A5005088657- RNA regulation and disease
- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- RNA Research and Splicing
- Advanced Proteomics Techniques and Applications
- RNA modifications and cancer
- interferon and immune responses
- Genomics and Phylogenetic Studies
- Bacterial Identification and Susceptibility Testing
- Yersinia bacterium, plague, ectoparasites research
- Viral Infections and Immunology Research
- Molecular Biology Techniques and Applications
- Machine Learning in Bioinformatics
- Virus-based gene therapy research
- Vibrio bacteria research studies
Pirogov Russian National Research Medical University
2017-2025
Federal Medical-Biological Agency
2024-2025
Federal Research and Clinical Center of Physical-Chemical Medicine named after Y.M. Lopukhin
2020-2023
Institute of Biomedical Chemistry
2017-2020
Introduction Bacteroides fragilis (Bf)’s T6SS locus has been characterized and shown to have functional activity in competition experiments. It demonstrated that symbiont nontoxigenic Bf strains a more effective “weapon” effect on pathogenic Bf, which is realized through the of effector-immune (E-I) protein pairs. Intensive study structure led an understanding certain issues related its activity, but exact regulatory mechanisms E-I pair remain unclear. Proteomic annotation components...
The proteogenomic search pipeline developed in this work has been applied for reanalysis of 40 publicly available shotgun proteomic datasets from various human tissues comprising more than 8000 individual LC-MS/MS runs, which 5442 .raw data files were processed total. This was focused on searching ADAR-mediated RNA editing events, their clustering across samples different origins, and classification. In total, 33 recoded protein sites identified 21 datasets. Of those, 18 detected at least...
Adenosine-to-inosine RNA editing is one of the most common types editing, a posttranscriptional modification made by special enzymes. We present proteomic study on this phenomenon for Drosophila melanogaster. Three proteome data sets were used in study: two taken from public repository and third obtained here. A customized protein sequence database was generated using results genome-wide adenosine-to-inosine studies applied identifying edited proteins. The total number 68 peptides belonging...
Cancer cell lines responded differentially to type I interferon treatment in models of oncolytic therapy using vesicular stomatitis virus (VSV). Two opposite cases were considered this study, glioblastoma DBTRG-05MG and osteosarcoma HOS exhibiting resistance sensitivity VSV after the treatment, respectively. Type responses compared for these by integrative analysis transcriptome, proteome, RNA editome identify molecular factors determining differential effects observed. Adenosine-to-inosine...
Mass spectrometry-based proteome analysis implies matching the mass spectra of proteolytic peptides to amino acid sequences predicted from genomic sequences. Reliability peptide variant identification in proteogenomic studies is often lacking. We propose a way interpret shotgun proteomics results, specifically data-dependent acquisition mode, as protein sequence coverage by multiple reads it done nucleic sequencing for calling single nucleotide variants. Multiple each position could be...
Adenosine-to-inosine RNA editing is an enzymatic post-transcriptional modification which modulates immunity and neural transmission in multicellular organisms. In particular, it involves of mRNA codons with the resulting amino acid substitutions. We identified such sites for developmental proteomes Drosophila melanogaster at protein level using available data 15 stages fruit fly development from egg to imago 14 time points embryogenesis. total, 40 were obtained, each belonging a unique...
Adenosine-to-inosine RNA editing is one of the most common types editing, a posttranscriptional modification made by special enzymes. We present proteomic study on this phenomenon for Drosophila melanogaster. Three proteome data sets were used in study: two taken from public repository and third obtained here. A customized protein sequence database was generated using results genome-wide adenosine-to-inosine studies applied identifying edited proteins. The total number 68 peptides belonging...
Alternative splicing is one of the main regulation pathways in living cells beyond simple changes level protein expression. Most approaches proposed proteomics for identification specific isoforms require a preliminary deep transcriptomic analysis sample under study, which not always available, especially case re-analysis previously acquired data. Herein, we developed new algorithms and validation splice proteomic data absence RNA sequencing samples study. The bioinformatic were tested on...
Abstract Adenosine-to-inosine RNA editing is an enzymatic post-transcriptional modification which modulates immunity and neural transmission in multicellular organisms. Some of its functions are enforced through mRNA codons with the resulting amino acid substitutions. We identified these sites originated from for developmental proteomes Drosophila melanogaster at protein level using available proteomic data fifteen stages fruit fly development egg to imago fourteen time points embryogenesis....
Abstract Mass spectrometry-based proteome analysis usually implies matching mass spectra of proteolytic peptides to amino acid sequences predicted from nucleic sequences. At the same time, due stochastic nature method when it comes proteome-wide analysis, in which only a fraction are selected for sequencing, completeness protein sequence identification is undermined. Likewise, reliability peptide variant proteogenomic studies suffering. We propose way interpret shotgun proteomics results,...
Abstract The proteogenomic search pipeline developed in this work has been applied for re-analysis of 40 publicly available shotgun proteomic datasets from various human tissues comprising more than 8,000 individual LC-MS/MS runs, which 5442 .raw data files were processed total. scope was focused on searching ADAR-mediated RNA editing events, their clustering across samples different origin, and classification. In total, 33 recoded protein sites identified 21 datasets. Of those, 18 detected...