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Biology subjects

Tarasova, O.

Publications and source records attributed to Tarasova, O..

4 recordsLinked to original sources

Analysis of Seasonal and Long-Term Population Dynamics for Modeling Populations at Low Density: Experience with Light Traps

Methods for estimating and modeling the long-term and short-term adult flight dynamics of the conifer silk moth Dendrolimus superans (Lepidoptera: Lasiocampidae) are examined. The analysis uses light trap adult catch data collected over 21 years, from 2005 to 2025. Three models of adult flight are considered: a flight-initiation model driven by weather factors, an autoregressive model of long-term catch dynamics, and a binary model of seasonal catch. For the flight-initiation model, we propose estimating the accumulated temperature sum ST from the date when the first derivative of the remote sensing vegetation index NDVI becomes positive until the date of the first adult capture of the season. ST is shown to be sufficiently stable across all years of observation, with flight each year beginning after this temperature sum is reached. The second model demonstrates that the long-term light trap catch time series is well described by a second-order autoregressive model AR(2), in which the catch of the current year depends on catches from the two preceding years. This long-term series is compared with a previously studied larval population density series of the Siberian silk moth; both are shown to be AR(2) series with similar coefficient values, which suggesting that adult catch data may serve as a proxy for absolute larval population density. In the third model, we describe the transition from absolute-scale seasonal catch dynamics (number of adults per day) to a binary scale (0, 1), where 0 denotes days on which no adults were attracted to the trap, and 1 denotes days on which at least one individual was captured. The seasonal absolute catch series is thereby transformed into a binary series of zeros and ones, and relationships between adjacent values in such a binary series are examined. A linear relationship between the absolute and binary seasonal dynamics series is demonstrated, making it possible to estimate absolute catches from binary catch values and to analyze seasonal flight in sparse pest populations. This potentially opens new avenues for understanding how outbreak populations function at chronically low density. Author summaryForest pests can cause catastrophic damage, yet predicting their outbreaks remains challenging. During periods of low population density, standard monitoring methods become labor-intensive and uninformative, while the transition to an outbreak often occurs unexpectedly. Using a 21-year dataset of adult Siberian silk moth (Dendrolimus superans) captures from light traps, we developed an approach combining three complementary models. First, we showed that moth flight begins upon reaching a specific temperature sum, with the starting point determined by NDVI vegetation index dynamics rather than a calendar date--making the forecast more ecologically relevant. Second, long-term adult population dynamics follow a second-order autoregressive model AR(2), matching the dynamics previously observed for larval populations. This establishes light trap data as a reliable proxy for absolute population density when ground surveys are impractical. Third, we introduced a method to analyze seasonal flight using binary data (presence/absence of moths per day), which we showed is linearly related to absolute abundance. This enables studying population dynamics during periods of extremely low density, when traditional methods fail. Our approach opens new possibilities for early warning systems to detect when a population risks transitioning from a latent state to an outbreak phase.

ecology↗

HIV-1 drug resistance profiling using amino acid sequence space cartography

Human immunodeficiency virus (HIV) drug resistance is a global healthcare issue. The emergence of drug resistance demands treatment adaptation. Computational methods predicting the drug resistance profile from genomic data of HIV isolates are advantageous for monitoring drug resistance in patients. Yet, the currently existing computational methods for drug resistance prediction are either not suitable for complex mutational patterns in emerging HIV strains or lack interpretability of prediction results which is of paramount importance in clinical practice. Hence, to overcome these limitations, new approaches for the HIV drug resistance prediction combining high accuracy and interpretability are required. In this work, a new methodology for the analysis of protein sequence data based on the application of generative topographic mapping was developed and applied for HIV drug resistance profiling. It allowed achieving high accuracy of resistance predictions and intuitive interpretation of prediction results. The developed approach was successfully applied for the prediction of HIV resistance towards protease, reverse-transcriptase and integrase inhibitors and in-depth analysis of HIV resistance-inducing mutation patterns. Hence, it can serve as an efficient and interpretable tool to suggest optimal treatment regimens.

bioinformatics↗

Comprehensive analysis of HIV elite controllers and progressors' transcriptional profiles from CD8+ T lymphocytes demonstrates heterogeneity of pathways and master regulators, which may be essential for disease nonprogression

Cytotoxic and noncytotoxic CD8+ T lymphocyte responses are essential for the control of HIV infection. Understanding the mechanisms underlying HIV control in elite controllers (ECs), who do not progress to AIDS for many years without treatment, may facilitate the development of new effective therapeutic strategies. We performed a comprehensive analysis of the transcriptional profiles of CD8+ cells from ECs and treated and untreated progressors using an original pipeline. Cluster analysis enabled the identification of five distinct groups (EC groups 1-5) of ECs based on their transcription profiles. Profiles of EC groups 2-4 were associated with different numbers of differentially expressed genes, but the corresponding genes shared the same cellular processes. These three groups were associated with increased metabolism, survival, proliferation, and the absence of an "exhausted" phenotype of CD8+ lymphocytes, compared to untreated progressors. The transcriptional profiles of EC group 1 were opposite to those of EC groups 2-4 and similar to those of the treated progressors. This group may be associated with residual dysfunction of T lymphocytes. The EC group 5 was indistinguishable from normal. EC groups 1 and 5 can have mechanisms of nonprogression unrelated to CD8+ cells. The transcription changes in CD8+ lymphocytes from ECs may be attributable to the receptors that modulate the functional states of CD8+ cells. We identified 22 receptors, which are potential master regulators and may be responsible for the observed expression changes of CD8+ cells in ECs. These receptors can be considered potential targets of therapeutic intervention, which may decelerate disease progression. IMPORTANCEA small group of HIV-infected individuals, known as elite controllers (ECs), do not develop AIDS for many years, despite being untreated. Understanding the mechanisms governing HIV control in ECs may help develop new effective therapeutic strategies. Since CD8+ T lymphocytes seem to play a significant role in HIV control, we analyzed the large number of transcriptional profiles in total CD8+ cells from ECs, treated, and untreated progressors. We found distinct groups of ECs, which may have different mechanisms governing HIV nonprogression, and we identified related pathways and cellular processes that are dissimilar from those in progressors. We also identified master regulators, key proteins in the signaling network that can be responsible for observed transcriptional changes in CD8+ cells from ECs and may be essential for disease nonprogression. These proteins may represent potential targets for therapeutic interventions.

microbiology↗

Novel allosteric mechanism of p53 activation by small molecules for targeted anticancer therapy

Given the immense significance of p53 restoration for anti-cancer therapy, elucidation of the mechanisms of action of p53-activating molecules is of the utmost importance. Here we report a discovery of novel allosteric modulation of p53 by small molecules, which is an unexpected turn in the p53 story. We identified a structural element involved in p53 regulation, whose targeting by RITA, PpIX and licofelone block the binding of p53 inhibitors, MDM2 and MDMX. Deletion and mutation analysis followed by molecular modeling, identified the key p53 residues S33 and S37 targeted by RITA and PpIX. We propose that the binding of small molecules to the identified site induces a conformational trap preventing p53 from the interaction with MDM2 and MDMX. These results point to a high potential of allosteric activators. Our study provides the basis for the development of therapeutics with a novel mechanism of action, thus extending the p53 pharmacological potential.

cancer biology↗