Project description:We treated L929 cells with TNF for six time points and the samples containing TNFR1 complexes were collected by affinity purification and analyzed by SWATH-MS. Accurate and consistent quantification across 18 IP samples showed dynamic profiles of the TNFR1 complex components across six time points.
Project description:We treated wildtype and RIP3 knockout L929 with TNF for 8 time points respectively, and used SWATH-MS to quantify dynamic proteomic change of these two cell lines under a serial TNF treatments.
Project description:Human glutamatergic neurons in culture were exposed to 1 nM secreted amyloid precursor protein alpha over a time course (0, 2, 6 and 24 h) and changes in the proteome were identified with SWATH-MS.
Project description:This project applies SWATH approach to analyse ex-diagnostic sheep serum samples from actual clinical cases submitted to The University of Queensland's School of Veterinary Science, Veterinary Laboratory Services (VLS) compared with serum of normal sheep.
Project description:This dataset consists of 44 raw MS files, comprising 27 DIA (SWATH) and 15 DDA runs on a TripleTOF 5600 and of two raw mass spectrometry files acquired on a Q Exactive. The composition of the dataset is described in the manuscript by Tsou et al., titled: "DIA-Umpire: comprehensive computational framework for data independent acquisition proteomics", Nature Methods, in press Raw files are deposited here in ProteomeXchange and are associated with the DIA-Umpire processed data. All DIA-Umpire processed results for each sample together with DDA results are deposited in separated folders. Also see the "DataSampleID.xlsx" associated with this Readme file. Internal reference from the Gingras lab ProHits implementation: Project 94, Export version VS2 (Tsou_DIA-Umpire)
Project description:Apolipoprotein C-III was recently acknowledged as a prognostic marker for cardiovascular risk. High levels of Apo-CIII strongly correlate with hypertriglyceridemia and are associated with atherosclerosis and coronary heart disease (CAD). Aim of the present research was to study the plasma proteome profiles of stable CAD patients characterized by different levels of total Apo-CIII. Two subgroups of CAD patients with divergent concentrations (under and upper the median concentration of the population distribution=10mg/dL) of total circulating Apo C-III were examined using a shotgun proteomic approach. 180 plasma proteins of CAD patients were quantified and the data were analyzed by bioinformatic tools and multivariate statistics. The fold change analysis and the Partial Least Square Discriminant Analysis showed a clear separation of the two groups. The dynamic processes that involve Apo C-III concentration in blood and its relation with all other plasma proteins were considered. Lipoproteins (Apo C-II and Apo E), retinol-binding protein 4 and vitronectin were up-regulated in patients with high Apo C-III, while alpha 1-antitrypsin was down-regulated. In this pilot study, the different expression of plasma proteins through the entire range of concentrations of Apo C-III was defined, suggesting possible new players involved in the APO C-III-associated process of arterial damage
Project description:Clostridium cellulovorans is among the most promising candidates for consolidated bioprocessing (CBP) of cellulosic biomass to liquid biofuels (e.g. ethanol, butanol). C. cellulovoranscan metabolize all the main plant polysaccharides (i.e. cellulose, hemicellusoses and pectins). Unlike other well established cellulolytic microorganisms, C. cellulovorans most abundant catabolite is butyrate. This attracted attention on this strain as potential butanol producer since most reactions involved in butyrate and butanol synthetic pathway from acetyl-coA are common. Recent studies demonstrated that the introduction of a single heterologous alcohol/aldehyde dehydrogenase can significantly divert the branching-point intermediate, i.e. butyryl-CoA, towards butanol production in this strain. In spite of the potential of C. cellulovorans for application in CBP of plant biomass, engineering its metabolic pathways towards industrial utilization still requires enhanced understanding of its metabolism. Few recent studies aimed at understanding the regulation of C. cellulovorans central carbon metabolism in response to different substrate availability, which seem insufficient for the aforementioned purposes. The present study aimed at improving comprehension of cellulose metabolism in C. cellulovorans by comparing growth kinetics, substrate consumption/product accumulation and whole-cell soluble proteome with those of C. cellulovorans grown on a soluble carbohydrate, i.e. glucose, as the main carbon source. Modulations of the central carbon metabolism in response to changes in the growth substrate were detected, including the regulation of glycolytic enzymes, fermentation pathways and nitrogen assimilation. Our data suggest that a higher energy expenditure occurs in cellulose-grown C. cellulovorans which induces up-regulation of ATP synthetic pathways, e.g. acetate production and ATP synthase.
Project description:Mouse primary astrocytes in culture were exposed to 1 nM secreted amyloid precursor protein alpha (sAPPalpha) or PBS (control) for 2 h or 6 h and changes in the cellular proteome or secretome respectively were quantified by SWATH-MS.
Project description:Disease resistance in plants depends on a molecular dialogue with microbes that involves many known chemical effectors, but the time course of the interaction and the influence of the environment are largely unknown. The outcome of host–pathogen interactions is thought to reflect the offensive and defensive capabilities of both players. When plants interact with Pseudomonas syringae, several well-characterized virulence factors contribute to early bacterial pathogenicity, including the type III secretion system (T3SS), which must be activated by signals from the plant and environment to allow the secretion of virulence effectors. The manner in which these signals regulate T3SS activity is still unclear. Here, we strengthen the paradigm of the plant–pathogen molecular dialogue by addressing overlooked details concerning the timing of interactions, specifically the role of plant signals and temperature on the regulation of bacterial virulence during the first few hours of the interaction. Whole-genome expression profiling after 1 h revealed that the perception of plant signals from kiwifruit or tomato extracts anticipates T3SS expression in P. syringae pv. actinidiae compared to apoplast-like conditions, facilitating more efficient effector transport in planta, as revealed by the induction of a temperature-dependent hypersensitive response in the non-host plant Arabidopsis thaliana Col-0. Our results show that, in the arms race between plants and bacteria, the temperature-dependent timing of bacterial virulence versus the induction of plant defenses is probably one of the fundamental parameters governing the outcome of the interaction.
Project description:Combination of butanol-hyperproducing and hypertolerant phenotypes is essential for developing microbial strains suitable for industrial production of bio-butanol, i.e. one of most promising liquid biofuels. Clostridium cellulovorans is among the microbial strains with the highest potential for direct production of n-butanol from lignocellulosic wastes, a process that would significantly reduce the cost of bio-butanol. However, butanol exhibits higher toxicity compared to ethanol and C. cellulovorans tolerance to this solvent is low. In the present investigation, comparative proteomics was used to study the response of C. cellulovorans to butanol challenge and understand the tolerance mechanisms activated in this condition. The most important response concerned modulation of protein biosynthesis, folding and degradation. Coherent with previous studies on other bacteria, several heat shock proteins (involved in protein quality control) were upregulated. Globally, our data indicates that protein biosynthesis is reduced, likely not to overload heat shock proteins. Several additional metabolic adaptations were triggered by butanol exposure such as the upregulation of V- and F-type ATPases (involved in ATP synthesis/generation of proton motive force), enzymes involved in amino acid biosynthesis, proteins involved in cell envelope re-arrangement and a redistribution of carbon flux through fermentative pathways. These analyses eventually suggested several potential gene targets for metabolic engineering strategies aimed at improving butanol tolerance in C. cellulovorans.