Biology subjects

Martynov, A.

Publications and source records attributed to Martynov, A..

8 recordsLinked to original sources

bioRxiv2021

Long-Term Persistence of Plasmids Targeted by CRISPR Interference in Bacterial Populations

CRISPR-Cas systems provide prokaryotes with an RNA-guided defense against foreign mobile genetic elements (MGEs) such as plasmids and viruses. A common mechanism by which MGEs avoid interference by CRISPR consists of acquisition of escape mutations in regions targeted by CRISPR. Here, using microbiological, live microscopy, and microfluidics analyses we demonstrated that plasmids can persist in Escherichia coli cells at conditions of continuous targeting by the type I-E CRISPR-Cas system without acquiring any genetic alterations. We used mathematical modeling to show how plasmid persistence in a subpopulation of cells mounting CRISPR interference is achieved due to the stochastic nature of CRISPR interference and plasmid replication events. We hypothesize that the observed complex dynamics provides bacterial populations with long-term benefits due to the presence of mobile genetic elements in some cells, leading to diversification of phenotypes in the entire community and allowing rapid changes in the population structure to meet the demands of a changing environment.

microbiology↗

bioRxiv2020

Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

BackgroundCladobranch sea slugs represent roughly half of the biodiversity of soft-bodied, marine gastropod molluscs (Nudibranchia) on the planet. Despite their global distribution from shallow waters to the deep sea, from tropical into polar seas, and their important role in marine ecosystems and for humans (as bioindicators and providers of medical drug leads), the evolutionary history of cladobranch sea slugs is not yet fully understood. Here, we amplify the current knowledge on the phylogenetic relationships by extending the cladobranch and outgroup taxon sampling using transcriptome data. ResultsWe generated new transcriptome data for 19 species of cladobranch sea slugs and two additional outgroup taxa. We complemented our taxon sampling with previously published transcriptome data, resulting in a final supermatrix covering 56 species from all but one accepted cladobranch superfamilies. Transcriptome assembly using six different assemblers, selection of those assemblies providing the largest amount of potentially phylogenetically informative sites, and quality-driven compilation of data sets resulted in three different supermatrices: one with a full coverage of genes per species (446 single-copy protein-coding genes) and two with a less stringent coverage (667 genes with 98.9% partition coverage and 1,767 genes with 86% partition coverage, respectively). We used these supermatrices to infer statistically robust maximum-likelihood trees. All analyses, irrespective of the data set, indicate maximum statistical support for all major splits and phylogenetic relationships on family level. The only discordance between the inferred trees is the position of Embletonia pulchra. Extensive testing using Four-cluster Likelihood Mapping, Approximately Unbiased tests, and Quartet Scores revealed that its position is not due to any informative phylogenetic signal, but caused by confounding signal. ConclusionsOur data matrices and the inferred trees inferred can serve as a solid foundation for future work on the taxonomy and evolutionary history of Cladobranchia. The correct placement of E. pulchra, however, proves challenging, even with large data sets. Moreover, quartet mapping shows that confounding signal present in the data is sufficient to explain the inferred position of E. pulchra, again leaving its phylogenetic position as an enigma.

evolutionary biology↗

bioRxiv2020

Improving vaccine efficacy based on non-covalent photoinactivation of microorganisms - sources vaccine antigens (MSVA)

One of the most promising methods for non-covalent inactivation of vaccine-producing microorganisms is the use of photoinactivation using riboflavin derivatives. The study used a dynamic combinatorial derivative of riboflavin - succinyl-maleinyl riboflavin. Corpuscular vaccines are divided into the following groups: from 2AB to 5AB - bacteria were inactivated by riboflavin derivative and blue light, and groups from 6AB to 9AB were inactivated by formalin (0.1% formalin in 9 log CFU was kept for 2 weeks in an thermostat and then sterility was determined - bacterial growth was not observed). A dynamic derivative of riboflavin at a final concentration of 0.02% can photo inactivate 6 time more bacteria P. Aeruginosa and E. coli than riboflavin. The minimum effective blue light emitter power (450 nm) for the photodynamic inactivation of both P. aeruginosa and E. coli is 1024.2 mW / cm2. In groups of mice pre-vaccinated intraperitoneally with corpuscular photo inactivated vaccines based on suspensions of and E. coli at doses of 0.5-1.0 ml 4 log (CFU) / mL, 100% survival of all animals was observed, whereas in control group with the same type of vaccines but formalin-treated vaccines, it failed to achieve a 100% protective effect.

microbiology↗

bioRxiv2018

The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water

The semi-aquatic bugs conquered water surfaces worldwide and occupy ponds, streams, lakes, mangroves, and even open oceans. As such, they inspired a range of scientific studies from ecology and evolution to developmental genetics and hydrodynamics of fluid locomotion. However, the lack of a representative water strider genome hinders thorough investigations of the mechanisms underlying the processes of adaptation and diversification in this group. Here we report the sequencing and manual annotation of the Gerris buenoi (G. buenoi) genome, the first water strider genome to be sequenced so far. G. buenoi genome is about 1 000Mb and the sequencing effort recovered 20 949 predicted protein-coding genes. Manual annotation uncovered a number of local (tandem and proximal) gene duplications and expansions of gene families known for their importance in a variety of processes associated with morphological and physiological adaptations to water surface lifestyle. These expansions affect key processes such as growth, vision, desiccation resistance, detoxification, olfaction and epigenetic components. Strikingly, the G. buenoi genome contains three Insulin Receptors, a unique case among metazoans, suggesting key changes in the rewiring and function of the insulin pathway. Other genomic changes include wavelength sensitivity shifts in opsin proteins likely in association with the requirements of vision in water habitats. Our findings suggest that local gene duplications might have had an important role during the evolution of water striders. These findings along with the G. buenoi genome open exciting research opportunities to understand adaptation and genome evolution of this unique hemimetabolous insect.

