A5011845016- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- DNA Repair Mechanisms
- RNA modifications and cancer
- Chromosomal and Genetic Variations
- Machine Learning in Bioinformatics
- Genomics and Chromatin Dynamics
- CRISPR and Genetic Engineering
- Cancer Genomics and Diagnostics
- SARS-CoV-2 and COVID-19 Research
- Evolution and Genetic Dynamics
- Animal Virus Infections Studies
- Cancer-related molecular mechanisms research
- Protist diversity and phylogeny
- Bacteriophages and microbial interactions
- Fungal and yeast genetics research
- T-cell and B-cell Immunology
- Virus-based gene therapy research
- Bacterial Genetics and Biotechnology
- Genetics, Bioinformatics, and Biomedical Research
- RNA regulation and disease
- Genetic diversity and population structure
- Cancer-related Molecular Pathways
- Bioinformatics and Genomic Networks
University of Ostrava
2024-2025
National Center for Biotechnology Information
2015-2024
National Institutes of Health
2015-2024
United States National Library of Medicine
2023
Institute of Cytology and Genetics
2007-2021
Siberian Branch of the Russian Academy of Sciences
2004-2019
Evolutionary Genomics (United States)
2016
Novosibirsk State University
2015-2016
Washington University in St. Louis
2009
University of Pittsburgh
2008
We describe the draft genome of microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count a consequence an elevated rate duplication resulting in tandem clusters. More than third Daphnia's genes have no detectable homologs any other available proteome, most amplified families are specific to lineage. coexpansion interacting within metabolic pathways suggests that maintenance duplicated not random, analysis expression under different...
Sequencing the genomes of multiple, taxonomically diverse eukaryotes enables in-depth comparative-genomic analysis which is expected to help in reconstructing ancestral eukaryotic and major events evolution making functional predictions for currently uncharacterized conserved genes.We examined evolutionary patterns recently constructed set 5,873 clusters predicted orthologs (eukaryotic orthologous groups or KOGs) from seven genomes: Caenorhabditis elegans, Drosophila melanogaster, Homo...
The "knockout-rate" prediction holds that essential genes should be more evolutionarily conserved than are nonessential genes. This is because negative (purifying) selection acting on expected to stringent for genes, which functionally dispensable and/or redundant. However, a recent survey of evolutionary distances between Saccharomyces cerevisiae and Caenorhabditis elegans proteins did not reveal any difference the rates evolution An analysis mouse rat orthologous also found evolved at...
Prochlorococcus marinus , the dominant photosynthetic organism in ocean, is found two main ecological forms: high-light-adapted genotypes upper part of water column and low-light-adapted at bottom illuminated layer. P. SS120, complete genome sequence reported here, an extremely form. The SS120 composed a single circular chromosome 1,751,080 bp with average G+C content 36.4%. It contains 1,884 predicted protein-coding genes size 825 bp, rRNA operon, 40 tRNA genes. Together 1.66-Mbp MED4, one...
Lineage-specific gene loss, to a large extent, accounts for the differences in repertoires between genomes, particularly among eukaryotes. We derived parsimonious scenario of losses eukaryotic orthologous groups (KOGs) from seven complete genomes. The involves substantial loss fungi, nematodes, and insects. Based on this evolutionary estimates divergence times major phyla, we introduce numerical measure, propensity (PGL). explore connection be lost evolution (PGL value), protein sequence...
During a systematic analysis of conserved gene context in prokaryotic genomes, previously undetected, complex, partially neighborhood consisting more than 20 genes was discovered most Archaea (with the exception Thermoplasma acidophilum and Halobacterium NRC-1) some bacteria, including hyperthermophiles Thermotoga maritima Aquifex aeolicus. The composition order this vary greatly between species, but all versions have stable, core that consists five genes. One encodes predicted DNA helicase,...
