Publications by authors named "Oxana A Volkova"
This is data on the microbial diversity in the floating cyanobacterial community and sediment samples from the lake Solenoe (Novosibirsk region, Russia) obtained by metagenomic methods. Such a detailed data of the microbial diversity of the Novosibirsk oblast lake ecosystem was carried out for the first time. The purpose of our work was to reveal microbial taxonomic diversity and abundance, metabolic pathways and new enzyme findings the studied lake ecosystem using the next-generation sequencing (NGS) technology and metagenomic analysis.
View Article and Find Full Text PDFRNA plays an important role in the intracellular cell life and in the organism in general. Besides the well-established protein coding RNAs (messenger RNAs, mRNAs), long non-coding RNAs (lncRNAs) have gained the attention of recent researchers. Although lncRNAs have been classified as non-coding, some authors reported the presence of corresponding sequences in ribosome profiling data (Ribo-seq).
View Article and Find Full Text PDFRibosome profiling technology (Ribo-Seq) allowed to highlight more details of mRNA translation in cell and get additional information on importance of mRNA sequence features for this process. Application of translation inhibitors like harringtonine and cycloheximide along with mRNA-Seq technique helped to assess such important characteristic as translation efficiency. We assessed the translational importance of features of mRNA sequences with the help of statistical analysis of Ribo-Seq and mRNA-Seq data.
View Article and Find Full Text PDFHidden coding potential of eukaryotic genomes: nonAUG started ORFs.
J Biomol Struct Dyn
October 2013
Article Synopsis
- * Recent studies show that alternative translation from non-AUG codons, as well as weak AUG contexts, is significant in the creation of diverse eukaryotic protein landscapes.
- * This research analyzes mRNA characteristics in yeast and mammals, finding that certain sequence features in upstream ORFs (uORFs) and stable downstream structures may enhance the recognition of non-AUG start codons by ribosomes.
Article Synopsis
- * Researchers analyzed mRNA sequences in two plants, Arabidopsis thaliana and Oryza sativa, finding that those with the UGA terminator had more nonsense codons, likely due to weak natural selection.
- * They discovered a correlation between the presence of tandem stop codons and the amino acid composition of proteins, specifically noting that glycine at the protein's C-terminal was linked to higher frequencies of reserve stop signals in UGA-containing mRNAs.
Article Synopsis
- - The study investigates how the nucleotide context around the AUG start codon affects translation initiation in eukaryotic ribosomes, particularly focusing on the role of specific nucleotides in the +4, +5, and +6 positions.
- - It was found that the presence of guanine (G) in the +4 position is significant for the GnnAUG context, while the context AnnAUG leads to an increased occurrence of serine in the second amino acid position.
- - Overall, the efficiency of the translation initiation process may be influenced by the interaction between both the 5'- and 3'-context regions, as well as the specific amino acids present in the early protein-coding sequence.
It is known that eukaryotic ribosomes are able to translate small ORFs and reinitiate translation at downstream start codons. However, this mechanism is widely considered to be inefficient and it is not commonly taken into account. We compiled a sample of human mRNAs containing small upstream ORFs overlapping with annotated protein coding sequences.
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