Project description:BioID2 Zebrafish Interaction Proteomics analyzed by nanoscale capillary LC coupled to a Fusion Lumos OT with label-free quantitation.
Project description:The fidelity of signal transmission requires the binding of regulatory molecules to their cognate targets. However, the crowded cell interior risks off-target interactions between proteins that are functionally unrelated. Understanding the constraints this imposes on cell systems evolution requires the fitness cost of spurious interactions to be quantified. Towards this end, we express human tyrosine kinases in the budding yeast S. cerevisiae. Yeast lacks bona fide tyrosine kinases and so the majority of resulting pY sites are functionless and artificial. We express 24 unique tyrosine kinases in total and perform phosphoproteomics in each case, resulting in ~30,000 phosphosites sites mapping to 3500 phosphoproteins. Examination of the fitness costs in each strain reveals a strong correlation between the number of spurious pY sites generated and negative effects on growth. Moreover, the prediction of pY effects on protein structure and on protein function (conservation-based) reveals potential for the widespread perturbation of the yeast proteome. Comparing the spurious pY sites (pre-selection) with native pY sites in human (post-selection) also demonstrates the recurrent modification of proteins and sites with no homology to native substrates. However, examination of these data together (fitness and phosphoproteomics) strongly suggests that a large number of the pY sites generated have a negligible effect on fitness. Finally, we test the hypothesis of pY counter-selection following the emergence of tyrosine kinases in metazoan species, but find no strong evidence for proteome-wide selection against spurious Y phosphorylation.
Project description:This study reports the first characterization of the intracellular proteome of peripheral blood mononuclear cells (PBMC) isolated from subjects diagnosed with primary open angle glaucoma (POAG)by shot-gun proteomics. Glaucoma is a chronic optic neuropathy and among the first causes of irreversible blindness on a global scale. Several recent data have pointed out alterations of immune system processes in glaucoma subjects. Very recently, oxygen consumption rate (OCR) and NAD levels have been proposed as biomarkers of disease severity.
Project description:Investigation of gene expression changes in a DvH genotype ES10-5, a strain isolated from population ES10 which has been evolved under salt stress for 5000 generations. The gene expression was compared to a gentype ES9-11 isolated from ES9 evolved under the same condition for 1200 generations and the ancestral strain. The genotype ES10-5 was characterized in this study. ES9-11 was isolated and characterized in Zhou A et al., 2013. Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution. ISME J, 7(9), 1790-1802
Project description:Label free quantititative phosphoproteomics analysis following TiO2 enrichment, nanoscale capillary chromatography and high resolution tandem mass spectrometry.
Project description:The CEBPA transcription factor is frequently mutated in acute myeloid leukemia (AML). Mutations in the CEBPA gene, which are typically biallelic, result in the production of a shorter isoform known as p30. Both the canonical 42-kDa isoform (p42) and the AML-associated p30 isoform bind chromatin and activate transcription, but the specific transcriptional programs controlled by each protein and how they are linked to a selective advantage in AML is not well understood. Here, we show that cells expressing the AML-associated p30 have reduced baseline inflammatory gene expression and display altered dynamics of transcriptional induction in response to LPS, consequently impacting cytokine secretion. This confers p30-expressing cells an increased resistance to the adverse effects of prolonged exposure to inflammatory signals. Mechanistically, we show that these differences primarily result from the differential regulation of AP-1 family proteins. In addition, we find that the altered function of the AP-1 member ATF4 in p30-expressing cells alters their response to ER stress. Collectively, these findings uncover a novel link between mutant CEBPA, inflammation and the stress response, potentially revealing a new vulnerability in AML.
Project description:Using omics tools with the SARS-CoV-2 infected Syrian hamster as model for COVID-19, along with published datasets from COVID-19 patients, Nouailles et al. present a detailed longitudinal analysis of systemic and pulmonary quantitative and qualitative immune responses in a moderate disease setting. Targeted analysis of the alveolar and microvascular niche revealed a dominant role for monocyte-derived macrophages and endothelial cells regarding early anti-viral genes as well as pro-inflammatory and T cell recruiting chemokine expression. Recruitment of cytotoxic effector T cells coincided with viral clearance. This combined response was favorable for a moderate and self-limited disease course.
Project description:Aim of the study was to profile and quantify the proteins head region of D. melanogaster that are changing as a result of phytohormone administration. Data-independent acquisition (DIA) bases quantitative proteomics approach were used to achieve this aim. An Orbitrap Fusion Tribrid mass spectrometer (Thermo Fischer Scientific, Bremen, Germany) connected to the Easy- nLC-1200 nanoflow liquid chromatography system (Thermo Scientific) was used for data acquisition.