Publications by authors named "Dmitry N Konanov"
Article Synopsis
- The study focuses on the role of mobile genetic elements in spreading biocide and antibiotic resistance among bacteria, specifically the qacEΔ1 gene that provides resistance to quaternary ammonium compounds (QACs).
- Researchers developed a TaqMan real-time PCR assay to detect the qacEΔ1 gene in Gram-negative bacteria, which can accurately identify even low quantities (as few as 80 copies) without false results.
- This assay serves as a rapid, sensitive, and specific method for monitoring QAC resistance, tracking the spread of class 1 integrons, and predicting multidrug-resistant (MDR) traits in Gram-negative bacteria.
Article Synopsis
- Inflammatory bowel diseases (IBD) are widespread but often show no symptoms early on, highlighting the need for effective, non-invasive diagnostic methods.
- This study proposes a technique to monitor IBD development by analyzing volatile organic compounds (VOCs) produced by gut microbiota using HS GC/MS during different inflammation stages in a rat model.
- Results showed significant changes in the metabolomic profile, particularly in short-chain fatty acids, during acute and remission phases of IBD, indicating potential biomarkers for early detection and monitoring of the disease.
Motivation: The Oxford Nanopore technology has a great potential for the analysis of methylated motifs in genomes, including whole-genome methylome profiling. However, we found that there are no methylation motifs detection algorithms, which would be sensitive enough and return deterministic results. Thus, the MEME suit does not extract all Helicobacter pylori methylation sites de novo even using the iterative approach implemented in the most up-to-date methylation analysis tool Nanodisco.
View Article and Find Full Text PDFUnlabelled: Circulating serum miRNA are increasingly used as biomarkers and potential treatment targets in several clinical scenarios, including cardiovascular diseases. However, the current data on circulating miRNA in thoracic aorta aneurism (TAA) patients are inconclusive. The aim of the present study is to compare the levels of several circulating miRNA in patients with degenerative TAA, coronary artery disease (CAD), and controls for special profile identification.
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- Microorganisms and their hosts communicate through secreted proteins and small molecules, including volatile compounds (VOCs) like butyrate and propionate, which impact intestinal and immune functions.
- The study focuses on analyzing the VOC secretome of specific bacteria from the intestinal microbiota, particularly their outer membrane vesicles (OMVs), which may have effects beyond the gut.
- More than 60 VOCs were identified in bacterial culture media, including fatty acids and amino acid derivatives, with the first characterization of Bacteroides species' OMVs and their associated volatile compounds.
The study of individual fungi and their communities is of great interest to modern biology because they might be both producers of useful compounds, such as antibiotics and organic acids, and pathogens of various diseases. And certain features associated with the functional capabilities of fungi are determined by differences in gene content. Information about gene content is most often taken from the results of functional annotation of the whole genome.
View Article and Find Full Text PDFBioCAT: Search for biosynthetic gene clusters producing nonribosomal peptides with known structure.
Comput Struct Biotechnol J
March 2022
Nonribosomal peptides are a class of secondary metabolites synthesized by multimodular enzymes named nonribosomal peptide synthetases and mainly produced by bacteria and fungi. NMR, LC-MS/MS and other analytical methods allow to determine a peptide structure precisely, but it is often not a trivial task to find natural producers of them. There are cases when potential producers should be found among hundreds of strains, for instance, when analyzing metagenomic data.
View Article and Find Full Text PDFShort-chain fatty acids are metabolites widely presented in many natural sources, including human feces and blood. Estimation of their composition is a common procedure, usually performed using nuclear magnetic resonance or gas chromatography with a flame ionization detector. However, the commonly used methods often depend on specific sample preparation, such as filtration and homogenization.
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