Biology subjects

Gusev, O. A.

Publications and source records attributed to Gusev, O. A..

5 recordsLinked to original sources

bioRxiv2025

Full-length isoform constructor (FLIC) - a tool for isoform discovery based on long reads

Advances in high-throughput sequencing have illuminated a complexity of transcriptome landscape in eukaryotes. An inherent part of this complexity is the presence of multiple isoforms generated by the alternative splicing and the use of alternative transcription start and polyadenylation sites. However, currently available tools have limited capacity to infer full-length isoforms. To address this problem, we developed a new pipeline, FLIC (Full-Length Isoform Constructor). FLIC is based on the long-read transcriptome data and integrates several key features: 1) utilizing biological replicate concordance to filter out noise and artifacts; 2) employing peak calling to precisely identify transcription start and polyadenylation sites; 3) enabling robust isoform reconstruction with minimal reliance on existing annotations. We evaluated FLIC using a dedicated set of real and simulated data of Arabidopsis thaliana cDNA sequencing. Results demonstrate that FLIC accurately reconstructs known and novel isoforms, outperforming existing tools, especially in the absence of reference annotations. A direct comparison with CAGE, currently regarded as golden standard for TSS identification shows that FLIC is equally accurate, while being much less time-consuming. Thus FLIC provides a valuable tool for comprehensive transcript characterization, particularly for non-model organisms or when dealing with incomplete or inaccurate annotations.

bioinformatics↗

bioRxiv2024

Prediction and annotation of alternative transcription starts and promoter shift in the chicken genome

The promoter shift is a long known phenomenon which implies changes in the coordinates of a transcription start site (TSS). Analysis of CAGE experiments allows one to assess the impact and statistical significance of the shift. The promoter shift can be associated not only with the change of stages in early development or tissue differentiation, but also with the environmental influence on the cells. Differential promoter usage suggests non-constitutive expression activity of the regulated gene, which, in turn, suggests the usage of few sharp promoters. On the other hand, the housekeeping genes are assumed to demonstrate stable levels of expression while using multiple broad promoters. Additionally, the housekeeping genes are assumed to be normally expressed in most of the tissues. Our results show that many ubiquitously expressed genes use single sharp promoters and are subject to the significant promoter shift, which implies an additional level of complexity to the problem of definition of a housekeeping gene. The reaction of genes in cells and tissues to external stimuli is often studied in the context of differential gene expression. Our study employs a different approach of differential promoter usage, which takes the genes whose promoters undergo significant promoter shifting as the signatures of tissue response and phenotypic effect. Our results suggest that the difference in growth rate of chickens is controlled by the rate of metabolism of nutrients via the differential usage of promoters of the relevant genes.

bioinformatics↗

bioRxiv2020

Population genomics of two closely related anhydrobiotic midges reveals differences in adaptation to extreme desiccation

The sleeping chironomid Polypedilum vanderplanki is capable of anhydrobiosis, a striking example of adaptation to extreme desiccation. Tolerance to complete desiccation in this species is associated with the emergence of multiple paralogs of protective genes. One of the gene families highly expressed under anhydrobiosis and involved in this process are protein-L-isoaspartate (D-aspartate) O-methyltransferases (PIMTs). Recently, a closely related anhydrobiotic midge from Malawi, P. pembai, showing the ability to tolerate complete desiccation similar to that of P. vanderplanki, but experiences more frequent desiccation-rehydration cycles due to differences in ecology, was discovered. Here, we sequenced and assembled the genome of P. pembai and performed a population genomics analysis of several populations of P. vanderplanki and a population of P. pembai. We observe positive selection and radical changes in the genetic architecture of the PIMT locus between the two species, including multiple duplication events in the P. pembai lineage. In particular, PIMT-4, the most highly expressed of these PIMTs, is present in six copies in the P. pembai; these copies differ in expression profiles, suggesting possible sub- or neofunctionalization. The nucleotide diversity ({pi}) of the genomic region carrying these new genes is decreased in P. pembai, but not in the orthologous region carrying the ancestral gene in P. vanderplanki, providing evidence for a selective sweep associated with post-duplication adaptation in the former. Overall, our results suggest an extensive recent and likely ongoing, adaptation of the mechanisms of anhydrobiosis.

evolutionary biology↗

bioRxiv2019

Intracellular localization and gene expression analysis provide new insights on LEA proteins diversity in anhydrobiotic midge

Anhydrobiosis, an adaptive ability to withstand complete desiccation, is in insects limited to a single species: the nonbiting midge Polypedilum vanderplanki (the sleeping chironomid). Evolution of anhydrobiosis in a single representative of a large genus is associated with drastic changes in genome structure, including the emergence of new multimember gene families directly involved in desiccation tolerance. Among them, Late Embryogenesis Abundant (LEA) proteins, which protect other proteins from aggregation caused by desiccation, are believed to originate via horizontal gene transfer from a bacterial donor. To obtain new insights on the biological background of the expanded 27-member LEA protein group in P. vanderplanki, we investigated the expression of corresponding genes in a P. vanderplanki-derived cell line, capable of anhydrobiosis, in a normal state and during induction of desiccation tolerance. We found that all LEA proteins genes identified in P. vanderplankis genome except PvLea16 and PvLea17 are also expressed in Pv11 cells. Their expression was elevated in response to anhydrobiosis-inducing trehalose treatment. Expression patterns of PvLea genes were well preserved in Pv11 cells in comparison to P. vanderplankis larvae both in the control group and during the anhydrobiosis cycle. We also investigated localization of LEA proteins in Pv11 cells and Sf9 cells and found a different level of conservation in intracellular localization of the protein expressed in mammalian and insect cells.

molecular biology↗

bioRxiv2019

Genetic algorithm-based personalized models of human cardiac action potential

We present a novel genetic algorithm-based solution to determine the set of cardiomyocyte model parameters based on experimental human action potential (AP) recordings. The novel approach is based on AP waveform dependence on the heart rate. In order to find the steady-state solution, optimized parameters include conductivities of ionic channels and exchangers augmented by slow variables, intracellular sodium concentration and sarcoplasmic reticulum calcium load. The algorithm is enhanced by a novel mutation operator, based on Cauchy distribution along a random direction in parameter space. We also demonstrate that increasing the number of elite organisms up to 7% results in faster convergence. Test runs indicate that algorithm error is below 5% for IKr, 7% for IK1 and INa and 13% for ICaL. Experimental signal-to-noise ratio above 28 dB was sufficient for high quality algorithm performance. The algorithm validation using optical mapping recordings of human ventricular AP demonstrated low error that was below 6 mV for AP waveform and less than 16 ms for AP duration. Further validation of the personalized models was done using mRNA expression profile of two donor hearts. The mRNA-based model reproduced AP waveform dependence on cycle length with 13 mV accuracy and AP duration with 20 ms accuracy.

biophysics↗