Project description:We propose a novel approach for FPOP data analysis, utilizing DIA data. The HbHp protein complex was analyzed by FPOP and measured on timsToF SCP in DIA, DDA and MS modes. The IDs of modified peptides were quantified for each acquisition mode and the extent of modification was calculated on the level of peptides. The reproducibility was evaluated by coefficients of variation.This work was mainly financially supported by the Czech Science Foundation (22-27695S), the Technology Agency of the Czech Republic (ODEEP-EU TH86010001), the Ministry of Education, Youth and Sports of the Czech Republic grant PHOTOMACHINES - Photosynthetic cell redesign for high yields of therapeutic peptides (CZ.02.01.01/00/22_008/0004624) and the Academy of Sciences of the Czech Republic (RVO: 61388971).
Project description:Genotype data from 55 Fulani individuals from Ziniare, Burkina Faso and 7 Czechs & Slovaks collected in Prague, Czech Republic The data was typed in Illumina Omni2.5-Octo BeadChip.
Project description:The spread of antimicrobial resistance (AMR), coupled with the decline in antibiotic development, has become a major public health concern. Recent studies estimate that around 700,000 people die each year from infections caused by multidrug-resistant (MDR) bacteria. This led the WHO to publish the ESKAPEE list of high priority pathogens for AMR, namely Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. and Escherichia coli. Among these, Gram-negative bacteria (K. pneumoniae, A. baumannii, P. aeruginosa, Enterobacter spp., and E. coli) are particularly overrepresented. This is mainly due to their high propensity to develop multiple resistance mechanisms, in addition to their intrinsic resistance to many antimicrobials, which is due to their membrane composition and the expression of broad-spectrum efflux pumps. One strategy to combat such AMR is the use of drug enhancers that are able to restore the antibacterial activity of poorly active antibiotics. In this context, we demonstrated that the polyamino-isoprenyl enhancer, NV716, efficiently potentiates the antibacterial activity of two families of multi-target Ser/Cys-based enzyme inhibitors, namely the oxadiazolone derivatives (OX) and the Cyclipostins and Cyclophostin analogs (CyC), against Enterobacter cloacae, while remaining inactive against other Gram-negative bacteria. We confirmed that NV716 potentiates some OX & CyC compounds by permeabilizing the outer membrane and thus by increasing the inhibitor accumulation as shown by fluorescence confocal microscopy. By using bio-orthogonal click-chemistry activity-based protein profiling (CC-ABPP) approach coupled to proteomic analysis, we also identified the target proteins of the best OX & CyC inhibitors from E. cloacae lysate, thereby confirming their multi-target nature. Interestingly, 6 of the latter proteins were also captured via CC-ABPP in P. aeruginosa lysate, and are highly conserved in all Gram-negative bacteria. These results provide proof of concept that both OX & CyC, if successfully potentiated, could be used against a wide range of ESKAPEE Gram-negative bacteria.
Project description:Generation of a new library of targeted mass spectrometry assays for accurate protein quantification in malignant and normal kidney tissue. Aliquots of primary tumor tissue lysates from 86 patients with initially localized renal cell carcinoma (RCC), 75 patients with metastatic RCC treated with sunitinib or pazopanib in the first line and 17 adjacent normal tissues treated at Masaryk Memorial Cancer Institute (MMCI) in Brno, Czech Republic, or University Hospital Pilsen (UHP), Czech Republic, were used to generate the spectral library. Two previously published datasets (dataset A and B) and two newly generated RCC datasets (dataset C and D) were analyzed using the newly generated library showing increased number of quantified peptides and proteins, depending on the size of the library and LC-MS/MS instrumentation. This PRIDE project also includes quantitative analysis results for all four datasets and raw files for dataset C and D. Dataset A is characterized in DOI: 10.1038/nm.3807. It consists of 18 samples from 9 RCC patients involving one cancer and non-cancerous sample per patient. Dataset B is characterized in DOI: 10.3390/biomedicines9091145. It consists of 16 tumor samples and 16 adjacent normal tissues from 16 mRCC patients treated at Masaryk Memorial Cancer Institute (MMCI) in Brno, Czech Republic. Dataset C involves only tumor tissues from dataset B. Half of them responded to sunitinib treatment in the first line three months after treatment initiation and half did not. Dataset D involves 16 RCC patients treated at University Hospital Pilsen (UHP), Czech Republic. All were localized at the time of initial diagnosis, half of the tumors developed distant metastasis in five years after the diagnosis.
Project description:In this study, we exposed Caenorhabditis elegans wild types N2 to water collected from six sources in the Dutch village Sneek. The sources were: wastewater from a hospital, a community (80 households), a nursing home, influent into the local municipal wastewater treatment plant, effluent of the wastewater treatment plant, and surface water samples. The goal of the experiment was to determine if C. elegans can be used to identify pollutants in the water by transcriptional profiling. Age synchronized worms at developmental L4 larval stage were exposed to treatment for 24 hours. After flash freezing the samples, RNA was isolated, labeled and hybridized on oligo microarray (Agilent) slides.
Project description:Transgenic Arabidopsis seedlings RV86-5 (contains a dexamethasone-inducible ubiquitin variant that contains Arg instead of Lys at position 48; ̈Schlögelhofer et al., 2005) were surface-sterilized and sown on Uhelon 120T (Silk & Progress, Czech Republic) mesh placed on 1% (w/v) agar containing a half-strength Murashige and Skoog medium (pH 5.7), stratified at 4 °C for 3 d, and cultivated at 21 °C/19 °C day/night temperatures, with a 16 h photoperiod (90 μmol m−2 s−1 light intensity) for 14 d. On the fourteenth day (after the first 2 h of the day period), the Uhelon mesh with the seedlings was transferred onto a new solid medium supplemented with (i) 5×10−4% (v/v) DMSO (mock); (ii) 0.7 or 7.0 μM dexamethasone (DEX) and rinsed with DMSO or DEX-supplemented water for mock and DEX-treated seedlings, respectively, and incubated for 24 hours.