Expression of Arabidopsis WEE1 in tobacco induces unexpected morphological and developmental changes.
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ABSTRACT:
SUBMITTER: Siciliano I
PROVIDER: S-EPMC6581958 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND: Tobacco etch potyvirus (TEV) has been extensively used as model system for the study of positive-sense RNA virus infecting plants. TEV ability to infect Arabidopsis thaliana varies among ecotypes. In this study, changes in gene expression of A. thaliana ecotype Ler infected with TEV have been explored using long-oligonucleotide arrays. A. thaliana Ler is a susceptible host that allows systemic movement, although the viral load is low and syndrome induced ranges from asymptomatic to mild. Gene expression profiles were monitored in whole plants 21 days post-inoculation (dpi). Microarrays contained 26,173 protein-coding genes and 87 miRNAs. RESULTS: Expression analysis identified 1727 genes that displayed significant and consistent changes in expression levels either up or down, in infected plants. Identified TEV-responsive genes encode a diverse array of functional categories that include responses to biotic (such as the systemic acquired resistance pathway and hypersensitive responses) and abiotic stresses (droughtness, salinity, temperature, and wounding). The expression of many different transcription factors was also significantly affected, including members of the R2R3-MYB family and ABA-inducible TFs. In concordance with several other plant and animal viruses, the expression of heat-shock proteins (HSP) was also increased. Finally, we have associated functional GO categories with KEGG biochemical pathways, and found that many of the altered biological functions are controlled by changes in basal metabolism. CONCLUSION: TEV infection significantly impacts a wide array of cellular processes, in particular, stress-response pathways, including the systemic acquired resistance and hypersensitive responses. However, many of the observed alterations may represent a global response to viral infection rather than being specific of TEV.
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Project description:Thrombin is a Na[Formula: see text]-activated serine protease existing in two forms targeted to procoagulant and anticoagulant activities, respectively. There is one Na[Formula: see text]-binding site that has been the focus of the study of the thrombin. However, molecular dynamics (MD) simulations suggest that there might be actually two Na[Formula: see text]-binding sites in thrombin and that Na[Formula: see text] ions can even bind to two sites simultaneously. In this study, we performed 12 independent 2-µs all-atom MD simulations for the wild-type (WT) thrombin and we studied the effects of the different Na[Formula: see text] binding modes on thrombin. From the root-mean-square fluctuations (RMSF) for the [Formula: see text]-carbons, we see that the atomic fluctuations mainly change in the 60s, 170s, and 220s loops, and the connection (residue 167 to 170). The correlation matrices for different binding modes suggest regions that may play an important role in thrombin's allosteric response and provide us a possible allosteric pathway for the sodium binding. Amorim-Hennig (AH) clustering tells us how the structure of the regions of interest changes on sodium binding. Principal component analysis (PCA) shows us how the different regions of thrombin change conformation together with sodium binding. Solvent-accessible surface area (SASA) exposes the conformational change in exosite I and catalytic triad. Finally, we argue that the double binding mode might be an inactive mode and that the kinetic scheme for the Na[Formula: see text] binding to thrombin might be a multiple-step mechanism rather than a 2-step mechanism.
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Project description:BackgroundWhile smoking is known to associate with development of multiple diseases, the underlying mechanisms are still poorly understood. Tobacco smoking can modify the chemical integrity of DNA leading to changes in transcriptional activity, partly through an altered epigenetic state. We aimed to investigate the impact of smoking on lung cells collected from bronchoalveolar lavage (BAL).MethodsWe profiled changes in DNA methylation (5mC) and its oxidised form hydroxymethylation (5hmC) using conventional bisulphite (BS) treatment and oxidative bisulphite treatment with Illumina Infinium MethylationEPIC BeadChip, and examined gene expression by RNA-seq in healthy smokers.FindingsWe identified 1667 total 5mC + 5hmC, 1756 5mC and 67 5hmC differentially methylated positions (DMPs) between smokers and non-smokers (FDR-adjusted P <.05, absolute Δβ >0.15). Both 5mC DMPs and to a lesser extent 5mC + 5hmC were predominantly hypomethylated. In contrast, almost all 5hmC DMPs were hypermethylated, supporting the hypothesis that smoking-associated oxidative stress can lead to DNA demethylation, via the established sequential oxidation of which 5hmC is the first step. While we confirmed differential methylation of previously reported smoking-associated 5mC + 5hmC CpGs using former generations of BeadChips in alveolar macrophages, the large majority of identified DMPs, 5mC + 5hmC (1639/1667), 5mC (1738/1756), and 5hmC (67/67), have not been previously reported. Most of these novel smoking-associating sites are specific to the EPIC BeadChip and, interestingly, many of them are associated to FANTOM5 enhancers. Transcriptional changes affecting 633 transcripts were consistent with DNA methylation profiles and converged to alteration of genes involved in migration, signalling and inflammatory response of immune cells.InterpretationCollectively, these findings suggest that tobacco smoke exposure epigenetically modifies BAL cells, possibly involving a continuous active demethylation and subsequent increased activity of inflammatory processes in the lungs. FUND: The study was supported by the Swedish Research Council, the Swedish Heart-Lung Foundation, the Stockholm County Council (ALF), the King Gustav's and Queen Victoria's Freemasons' Foundation, Knut and Alice Wallenberg Foundation, Neuro Sweden, and the Swedish MS foundation.