Deinococcus radiodurans R1 (DEIRA) is a bacterium best known for its extreme resistance to the lethal effects of ionizing radiation, but molecular mechanisms underlying this phenotype remain poorly understood. To define repertoire DEIRA genes responding acute irradiation (15 kGy), transcriptome dynamics were examined in cells representing early, middle, and late phases recovery by using DNA microarrays covering ≈94% predicted genes. At least at one time point during recovery, 832 (28%...
Instead of the immunoglobulin-type antigen receptors jawed vertebrates, jawless fish have variable lymphocyte (VLRs), which consist leucine-rich repeat (LRR) modules. Somatic diversification VLR gene is shown here to occur through a multistep assembly LRR modules randomly selected from large bank flanking cassettes. The predicted concave surface lined with hypervariable positively residues, and computational analysis suggests repertoire about 10(14) unique receptors. Lamprey immunized...
The availability of multiple complete genome sequences from diverse taxa prompts the development new phylogenetic approaches, which attempt to incorporate information derived comparative analysis gene sets or large subsets thereof. Such attempts are particularly relevant because major role horizontal transfer and lineage-specific loss, at least in evolution prokaryotes.Five largely independent approaches were employed construct trees for completely sequenced bacterial archaeal genomes: i)...
We have determined the complete 1,694,969-nt sequence of GC-rich genome Methanopyrus kandleri by using a whole direct sequencing approach. This approach is based on unlinking genomic DNA with ThermoFidelase version M. topoisomerase V and cycle directed 2′-modified oligonucleotides (Fimers). Sequencing redundancy (3.3×) was sufficient to assemble less than one error per 40 kb. Using combination database searches coding potential prediction, 1,692 protein-coding genes 39 for structural RNAs...
Relative positions of nematodes, arthropods, and chordates in animal phylogeny remain uncertain. The traditional tree topology joins arthropods with a coelomate clade, whereas which lack coelome, occupy basal position. However, the current leading hypothesis, based on phylogenetic trees for 18S ribosomal RNA several proteins, nematodes clade molting animals, Ecdysozoa. We performed analysis over 500 sets orthologous are represented plants, fungi, using maximum likelihood, parsimony, distance...
The rhomboid family of polytopic membrane proteins shows a level evolutionary conservation unique among proteins. They are present in nearly all the sequenced genomes archaea, bacteria and eukaryotes, with exception several species small genomes. On basis experimental studies developmental regulator from Drosophila AarA protein bacterium Providencia stuartii, rhomboids thought to be intramembrane serine proteases whose signaling function is conserved eukaryotes prokaryotes.Phylogenetic tree...
A feature of Ig hypermutation is the presence hypermutable DNA sequences that are preferentially found in V regions genes. Among these, RGYW/WRCY most pronounced motif (G:C a mutable position; R=A/G, Y=C/T, and W=A/T). However, molecular basis for high mutability RGYW was not known until recently. The discovery activation-induced cytidine deaminase targets encoding regions, has enabled analysis its targeting properties when expressed outside context hypermutation. We analyzed these data...
The Xist locus plays a central role in the regulation of X chromosome inactivation mammals, although its exact mode action remains to be elucidated. Evolutionary studies are important identifying conserved genomic regions and defining their possible function. Here we report cloning, sequence analysis, detailed characterization gene from four closely related species common vole (field mouse), Microtus arvalis . Our analysis reveals that there is overall conservation structure both between...
A computational method was developed for delineating connected gene neighborhoods in bacterial and archaeal genomes. These are not typically present, their entirety, any single genome, but held together by overlapping, partially conserved arrays. The procedure applied to comparing the orders of orthologous genes, which were extracted from database Clusters Orthologous Groups proteins (COGs), 31 prokaryotic genomes resulted identification 188 clusters arrays, included 1001 2890 COGs....
Numerous eukaryotic proteins contain multiple domains. Certain domains show a tendency to occur in diverse domain architectures and can be considered “promiscuous.” These promiscuous are, typically, involved protein–protein interactions play crucial roles interaction networks, particularly those that contribute signal transduction. A systematic comparative-genomic analysis of eukaryotes is described. Two quantitative measures promiscuity are introduced applied the 28 genomes eukaryotes....