Publications by authors named "S A Khmeleva"
Article Synopsis
- The ring rot of potato, caused by a bacterial pathogen, is a quarantine disease that threatens the global potato industry, making its detection crucial for control efforts.
- A new detection system combines CRISPR/Cas13a with NASBA for identifying viable bacteria in potato tubers, allowing for both instrumental and visual detection methods.
- The system shows a limit of detection as low as 1000 RNA copies per reaction and can be performed in under 2 hours, potentially serving as a routine on-site testing method.
The use of CRISPR/Cas nucleases for the development of DNA diagnostic systems in out-of-laboratory conditions (point-of-need testing, PONT) has demonstrated rapid growth in the last few years, starting with the appearance in 2017-2018 of the first diagnostic platforms known as DETECTR and SHERLOCK. The platforms are based on a combination of methods of nucleic acid isothermal amplification with selective CRISPR/Cas detection of target amplicons. This significantly improves the sensitivity and specificity of PONT, making them comparable with or even superior to the sensitivity and specificity of polymerase chain reaction, considered as the "gold standard" of DNA diagnostics.
View Article and Find Full Text PDFThe approach based on a combination of isothermal recombinase polymerase amplification (RPA), 2'-deoxyuridine-5'-triphosphate modified with tyrosine aromatic group (dUTP-Y1), and direct voltammetric detection of RPA product carrying electroactive labels was successfully applied to the potato pathogen Dickeya solani. The artificial nucleotide dUTP-Y1 demonstrated a good compatibility with RPA, enabling by targeting a section of D. solani genome with a unique sequence to produce the full-size modified products at high levels of substitution of dTTP by dUTP-Y1 (up to 80-90 %) in the reaction mixture.
View Article and Find Full Text PDFThree novel 2'-deoxyuridine-5'-triphosphates modified with 4-nitrophenyl groups via various linkers (dUTP-N1, dUTP-N2, and dUTP-N3) were tested as bearers of reducible electroactive labels as well as substrates suitable for enzymes used in polymerase chain reaction (PCR) and recombinase polymerase amplification (RPA) with a potential application to direct electrochemical detection of double-stranded deoxyribonucleic acid (dsDNA). In cyclic and square wave voltammograms on carbon screen printed electrodes, the labeled dUTP have demonstrated distinct reduction peaks at potentials of -0.7 V to -0.
View Article and Find Full Text PDFArticle Synopsis
- Oxford Nanopore Technologies' long-read RNA sequencing enables detailed analysis of transcript isoforms and alternative splicing (AS) profiles, allowing researchers to quantify different splice variants and their abundances.
- The study applied a method known as gene set enrichment analysis to expose the biological pathways affected by AS changes in human liver tissue and cancer cell lines (HepG2 and Huh7).
- By utilizing a method called the graded tissue specificity index, the research identified specific groups of genes with splice variants unique to liver tissue and the cell lines studied, many of which are significant for understanding cancer development.