Project description:A pluripotent inducible cell line was generated from Arabidopsis to address the limitations of traditional in planta dicot systems and to develop a well-controlled experimental setup where the individual regulatory check points of chloroplast development could be defined. Following light exposure, this cell line was shown to differentiate into photosynthetically active cells with functional chloroplasts providing an experimental system with a temporal gradient of chloroplast development. Using this unique cell line from the dicot Arabidopsis we could demonstrate that the development from a proplastid to a functional chloroplast, and thereby the establishment of photosynthesis, is dependent on a regulatory mechanism involving two distinct phases. First, light exposure triggers an initial change in gene expression, metabolite profile, chlorophyll accumulation and plastid structure. Secondly, a second signal, most likely triggered by activation of the chloroplast, is required for full transition to a functional chloroplast and the shift from heterotrophic to photoautotrophic metabolism.
Project description:A "Cartes d'Identite des Tumeurs" (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net). Hepatoblastoma, the most common pediatric liver cancer, is tightly linked to excessive Wnt/C/B?B=-catenin signaling. Microarray analysis identifitwo tumor subclasses resembling distinct phases of liver development typified by gains of chromosomes 8q and 2p and upregulated Myc signaling.
Project description:Identification of target transcripts for the putative chloroplast RNA binding protein CFM2 in Zea mays. CFM2 was immunoprecipitated from a chloroplast extract. Chloroplast extracts were prepared from WT tissue. RNA from the pellet and from the supernatant for each pulldown was labelled with different fluoro-dyes and hybridized onto an array covering the complete maize chloroplast genome. Messages enriched in the immunoprecipitate from WT tissue are likely targets for CFM2.
Project description:The experiment was made do to assess the influence of increased salt concentration on cucumber chloroplast transcription. We used 0,4M NaCl water solution and we checked its influence on plants after 0, 4, 8, 24, 48 hours. We have also measured changes in chloroplast gene expression after recovery of plants in water (48 hours of 0,4M NaCl solution treatment followed by 48 hours in clean water). Other growth conditions weren't changed comparing to those of standard plants growth in our experiments (check: versatile chamber growth protocol)
Project description:Since little information is available on the processes in the liver associated with the natural history during chronic HBV infections, we now examined hepatic transcriptomes to identify distinctive gene expression profiles in the HBV clinical phases. We show that the transcriptomes of mild fibrotic, HBV-infected livers were significantly different from those with comorbidities. Across the clinical HBV phases, comparable intrahepatic ISG expression was observed. However, global transcription was most distinctive between the immunotolerant and the immunoactive phases (n=92 genes), followed by the immunotolerant and the HBeAg-negative hepatitis phase (n=71 genes), and the immunotolerant and the inactive carrier phase (n=46 genes). Among these were CD19, TNFRSF13C, granzyme H, and KIR2DS3. Moreover, during these clinical phases, 4 intrinsic functional clusters (IFC) with distinctive transcriptional activity were identified by combined global module analysis. These discriminative clusters contained B-cell and cell cycle-related genes, which were highly expressed in liver during the immunoactive phase; and NK-cell and mitochondria respiration-related genes in the HBeAg-negative hepatitis phase. Our data define distinctive transcriptomes in the liver during HBV clinical phases. We observed important differences between the liver and blood in transcription levels of ISG and cell cycle genes, but, strikingly, also a high degree of overlap in expression patterns of B- and NK-cell genes during the immune active phases. Overall design: we analyzed a cohort of FFPE biopsies collected from the livers of well-characterized chronic HBV patients (n=74) and archived for up to 30 years. Differential gene expression analysis , global module analysis, and unsupervised clustering analysis were performed by employing the WG-DASL assay on liver transcriptomes from chronic HBV patients with and without concomitant NASH or advanced fibrosis, or between different HBV clinical phases.
Project description:Bienertia sinuspersici performs C4 photosynthesis without Kranz anatomy through subcellular compartmentalization of carbon fixation within individual cells. In this species, central compartment chloroplasts (C) and peripheral chloroplasts (P) collaborate with cytosolic and mitochondrial components in a NAD-ME type C4 cycle. How the two functionally different chloroplast types can develop within individual cells and the mechanism of import of nuclear encoded, plastid targeted proteins are currently unknown. We used 454 sequencing in combination with large scale label-free proteomics to determine the distribution of photosynthesis-related proteins. Subcellular localization of 169 protein was determined through comparison of protein abundance in four different subcellular fractions. 39 out of the 120 chloroplastic proteins showed differential accumulation between the two chloroplast types. Rubisco, RPP regenerative phase and PSII related proteins accumulated in C chloroplasts whereas C4 related proteins and the NDH complex were more abundant in P chloroplasts. Comparison of transit peptides of differential accumulating proteins indicated no obvious sequence homology or similarities in physico-chemical properties between members of the same group. Protein composition analysis of the central compartment indicated that mitochondria and peroxisomes are the only major components besides chloroplasts in this compartment. The combined information from subcellular and developmental protein profiling was used to generate a first draft of the protein machinery involved in single-cell C4 photosynthesis.
Project description:Protein N-termini are prone to post translational modification and are major determinants of protein stability in bacteria, eukaryotes, and perhaps also in chloroplasts. Most chloroplast proteins undergo N-terminal maturation, but this is poorly understood due to insufficient experimental information and the N-termini of mature chloroplast proteins cannot be accurately predicted. This motivated an extensive characterization of chloroplast protein N-termini using terminal amine isotopic labeling of substrates (TAILS). Many nuclear-encoded plastid proteins accumulated with two or three different N-termini; we evaluated the significance of these different proteoforms. Ala, Val, Thr (often in N-Î? acetylated form) and Ser were the most frequently observed N-terminal residues, even after normalization for their frequency in the plastid proteome, while other residues were absent or highly under-represented. Plastid-encoded proteins showed a similar distribution of N-terminal residues, but with a higher frequency of Met. Infrequent residues such as Ile, Arg, Cys, Pro, Asp and Glu were observed for several abundant proteins likely reflecting functional regulation through their N-termini. In contrast, the thylakoid lumenal proteome showed a wide diversity of N-terminal residues, including those typically associated with instability (Asp, Glu, Leu, Phe). We propose that after cleavage of the chloroplast transit peptide by stromal processing peptidase, additional processing by unidentified peptidases occurs to avoid unstable or otherwise unfavorable N-terminal residues. The possibility of a chloroplast N-end rule is discussed. This work provides a baseline for understanding N-terminal processing and maturation of chloroplast proteins.
Project description:OE17 and OE23 are chloroplast targeted proteins. RNA co-immunoprecipitation was performed using antibodies raised against these proteins. RNA from the pellet and from the supernatent for each pulldown was labeled with different fluoro-dyes.