Analysis of the Diversity and Functional Potential of Bacterial Communities in Tuberculomas.

The dynamics of lung microbiota in tuberculosis remains poorly understood. Sequencing of variable regions of the 16S rRNA gene from surgically excised tuberculosis foci and biopsy specimens of normal lung tissue allowed characterization of the diversity and predictive potential of bacterial communities. Taxonomic diversity indices attested to differences in the structure of microbial communities between "healthy" lungs and tuberculomas. The microbial composition of "healthy" lungs varied in taxonomic diversity and was presented by both gram-positive and gram-negative bacteria with sufficiently similar metabolic potential. The microbiota of the examined tuberculomas consisted of Mycobacterium tuberculosis in 99.9% of cases. A significant part of the metabolic pathways predicted by PICRUSt2 included cholesterol catabolism, sulfate assimilation, and various pathways for the biosynthesis of cell wall components.

[Age Dynamics of Telomere Length in Endemic Baikal Planarians].

Age-related changes in telomere length (TL) in somatic tissues are not limited only to shortening. It is known that many organisms show different TL dynamics. Such species specificity indicates the complexity of the mechanisms involved in the regulation of TL. Owing to their morphological, physiological, and ecological features, Baikal planarians are an interesting model for studying the TL dynamics and the factors influencing it in comparison with species living outside Baikal. In this work, we investigated telomerase activity and age-related changes in TL in three endemic species of planarians from the Dendrocoelidae family. Two species are giant deep-water species (7-12 cm long, Sorocelis hepatizon and Rimacephalus arecepta), and one is a coastal shallow species (1 cm long, Baikalobia guttata). In addition, we investigated the telomere biology in another small Siberian species from the Planariidae family (2 cm in length, Phagocata sibirica), which is not found in Baikal. TL and telomerase activity were determined using real-time PCR and the TRAP method. Three types of age-related TL dynamics were detected with active telomerase: (1) TL shortening at the juvenile stage of development and subsequent maintenance (R. arecepta, Ph. sibirica), (2) gradual TL shortening during ontogeny (S. hepatizon) and (3) cyclic dynamics of TL (B. guttata). Thus, the changes of TL in the studied planarians does not have an obvious connection with body size, habitat depth, phylogenetic relationship and is probably a consequence of species features in the regulation of telomerase activity.

[Molecular phylogenetic analysis of Diacyclops and Acanthocyclops (Copepoda: Cyclopoida) from Lake Baikal].

Lake Baikal is inhabited by a relatively large number of cyclopid species, many of which are endemics. Two genera, Diacyclops Kiefer, 1927 and Acanthocyclops Kiefer, 1927, are the most specious in the lake. Taxonomic discrimination of the majority of representatives of these genera is difficult owing to their high morphological similarities and poor standard description. In this study, a molecular phylogenetic analysis of Lake Baikal members of the Diacyclops/Acanthocyclops group is performed on the basis of mitochondrial cytochrome c oxidase subunit I (COI) gene. It is shown that a fragment of COI 1000 bp long is sufficient for intragenus discrimination of the cyclopids of Lake Baikal. The issues of Diacyclops/Acanthocyclops taxonomy are reflected in the obtained molecular data. Two distinct phylogenetic groups of Diacyclops genus with uncertain taxonomic status are revealed.

[A simple and effective method for assessing chromatin diminution values in copepods using qPCR].

The value of chromatin diminution (CD) in different species of freshwater cyclopoid copepods can differ significantly. The biological and evolutionary roles of these differences remain unclear. To expand the knowledge on CD distribution and magnitude in this group of copepods, a quick method for its evaluation was required. This study proposes a simple approach for CD assessment in copepods using quantitative realtime PCR (qPCR). The magnitude of changes in the genome size was assessed by comparing fluorescence curves of qPCR fragments of target genes for pre- and post-diminution materials. The method was tested on four cyclopoid copepods species. In Cyclops kolensis, CD was assessed as 95.3 ± 1.2; in Acanthocyclops vernalis it was assessed at 94.6 ± 0.8%; at C. insignis, it was 82.3 ± 5.2%; and for the first time, CD was found in Megacyclops viridis at 91.1 ± 2.6%. The advantages of our approach are its rapidity, simplicity and minimal requirements of materials studied.

[MtDNA Polymorphism of Lake Baikal Epischura--A Key Endemic Species of the Plankton Community].

The population structure of Epischura baicalensis Sars (Copepoda, Calanoida), one of the key endemic species of the plankton community of Lake Baikal was studied. An analysis of mitochondrial DNA polymorphism revealed no genetic differences between Epischura sampled in the different basins of the lake or in the winter-spring/summer generations. Baikal Epischura is represented by a single panmictic population with a high level of mtDNA haplotype diversity.

[Length and structure of telomeric DNA in three species of Baikal gastropods (Caenogastropoda: Hydrobioidea: Benedictiidae)].

The structure of telomeric repeat (TTAGGG)n was determined and the length of telomeric DNA (tDNA) was measured in three species of gastropods from the family Benedictiidae that are endemic to Lake Baikal. Fluorescence in situ hybridization (FISH) confirmed the localization of a telomeric repeat at the chromosome ends. The sizes of tDNA in "giant" eurybathic, psammo-pelobiontic species Benedictia fragilis and shallow water litho-psammobiontic species B. baicalensis with medium shell sizes were similar (16 ± 2.9 and 15 ± 2.1 kb, respectively), but they had a greater length than that of the shallow water spongio-litobiontic species Kobeltocochlea martensiana with small shells (10.5 ± 1.5 kb). We discuss tendencies in age-related changes in tDNA length in snails and a possible mechanism for maintaining tDNA size in ontogeny.

[Genetic polymorphism of a pelagic fish species, little Baikal oilfish Comephorus dybowski, deduced from analysis of microsatellite loci].

Intraspecific genetic polymorphism of a Baikal Lake endemic, little Baikal oilfish (Comephorus dybowski Korotneff, 1905), was evaluated based on microsatellite analysis. Six microsatellite loci designed for the European sculpin, Cottus gobio, were used. Each locus was typed using 25 to 35 individuals from each of the Baikal trenches (southern, middle, and northern). Analysis of genetic differentiation (F(ST) and R(ST)) revealed no statistical significant differences between the samples. The data showed that the target species was represented by a single panmictic stable population.

The evolutionary relationships of two families of cottoid fishes of Lake Baikal (east Siberia) as suggested by analysis of mitochondrial DNA.

Fragments of mtDNA genes Cyt B, ATPase 6, and ATPase 8 of six cottoid fishes species of Lake Baikal (East Siberia) were amplified and sequenced. In addition mtDNAs of the same fish were subjected to restriction analysis. The data obtained were used to construct phylogenetic trees. The topology of the ATPase tree differs from those of the Res (restriction) and Cyt B trees. Clustering of species within the trees confirms the viewpoint of Taliev (1955, Baicalian Sculpins (Cottoidei)) according to which Baikalian cottoids originate from two ancestral forms. The times of branching obtained do not confirm the existing viewpoint according to which the two golomyankas (Comephorus baicalensis and Comephorus dybowskii) are pre-Baikal (Myocene) relicts: these two species may have originated 1.2-1.8 million years ago in Baikal, and they seem to represent an example of rapid morphological evolution which resulted in the formation of a new family.