling pathway is activated in the skin of grapes grown at low-medium altitudes. The biosynthesis and accumulation of UV-absorbing compounds that are appreciated for winemaking were almost specifically triggered, which indicates that viticultural practices increasing solar UV incidence may improve grape features important to wine production. A total of 12 samples were hybridized. Grape skin RNA from berries ripening under a UV-transmitting filter (FUV+) and a UV-blocking filter (FUV-) was compared. Berry skin of two different ripening stages was analysed on each UV treatment. All samples were harvested simultaneously and a NaCl series was used to select the ripening degree in a non-invasive way. Three biological replicates were analyzed for each sample.