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result(s) for
"Petrova, Tatyana"
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A mitochondrial genome phylogeny of voles and lemmings (Rodentia: Arvicolinae): Evolutionary and taxonomic implications
by
Bodrov, Semyon Yu
,
Genelt-Yanovskiy, Evgeny A.
,
Abramson, Natalia I.
in
Analysis
,
Animals
,
Arvicolinae
2021
Arvicolinae is one of the most impressive placental radiations with over 150 extant and numerous extinct species that emerged since the Miocene in the Northern Hemisphere. The phylogeny of Arvicolinae has been studied intensively for several decades using morphological and genetic methods. Here, we sequenced 30 new mitochondrial genomes to better understand the evolutionary relationships among the major tribes and genera within the subfamily. The phylogenetic and molecular dating analyses based on 11,391 bp concatenated alignment of protein-coding mitochondrial genes confirmed the monophyly of the subfamily. While Bayesian analysis provided a high resolution across the entire tree, Maximum Likelihood tree reconstruction showed weak support for the ordering of divergence and interrelationships of tribal level taxa within the most ancient radiation. Both the interrelationships among tribes Lagurini, Ellobiusini and Arvicolini, comprising the largest radiation and the position of the genus Dinaromys within it also remained unresolved. For the first time complex relationships between genus level taxa within the species-rich tribe Arvicolini received full resolution. Particularly Lemmiscus was robustly placed as sister to the snow voles Chionomys in the tribe Arvicolini in contrast with a long-held belief of its affinity with Lagurini. Molecular dating of the origin of Arvicolinae and early divergences obtained from the mitogenome data were consistent with fossil records. The mtDNA estimates for putative ancestors of the most genera within Arvicolini appeared to be much older than it was previously proposed in paleontological studies.
Journal Article
The mitochondrial genome of the critically endangered enigmatic Kazakhstani endemic Selevinia betpakdalaensis (Rodentia: Gliridae) and its phylogenetic relationships with other dormouse species
by
Bodrov, Semyon Yu
,
Abramson, Natalia I.
,
Panitsina, Valentina A.
in
631/158/672
,
631/181/2480
,
631/181/757
2024
Dormice (family Gliridae) are an ancient group of rodents. It was fully dominant in the Oligocene and Early Miocene, and its current diversity is represented by a few extant species. A Kazakhstani endemic, the desert dormouse
Selevinia betpakdalaensis
is one of the most enigmatic dormouse species. Lack of genetic data has not allowed
Selevinia
to be included in previous molecular phylogenetic analyses. In the current study, we report the first genetic data on
S. betpakdalaensis
as well as mitochondrial genomes of
Myomimus roachi
and
Glirulus japonicus
(retrieved from museum specimens) and a mitogenome of
Graphiurus murinus
(assembled from SRA data). The assembled mitochondrial genomes were combined with available mitochondrial data from GenBank to reconstruct the mitochondrial phylogeny of Gliridae. Taking into account a distortion of the phylogeny as a result of an analysis of the saturated third codon position, we obtained for the first time a resolved phylogeny of the family. The first split within Gliridae was estimated as an average of 34.6 Mya, whereas divergence time of subfamilies Graphiurinae and Glirinae was assessed at 32.67 Mya. The phylogenetic analysis confirmed the relationship (previously shown based on cranial and mandibular morphology) between
Selevinia
and the
Myomimus.
Journal Article
Evaluation of the “Bottleneck” Effect in an Isolated Population of Microtus hartingi (Rodentia, Arvicolinae) from the Eastern Rhodopes (Bulgaria) by Methods of Integrative Analysis
by
Zorenko, Tanya A.