genomics↗

bioRxiv2017

A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)

The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.

genomics↗

bioRxiv2017

The anticancer activity and immune modulating properties of combinatorial ensemble complementary (antisense) microRNA (fRNA) in combination with the immunomodulator - glycoproteid lectin from B. subtilis B-7025

BackgroundMany adenocarcinomas have the ability to capture from an extracellular matrix the oligonucleotides and nanoparticles by pinocytosis, when the non-cancerous cells are not capable to capture the oligonucleotides and small liposomes. This provides selective accumulation of proposed protected oligonucleotides (fRNA) in cancer cells and also provides the absence toxicity in the fRNA.\n\nMaterials and methodsFor the immunotherapy we used immunotropic 70 kDa lectin B. subtilis B-7025. In vivo experiments were carried out in C57BL line mice in Lewis lung carcinoma. The cytotoxic activity, lymphocytes, macrophages was determined in vitro using the MTT assay.\n\nResults and discussionAnimal survival rate in groups receiving either the fRNA or Vaccine was 70 and 40%, respectively. Combined use fRNA and Vaccine has the advantage compared with the use these drugs in monotherapy, as the anticancer efficacy of the scheme is much higher, which is manifested in the primary tumor node and metastasis inhibition.

cancer biology↗

bioRxiv2017

Optimal Number Of Spacers In CRISPR Arrays

We estimate the number of spacers in a CRISPR array of a bacterium which maximizes its protection against a viral attack. The optimality follows from a competition between two trends: too few distinct spacers make the bacteria vulnerable to an attack by a virus with mutated corresponding protospacers, while an excessive variety of spacers dilutes the number of the CRISPR complexes armed with the most recent and thus most effective spacers. We first evaluate the optimal number of spacers in a simple scenario of an infection by a single viral species and later consider a more general case of multiple viral species. We find that depending on such parameters as the concentration of CRISPR-CAS interference complexes and its preference to arm with more recently acquired spacers, the rate of viral mutation, and the number of viral species, the predicted optimal array length lies within a range quite reasonable from the viewpoint of recent experiments.\n\nAuthor summaryCRISPR-Cas system is an adaptive immunity defense in bacteria and archaea against viruses. It works by accumulating in bacterial genome an array of spacers, or fragments of virus DNA from previous attacks. By matching spacers to corresponding parts of virus DNA called protospacers, CRISPR-Cas system identifies and destroys intruder DNA. Here we theoretically estimate the number of spacers that maximizes bacterial survival. This optimum emerges from a competition between two trends: More spacers allow a bacterium to hedge against mutations in viral protospacers. However, keeping too many spacers makes the older ones inefficient because of accumulation of mutations in corresponding protospacers in viruses. Thus, fewer CRISPR-Cas molecular machines are left armed with more efficient young spacers. We have shown that a higher efficiency of CRISPR-Cas system allows a bacterium to utilize more spacers, increasing the optimal array length. On contrary, a higher viral mutation rate makes older spacers useless and favors shorter arrays. A higher diversity in viral species reduces the efficiency of CRISPR-Cas but does not necessary lead to longer arrays. We think that our study provides a new viewpoint at a huge variety in the observed array lengths and adds relevance to evolutionary models of bacterial-phage coexistence.

systems biology↗

bioRxiv2017

Influence Of Non-Metabolic Microbial Growth Promotors (AMP Activators) On The Sensitivity To Antimicrobials In The Actually Multiresistant Microbial Strains

IntroductionThe control over multi-resistant nosocomial strains of microorganisms has been becoming increasingly urgent in recent years. We suggest a new paradigm that eliminates killing or inhibiting the growth of bacteria. Excluding bacteria death supresses the selection of resistant strains of microorganisms. We have developed such non-metabolite growth promoters, which in very low doses stimulate the rapid growth of many bacteria strains. The mechanism of action of the enhancers is caused by the activation of the cAMP high doses accumulation process in the microbial cells. cAMP itself is a substrate for phosphorylation including DNA polymerases.\n\nMaterials and methodsThe susceptible culture collection resistance strains Pseudomonas aeruginosa MDR Kharkov IMI1, Acinetobacter baumanii MDR Kharkov-IMI1, and Clebsiella pneumonia MDR Kharkov-IMI1 were used. The following antimicrobial agents of known potency were evaluated: ciprofloxacin, polymyxin, amikacin. The same broth, but containing 0.001% enhancers (under patenting), has been used for further passaging for MDR strains. Characteristics of bacterial growth were determined in a medium compared at the control group - the broth without enhancers.\n\nResults and discussionEnhancers contribute to a significant increase in the antimicrobial sensitivity to polymyxin, ciprofloxacin and amikacin in multi-resistant strains of bacteria. Changes in the growth characteristics and antimicrobial sensitivity are observed only in the second passage that demonstrates the need for the further studies of the molecular mechanisms of the cAMP effect on the division and growth of microbial cells.

microbiology↗