Alexandra Klimenko

• PhD
• Researcher at Institute of Cytology and Genetics, Russian Academy of Sciences

The use of CpGV strains as the basis for bioinsecticides is an effective and safe way to control Cydia pomonella. The research is aimed at the identification and study of new CpGV strains. Objects of identification and bioinformatic analysis: 18 CpGV strains. Sequencing was carried out on a NextSeq550. Genome assembly and annotation were carried ou...

We report a genome of CpGV from the bioresource collection of the Federal Research Center of Biological Plant Protection “State Collection of Entomoacariphages and Microorganisms.” Its sequence is 123,862 bp. The genome under study demonstrates a degree of similarity of more than 99% with reference NC_002816 from the NCBI RefSeq database.

Cydia pomonella granulovirus is a natural pathogen for Cydia pomonella that is used as a biocontrol agent of insect populations. The study of granulovirus virulence is of particular interest since the development of resistance in natural populations of C. pomonella has been observed during the long-term use of the Mexican isolate CpGV. In our study...

Wheat heading time is primarily governed by two loci: VRN-1 (response to vernalization) and PPD-1 (response to photoperiod). Five sets of near-isogenic lines (NILs) were studied with the aim of investigating the effect of the aforementioned genes on wheat vegetative period duration and 14 yield-related traits. Every NIL was sown in the hydroponic g...

Simple Summary Bacteria belonging to the Ralstonia genus are of great interest for study since this genus includes both phytopathogenic species and soil opportunistic human pathogens, forming two phylogenetic branches. The difference in phenotype of related species is formed by differences in how proteins and other molecules bacteria synthesize, as...

Modern computational biology makes widespread use of mathematical models of biological systems, in particular systems of ordinary differential equations, as well as models of dynamic systems described in other formalisms, such as agent-based models. Parameters are numerical values of quantities reflecting certain properties of a modeled system and...

Modern computational biology makes widespread use of mathematical models of biological systems, in particular systems of ordinary differential equations, as well as models of dynamic systems described in other formalisms, such as agent-based models. Parameters are numerical values of quantities reflecting certain properties of a modeled system and...

Nonribosomal peptides play an important role in the vital activity of bacteria and have an extremely broad field of biological activity. In particular, they act as antibiotics, toxins, surfactants, sidero-phores, and also perform a number of other specific functions. Biosynthesis of these molecules does not occur on ribosomes but by special enzymes...

Non-ribosomal peptides play an important role in the vital activity of bacteria and have an extremely broad field of biological activity. In particular, they act as antibiotics, toxins, surfactants, siderophores, and also perform a number of other specific functions. Biosynthesis of these molecules does not occur on ribosomes but by special enzymes...

Simple Summary Understanding what functions can be performed by members of the human gut microbial community and how they are interconnected can be very useful for the comprehension of this ecosystem’s function in human health and disease. Here, we propose an original approach to derive this information from metatranscriptomes and test it on public...

The maternally transmitted endocellular bacteria Wolbachia is a well-known symbiont of insects, demonstrating both negative and positive effects on host fitness. The previously found Wolbachia strain wMelPlus is characterized by a positive effect on the stress-resistance of its host Drosophila melanogaster, under heat stress conditions. This invest...

A number of methods for extracting the DNA of maternally inherited obligate intracellular bacteria Wolbachia from an insect host and its subsequent purification have been described in previous scholarship. As Wolbachia is present in the hosts’ organisms in rather low quantities, these techniques used to be quite labor-intensive. For this paper, we...

Protein abundance is crucial for the majority of genetically regulated cell functions to act properly in prokaryotic organisms. Therefore, developing bioinformatic methods for assessing the efficiency of different stages of gene expression is of great importance for predicting the actual protein abundance. One of these steps is the evaluation of tr...

In this study, we collected and systemized diverse information related to depressive and anxiety disorders as the first step on the way to investigate the associations between molecular genetics, electrophysiological, behavioral, and psychological characteristics of people. Keeping that in mind, we developed an internet resource including a databas...

Simple Summary Motile bacteria are widespread in various water ecosystems along with nonmotile species, which posits the question: what makes motility an advantage in such habitats, and under what conditions? This simulation study addresses these problems using a computer model of competition of two microbial species: Nomad of a motile population a...

Current biology tasks are impracticable without bioinformatic data processing. Information technologies and the newest computers provide the ability to automatically execute algorithms on an extensive data set and store either strong- or weak-structured data. A well-designed architecture of such data warehouses increases the reproducibility of inve...

Autism spectrum disorder (ASD) is characterized by uncommon genetic heterogeneity and a high heritability concurrently. Most autoimmune disorders (AID), similarly to ASD, are characterized by impressive genetic heterogeneity and heritability. We conducted gene-set analyses and revealed that 584 out of 992 genes (59%) included in a new release of th...

The results of our simulations show that motile forms (as opposed to sedentary forms) have an advantage under nutrient-poor conditions corresponding to the environment in which marine bacteria live. There is a turning point in the magnitude of the migration penalty that determines whether the Nomadic strategy will be successful or not.

We have found out that those two classes of bacteria whose genomes contain and do not contain biosynthetic gene clusters of nonribosomal peptide synthetases substantially differentiate in preferred evolutionary strategies for optimizing primary structure of their gene coding sequences.

Autism spectrum disorder (ASD) has a strong and complex genetic component with an estimate of more than 1000 genes implicated cataloged in SFARI (Simon′s Foundation Autism Research Initiative) gene database. A significant part of both syndromic and idiopathic autism cases can be attributed to disorders caused by the mechanistic target of rapamycin...

Background: The study of the biological basis of anxiety, depression, and intellectual disabilities in humans is one of the most actual problems of modern neurophysiology. Of particular interest is the study of complex interactions between molecular genetic factors, electrophysiological properties of the nervous system, and the behavioral character...

There are two evolutionary trends in genome organization among microbes: towards either amplification or reduction. Which evolutionary scenario overcomes depends on environmental conditions and the complexity of gene networks determining phenotypic traits such as metabolic features of cells. In this simulation study, we have shown that the habitats...

Motivation: Protein synthesis is not a straight forward process and one gene locus can produce many isoforms, for example, by starting mRNA translation from alternative start sites. altORF evaluator (altORFev) predicts alternative open reading frames within eukaryotic mRNA translated by a linear scanning mechanism and its modifications (leaky scan...

Bacterial communities are closely interrelated systems consisting of numerous species making it challenging to analyze their structure and relations. At present, there are several experimental techniques providing heterogeneous data, concerning various aspects of this research object. The recent avalanche of available metagenomic data challenges no...

Background: Bacteriophages are known to be one of the driving forces of bacterial evolution. Besides promoting horizontal transfer of genes between cells, they may induce directional selection of cells (for instance, according to more or less resistance to phage infection). Switching between lysogenic and lytic pathways results in various types of...

Background Bacteriophages are known to be one of the driving forces of bacterial evolution. Besides promoting horizontal transfer of genes between cells, they may induce directional selection of cells (for instance, according to more or less resistance to phage infection). Switching between lysogenic and lytic pathways results in various types of (...

Bacterial communities are tightly interconnected systems consisting of numerous species making it challenging to analyze their structure and relations. There are several experimental techniques providing heterogeneous data concerning various aspects of this object. A recent avalanche of metagenomic data challenges not only biostatisticians but also...

Multiscale approaches for integrating submodels of various levels of biological organization into a single model became the major tool of systems biology. In this paper, we have constructed and simulated a set of multiscale models of spatially distributed microbial communities and study an influence of unevenly distributed environmental factors on...