,
Kryuchkova, Lyudmila Yu
,
Golenishchev, Fedor N.
in
Bulgaria
,
Cloning
,
Computed tomography
2022
An integrative analysis of an isolated population of Harting’s vole (Microtus hartingi) from the Eastern Rhodope Mountains (Bulgaria) was carried out by morphological and morphometric methods, computed tomography, Cytb variation data, and experimental hybridization. Substantial changes in the development of the skull and teeth were found. Nevertheless, those voles can live to the senex stage. A phylogenetic reconstruction based on Cytb sequences showed that M. hartingi from the Eastern Rhodopes forms a separate clade, which is a sister clade to the voles from Northeastern Greece (also from the foothills of the Rhodopes). M. hartingi from the Rhodopes is mostly isolated reproductively from M. h. ankaraensis from Anatolia (Turkey), as evidenced by a decrease in the proportion of pairs that started breeding, relatively high mortality of pups, and increased sterility of hybrid males. Possible time of isolation of the Rhodopean population and consequences of the “bottleneck” effect on its current state are discussed. At the same time, we believe that, at present, it is impossible to determine its taxonomic status. It is necessary to recognize M. hartingi from the Bulgarian Rhodopes as an endangered population and to include it in regional Red Lists of Bulgaria.
Journal Article
Effect of Flaxseed Mucilage on the Probiotic, Antioxidant, and Structural-Mechanical Properties of the Different Lactobacillus Cells
by
Kharina, Maria
,
Mikshina, Polina
,
Nikitina, Elena
in
Acidification
,
antioxidant activity
,
antioxidant properties
2023
A positive effect of flaxseed mucilage (FSM) addition (at concentrations of 0.1, 0.2, and 0.4%) to MRS and milk whey nutrient medium on the survival, auto-aggregation, hydrophobicity, adhesive, and antioxidant properties of L. bulgaricus, L. fermentum AG8, and L. plantarum AG9 was shown. It was found that the AG 8 strain became less sensitive to 7% NaCl concentrations (the cell survival rate in the experiment with 0.4% flaxseed mucilage increased by 10% compared to the control). Cultivation in the presence of FSM led to an increase in auto-aggregation, especially in the case of AG8 (from 60 to 85%) and AG9 (from 50 to 80%) strains, and an increase in hydrophobicity was seen: for L. fermentum AG8, it was from 30% to 62–72%, for L. fermentum AG9 from 30% to 35–42%, and for L. bulgaricus from 20% to 30%. The adhesive properties of the L. fermentum AG8 and L. plantarum AG9 cells increased from 0.472 to 1 nN (nanonewton) and from 0.630 to 2.5 nN, respectively. The presence of flaxseed mucilage increased the total phenolic content in cell-free supernatants after 48 h of cultivation. The concentration of 0.1–0.2% FSM increased the OH-scavenging activity of milk whey nutrient medium cell-free supernatants of strains AG8 and AG9 by 7–10%. Flaxseed mucilage can serve as a promising bioactive additive that elevates antioxidant activity, increases the resistance and survival of Lactobacillus cells in the gastrointestinal tract, and leads to the synthesis of lipase and α-glucosidase inhibitors. The co-culture of these lactic acid bacteria in the presence of FSM and milk components in the form of whey leads to the synthesis of lipase and α-glucosidase inhibitors more than the culturing on de Man, Rogosa, and Sharpe broth.
Journal Article
Compact Thermal Storage with Phase Change Material for Low-Temperature Waste Heat Recovery—Advances and Perspectives
by
Dzhonova-Atanasova, Daniela
,
Nakov, Svetoslav
,
Panyovska, Stela
in
Alternative energy sources
,
Cooling
,
Emissions
2022
The current interest in thermal energy storage is connected with increasing the efficiency of conventional fuel-dependent systems by storing the waste heat in low consumption periods, as well as with harvesting renewable energy sources with intermittent character. Many of the studies are directed towards compact solutions requiring less space than the commonly used hot water tanks. This is especially important for small capacity thermal systems in buildings, in family houses or small communities. There are many examples of thermal energy storage (TES) in the literature using the latent heat of phase change, but only a few are commercially available. There are no distinct generally accepted requirements for such TES systems. The present work fills that gap on the basis of the state of the art in the field. It reviews the most prospective designs among the available compact latent heat storage (LHS) systems in residential applications for hot water, heating and cooling and the methods for their investigation and optimization. It indicates the important characteristics of the most cost- and energy-efficient compact design of an LHS for waste heat utilization. The proper design provides the chosen targets at a reasonable cost, with a high heat transfer rate and effective insulation. It allows connection to multiple heat sources, coupling with a heat pump and integration into existing technologies and expected future scenarios for residential heating and cooling. Compact shell-tube type is distinguished for its advantages and commercial application.
