Role of ClpCP in respiratory and fermentative growth
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ABSTRACT: To determine metabolite concentrations and differences at the 48 hour time point for WT, ClpC mutant, srrAB mutant, and ClpC:srrAB double mutant
Project description:To investigate the processes affected when plants are exposed to 3-butenenitrile (3BN; allyl cyanide ACN), we performed a genome scale transcriptional profiling of Arabidopsis thaliana Col(0) and the nia1nia2 double mutant after 24 hour treatment with 3BN.
Project description:Retinal photoreceptors undergo daily renewal of their distal outer segments, a process indispensable for maintaining retinal health. Photoreceptor Outer Segment (POS) phagocytosis occurs as a daily peak, roughly about one hour after light onset. However, the underlying cellular and molecular mechanisms which initiate this process are still unknown. Here we show that, under constant darkness, mice deficient for core circadian clock genes (Per1 and Per2), lack a daily peak in POS phagocytosis. By qPCR analysis we found that core clock genes were rhythmic over 24h in both WT and Per1, Per2 double mutant whole retinas. More precise transcriptomics analysis of laser capture microdissected WT photoreceptors revealed no differentially expressed genes between time-points preceding and during the peak of POS phagocytosis. By contrast, we found that microdissected WT retinal pigment epithelium (RPE) had a number of genes that were differentially expressed at the peak phagocytic time-point compared to adjacent ones. We also found a number of differentially expressed genes in Per1, Per2 double mutant RPE compared to WT ones at the peak phagocytic time-point. Finally, based on STRING analysis we found a group of interacting genes which potentially drive POS phagocytosis in the RPE. This potential pathway consists of genes such as: Pacsin1, Syp, Camk2b and Camk2d among others. Our findings indicate that Per1 and Per2 are necessary clock components for driving POS phagocytosis and suggest that this process is transcriptionally driven by the RPE.
Project description:Retinal photoreceptors undergo daily renewal of their distal outer segments, a process indispensable for maintaining retinal health. Photoreceptor Outer Segment (POS) phagocytosis occurs as a daily peak, roughly about one hour after light onset. However, the underlying cellular and molecular mechanisms which initiate this process are still unknown. Here we show that, under constant darkness, mice deficient for core circadian clock genes (Per1 and Per2), lack a daily peak in POS phagocytosis. By qPCR analysis we found that core clock genes were rhythmic over 24h in both WT and Per1, Per2 double mutant whole retinas. More precise transcriptomics analysis of laser capture microdissected WT photoreceptors revealed no differentially expressed genes between time-points preceding and during the peak of POS phagocytosis. By contrast, we found that microdissected WT retinal pigment epithelium (RPE) had a number of genes that were differentially expressed at the peak phagocytic time-point compared to adjacent ones. We also found a number of differentially expressed genes in Per1, Per2 double mutant RPE compared to WT ones at the peak phagocytic time-point. Finally, based on STRING analysis we found a group of interacting genes which potentially drive POS phagocytosis in the RPE. This potential pathway consists of genes such as: Pacsin1, Syp, Camk2b and Camk2d among others. Our findings indicate that Per1 and Per2 are necessary clock components for driving POS phagocytosis and suggest that this process is transcriptionally driven by the RPE.
Project description:Purpose: The aim of this study was to compare transcriptome profiling (RNA-seq) of rice panicle tissue from resistant and suceptible lines at different time intervals infected with M.oryzae. The results were validated using Semi-quantitative PCR. Methods: Panicles from resistant and suceptible rice lines were inoculated with suspension having double distill water, Tween-20 without spores for 0 hour and same suspension with spores was used to inoculate for 48, 72 and 96 hour samples. After collection, samples were frozen on liquid nitrogen, and RNA was extracted using Spectrum™ Plant Total RNA Kit (Sigma). RNA libraries were prepared for sequencing using standard Illumina protocols. Results: Differential Expressed Genes were identified, comparing transcriptome of Control 0 hour vs 48, 72 and 96 hour post infection. Where we get 1070, 2383 and 1080 total significant genes at 48, 72, and 96 hour post infection respectively in HP2216. And, 1564, 1433 and 2263 total significant genes at 48, 72, and 96 hour post infection respectively in Tetep.
Project description:In this project, we report the bacterial proteome expression profile change for different time points when culturing in rapeseed cake substrate (RCS). Bacillus cereus tsu1 was cultured in RCS (25g/L) for 12 hours, 24 hours and 48 hours. At each time point, cells were stained with Sudan Black to monitor PHB accumulation. Bacterial cells were loaded with PHB after 12-hour culture and significant degradation of PHB was observed after 48-hour culture. Bacterial proteome profile changes were identified using tandem mass tags mass spectrometry (TMT-MS)-based quantitative proteomics analysis. From TMT proteomics analysis, 3,237 proteins were detected and quantified from the bacterial pellet protein extraction, from which proteins related with PHB biosynthesis and degradation were identified. Quantitative analysis revealed that 146 (between 12h and 24h samples), and 158 (between 12h and 48h) proteins showed significant differences. Several STRING protein interaction networks were developed for significantly changed protein related with sporulation and anaerobic respiration.
Project description:Francisella tularensis is a category A select agent based on its infectivity and virulence but disease mechanisms in F. tularensis infection remain poorly understood. A murine pulmonary model of infection was therefore employed to characterize the host immune response to F. tularensis infection and to discern differences in responses to infection with the highly virulent Type A F. tularensis strain Schu4 and to the less virulent Type B live vaccine strain (LVS). Mice were infected intranasally with F. tularensis Schu4 or LVS and organ lesions were assessed 48 and 120 hours after infection. Experiments were also conducted to assess and compare the host immune response to infection using global transcriptional analysis. Mice were infected via low dose aerosol with F. tularensis Schu4 or LVS strains, and transcriptional response in the lungs and spleen was monitored using full mouse genome microarrays at 12, 24, 48, and 120 hours after infection. We found differential and temporal differences in expression of cytokine and chemokine genes, CD molecules, apoptosis, leukocytes and adhesion receptors, and immunological signaling between infection with Schu4 and LVS strains. The transcriptional differences coincided with marked differences in the timing and extent of organ lesions in mice infected with the LVS and Schu4 strains. Thus, these studies revealed both temporal and qualitative differences in the host immune response to infection with virulent F. tularensis Schu4 compared to infection with LVS. 18 mice total, 2 uninfected controls, 2 mice per time point, time points were 12 hour/24 hour/48 hour/ 120 hour post infection, 2 infection groups: LVS and Schu4 infection. Lung and spleen were harvested at each time point, poly A RNA was extracted, converted to cDNA, labeled and hybridized in triplicate
Project description:In order to further our understanding of the metabolic network of the malaria parasite, Plasmodium falciparum, we carried out a concurrent transcriptomic and metabolomic study of the parasite's intraerythrocytic developmental cycle. These microarray data were generated to compare the expression levels of metabolic enzymes to the concentrations of their associated metabolites over the 48-hour life cycle.
Project description:Comparison of the expression profiles of nac45-2 nac86 mutant with col WT, and comparison of the expression profiles of NAC45 extopical induction with non-induction. Three-dye gene expression study with three biological replicates. Five-point time-series experiment and double-mutant vs wild-type comparison.