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:Contrasting levels of beta-diversity and underlying phylogenetic trends indicate different paths to chemical diversity in highland and lowland willow species
Martin Volf*, Jing Vir Leong, Paola de Lima Ferreira, Tereza Volfova, Petr Kozel, Pavel Matos-Maravi, Elvira Horandl, Natascha D. Wagner, Niko Luntamo, Juha-Pekka Salminen, Simon T. Segar, Brian E. Sedio
*Corresponding author: Martin Volf, volf@entu.cas.cz, tel. +420 387775038, Biology Centre, Czech Academy of Sciences, Institute of Entomology, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
Untargeted metabolomics data was generated for the above publication for 29 species of willows in the Czech Republic and Austria, encompassing an elevation gradient spanning >2500 m (from 175 to 2620 m asl). Extraction and instrumental methods are reported in Volf et al. 2023 Ecology Letters and Sedio et al. 2021 Frontiers in Ecology and Evolution, https://doi.org/10.3389/fevo.2021.679638
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:Untargeted metabolomics data generated for the above publication for 13 lowland willows in Czech Republic and Austria. Extraction and methods are reported in Leong et al. (Accepted) and Sedio et al. 2021 Frontiers in Ecology and Evolution, https://doi.org/10.3389/fevo.2021.679638 [doi:10.25345/C59Z90N8R] [dataset license: CC0 1.0 Universal (CC0 1.0)].
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:Main objective is to improve colorectal cancer (CRC) screening programme in the Czech Republic and decrease the disease incidence and mortality. The secondary aim is to verify the effectiveness of incorporation of the new minimally invasive device in the prevention programme.
Project description:Despite high vaccination coverage, pertussis is on the rise in many countries including Czech Republic. To better understand B. pertussis resurgence we compared the changes in genome structures between Czech vaccine and circulating strains and subsequently, we determined how these changes translated into global transcriptomic and proteomic profiles. The whole-genome sequencing revealed that both historical and recent isolates of B. pertussis display substantial variation in genome organization and cluster separately. The RNA-seq and LC-MS/MS analyses indicate that these variations translated into discretely separated transcriptomic and proteomic profiles. Compared to vaccine strains, recent isolates displayed increased expression of flagellar genes and decreased expression of polysaccharide capsule operon. Czech strains (Bp46, K10, Bp155, Bp318 and Bp6242)exhibited increased expression of T3SS and sulphate metabolism genes when compared to Tohama I. In spite of 50 years of vaccination the Czech vaccine strains (VS67, VS393 and VS401) differ from recent isolates to a lesser extent than from another vaccine strain Tohama I.
Project description:Contrasting levels of beta-diversity and underlying phylogenetic trends indicate different paths to chemical diversity in highland and lowland willow species
Martin Volf*, Jing Vir Leong, Paola de Lima Ferreira, Tereza Volfova, Petr Kozel, Pavel Matos-Maravi, Elvira Horandl, Natascha D. Wagner, Niko Luntamo, Juha-Pekka Salminen, Simon T. Segar, Brian E. Sedio
*Corresponding author: Martin Volf, volf@entu.cas.cz, tel. +420 387775038, Biology Centre, Czech Academy of Sciences, Institute of Entomology, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
Untargeted metabolomics data was generated for the above publication for 29 species of willows in the Czech Republic and Austria, encompassing an elevation gradient spanning >2500 m (from 175 to 2620 m asl). Extraction and instrumental methods are reported in Volf et al. 2023 Ecology Letters and Sedio et al. 2021 Frontiers in Ecology and Evolution, https://doi.org/10.3389/fevo.2021.679638