Journal Article
Resolving Rapid Radiation of Voles and Lemmings (Arvicolinae: Cricetinae, Rodentia) with QuaddRAD Sequencing and Transcriptome Analysis
by
Abramson, Natalia
,
Skalon, Elizaveta
,
Bondareva, Olga
in
Analysis
,
Arvicolinae
,
Diversification
2025
Voles and lemmings (subfamily Arvicolinae) remain some of the most difficult groups for disentangling phylogenetic relations owing to recent and very fast explosive radiation. The rapid radiation events are challenging for phylogenetic analysis and produce bushes of various shapes that are impossible to resolve with a straightforward approach using individual loci. Here using the quaddRAD-seq technique and transcriptomes, we tested whether data from the nuclear genome are consistent with trees inferred earlier from individual loci and from mitogenomes in topology and divergence dating. Both the transcriptome and quaddRAD-seq data convincingly place Arvicola as the earliest derivative within Arvicolini. This result is in agreement with the fossil record and conventional taxonomy. For the first time, whole-genome sequencing data resolved relations within the third radiation wave of the subfamily’s taxa, namely the tribes Arvicolini, Lagurini, and Ellobiusini, which have formed polytomy in mitochondrial trees in earlier articles. This study indicates that divergence dating is highly dependent on the number and position of calibration points in a tree and on taxa sampling. In terms of phylogenetic inference, the position of nodes with insufficient taxa representation is the most susceptible to errors.
Journal Article
Reconstruction of Pleistocene Evolutionary History of the Root Vole Alexandromys oeconomus (Cricetidae, Rodentia) in Northern Asia
by
Bodrov, Semyon Yu
,
Kuular, Aivar V.
,
Abramson, Natalia I.
in
Alexandromys oeconomus
,
Cytochrome
,
Cytochrome b
2025
Previous phylogeographic study of the root vole (Alexandromys oeconomus) revealed four mitochondrial cytochrome b lineages—North and Central European, North (=Central) Asian and Beringian. Three of them were studied in detail, while the North Asian lineage, which occupies the most extensive territory and is considered to be the place of origin for the species, was understudied. In the framework of the current study, we obtained 95 new sequences (34 localities) from the wide territory of Northern Asia and in total, examined 940 specimens from 181 localities throughout the species’ distribution range. The North Asian lineage was found to be more diverse than the Beringian and the European lineages. Southern Siberia and especially the Altai–Sayan region displayed the highest haplotype and nucleotide diversity, suggesting the region’s role as a genetic diversity hotspot. We suppose that the expansion of the North Asian lineage started from Western Transbaikalia. Its representatives colonised the territory from the Urals to the northern shore of the Okhotsk Sea, and then spread in the opposite direction, to Southern Siberia. As a result, a mixture of haplogroups is observed in the Altai–Sayan region. According to the BEAST analysis calibrated with the first A. oeconomus records, the MRCA of North Asian and Beringian lineages is dated back to ~0.82 Mya, and the first divergence within the North Asian lineage may have occurred ~0.6 Mya. When compared with colonisation times of other representatives of the Arvicolinae subfamily, our dating seems to be overestimated. In this regard, molecular data for dated fossil remains of the root vole are essential for subsequent studies.
Journal Article
A Cybertaxonomic Revision of the “Crocidura pergrisea” Species Complex with a Special Focus on Endemic Rocky Shrews: Crocidura armenica and Crocidura arispa (Soricidae)
by
Bodrov, Semyon Yu
,
Abramson, Natalia I.