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Project description:BackgroundCachexia is a multifactorial and multiorgan syndrome associated with cancer and other chronic diseases and characterized by severe involuntary body weight loss, disrupted metabolism, inflammation, anorexia, fatigue, and diminished quality of life. This syndrome affects around 50% of patients with colon cancer and is directly responsible for the death of at least 20% of all cancer patients. Systemic inflammation has been recently proposed to underline most of cachexia-related symptoms. Nevertheless, the exact mechanisms leading to the initiation of systemic inflammation have not yet been unveiled, as patients bearing the same tumour and disease stage may or may not present cachexia. We hypothesize a role for gut barrier disruption, which may elicit persistent immune activation in the host. To address this hypothesis, we analysed the healthy colon tissue, adjacent to the tumour.MethodsBlood and rectosigmoid colon samples (20 cm distal to tumour margin) obtained during surgery, from cachectic (CC = 25) or weight stable (WSC = 20) colon cancer patients, who signed the informed consent form, were submitted to morphological (light microscopy), immunological (immunohistochemistry and flow cytometry), and molecular (quantification of inflammatory factors by Luminex® xMAP) analyses.ResultsThere was no statistical difference in gender and age between groups. The content of plasma interleukin 6 (IL-6) and IL-8 was augmented in cachectic patients relative to those with stable weight (P = 0.047 and P = 0.009, respectively). The number of lymphocytic aggregates/field in the gut mucosa was higher in CC than in WSC (P = 0.019), in addition to those of the lamina propria (LP) eosinophils (P < 0.001) and fibroblasts (P < 0.001). The area occupied by goblet cells in the colon mucosa was decreased in CC (P = 0.016). The M1M2 macrophages percentage was increased in the colon of CC, in relation to WSC (P = 0.042). Protein expression of IL-7, IL-13, and transforming growth factor beta 3 in the colon was significantly increased in CC, compared with WSC (P = 0.02, P = 0.048, and P = 0.048, respectively), and a trend towards a higher content of granulocyte-colony stimulating factor in CC was also observed (P = 0.061). The results suggest an increased recruitment of immune cells to the colonic mucosa in CC, as compared with WSC, in a fashion that resembles repair response following injury, with higher tissue content of IL-13 and transforming growth factor beta 3.ConclusionsThe changes in the intestinal mucosa cellularity, along with modified cytokine expression in cachexia, indicate that gut barrier alterations are associated with the syndrome.
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Project description:Impairment or stimulation of the immune system by ionizing radiation (IR) impacts on immune surveillance of tumor cells and non-malignant cells and can either foster therapy response or side effects/toxicities of radiation therapy. For a better understanding of the mechanisms by which IR modulates T-cell activation and alters functional properties of these immune cells, we exposed human immortalized Jurkat cells and peripheral blood lymphocytes (PBL) to X-ray doses between 0.1 and 5?Gy. This resulted in cellular responses, which are typically observed also in naïve T-lymphocytes in response of T-cell receptor immune stimulation or mitogens. These responses include oscillations of cytosolic Ca2+, an upregulation of CD25 surface expression, interleukin-2 and interferon-? synthesis, elevated expression of Ca2+ sensitive K+ channels and an increase in cell diameter. The latter was sensitive to inhibition by the immunosuppressant cyclosporine A, Ca2+ buffer BAPTA-AM, and the CDK1-inhibitor RO3306, indicating the involvement of Ca2+-dependent immune activation and radiation-induced cell cycle arrest. Furthermore, on a functional level, Jurkat and PBL cell adhesion to endothelial cells was increased upon radiation exposure and was highly dependent on an upregulation of integrin beta-1 expression and clustering. In conclusion, we here report that IR impacts on immune activation and functional properties of T-lymphocytes that may have implications in both toxic effects and treatment response to combined radiation and immune therapy in cancer patients.
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