,
Winkler, Viola
in
Biological diversity
,
Computed tomography
,
Crocidura
2024
The extraction of museum DNA from a unique collection of samples of the “Crocidura pergrisea” species complex, which comprises local endemics of Central and West Asia, allowed us to determine their inter- and intragroup relationships. The first step of this study was the re-evaluation of heavily damaged type specimens of C. armenica via a microcomputed-tomography-based cybertaxonomic approach (CTtax), which enabled a precise description of the species’ morphology; three-dimensional models of the cybertypes were made available through the MorphoBank Repository. We developed the “AProMaDesU” pipeline on the basis of five requirements for micro-CT-based cyber-datasets in relation to mammalian collections. Our second step was a combination of several meticulous approaches to morphological investigation against a background of a cytb-based phylogeny, which helped us to make a taxonomic decision about the status of species of the “pergrisea” group, e.g., C. arispa, C. armenica, and C. serezkyensis, when the morphological results were partly incongruent with the molecular phylogeny. Nevertheless, under two assumptions, our findings preserved a separate species-level status of C. serezkyensis and C. arispa. In addition, we restored the species-level status of C. armenica. This taxonomic decision is based on our morphospace analysis, which revealed unique craniomandibular shape transformations within the rocky shrews that helped them with the transition to a new area of morphospace/trophic niches and consequently separated them from the other analyzed Crocidura groups.
Journal Article
A mitochondrial genome phylogeny of voles and lemmings
by
Bodrov, Semyon Yu
,
Abramson, Natalia I
,
Bondareva, Olga V
in
Analysis
,
Genetic aspects
,
Lemmings
2021
Arvicolinae is one of the most impressive placental radiations with over 150 extant and numerous extinct species that emerged since the Miocene in the Northern Hemisphere. The phylogeny of Arvicolinae has been studied intensively for several decades using morphological and genetic methods. Here, we sequenced 30 new mitochondrial genomes to better understand the evolutionary relationships among the major tribes and genera within the subfamily. The phylogenetic and molecular dating analyses based on 11,391 bp concatenated alignment of protein-coding mitochondrial genes confirmed the monophyly of the subfamily. While Bayesian analysis provided a high resolution across the entire tree, Maximum Likelihood tree reconstruction showed weak support for the ordering of divergence and interrelationships of tribal level taxa within the most ancient radiation. Both the interrelationships among tribes Lagurini, Ellobiusini and Arvicolini, comprising the largest radiation and the position of the genus Dinaromys within it also remained unresolved. For the first time complex relationships between genus level taxa within the species-rich tribe Arvicolini received full resolution. Particularly Lemmiscus was robustly placed as sister to the snow voles Chionomys in the tribe Arvicolini in contrast with a long-held belief of its affinity with Lagurini. Molecular dating of the origin of Arvicolinae and early divergences obtained from the mitogenome data were consistent with fossil records. The mtDNA estimates for putative ancestors of the most genera within Arvicolini appeared to be much older than it was previously proposed in paleontological studies.
Journal Article
Rehabilitation of Disturbed Lands with Industrial Wastewater Sludge
by
Petrova, Tatyana A.
,
Rudzisha, Edelina
,
Pashkevich, Mariya A.
in
Abandoned mines
,
Biodegradation
,
Biomass
2022
Wastelands of the mining industry are among the largest of disturbed areas that demand revitalization. To reduce environmental impact and to better manage these geo-resources, the formation of sustainable plant and soil complexes and the restoration of self-recovery soil function are critical points. The successful return of vegetative cover at post-mining sites requires eliminating the deficiency of organic matter. For this, we assessed the usability of non-traditional ameliorants to provide a better understanding of benefits from mutual dependencies of environmental resources. To prevent losses and to close resource cycles, we studied the applicability of wastewater sludge from the pulp and paper (SPP) industry as an amendment to counteract soil degradation and rehabilitate human-disturbed lands. Waste rock limestone, beresite, and phosphogypsum substrates of post-mining sites were used in vitro for the application of sludge and peat mixture and consequent grass seeding. The formed vegetative cover was analyzed to compare the germination and biomass growth on reconstructed soils. We assessed the efficiency of ameliorant combinations by two approaches: (1) the traditional technique of cutting-off plant material to measure the obtained plant biomass, and (2) digital image analysis for RGB-processed photographs of the vegetative cover (r2 = 0.75–0.95). The effect of SPP on plant cover biomass and grass height showed similar results: land rehabilitation with the formation of a 20 cm soil layer on mine waste dumps was environmentally suitable with an SPP:soil ratio of 1:3. However, excessive application (ratio 1:1 of SPP to the soil) negatively affected seed germination and plant vegetation.
Journal Article