Distortion of Population Statistics due to the Use of Different Methodological Approaches to the Construction of Genomic DNA Libraries.

Several different methods of DNA library preparation for paleogenetic studies are now available. However, the chemical reactions underlying each of them can affect the primary sequence of ancient DNA (aDNA) in the libraries and taint the results of a statistical analysis. In this paper, we compare the results of a sequencing of the aDNA libraries of a Bronze Age sample from burials of the Caucasian burial ground Klady, prepared using three different approaches: (1) shotgun sequencing, (2) strategies for selecting target genomic regions, and (3) strategies for selecting target genomic regions, including DNA pre-treatment with a mixture of uracil-DNA glycosylase (UDG) and endonuclease VIII. The impact of the studied approaches to genomic library preparation on the results of a secondary analysis of the statistical data, namely F4 statistics, ADMIXTURE, and principal component analysis (PCA), was analyzed. It was shown that preparation of genomic libraries without the use of UDG can result in distorted statistical data due to postmortem chemical modifications of the aDNA. This distortion can be alleviated by analyzing only the single nucleotide polymorphisms caused by transversions in the genome.

Unusual congenital polydactyly in mini-pigs from the breeding group of the Institute of Cytology and Genetics (Novosibirsk, Russia).

The article describes a new phenomenon in the breeding group of mini-pigs at the Institute of Cytology and Genetics (ICG, Novosibirsk): polydactyly (extra digits), which is unusual because the additional digits are situated at the lateral surface of legs or at the lateral and medial ones. This anomaly was f irst found here in 2017 in adult animals intended for culling due to incorrect positioning of the legs caused by f lexor tendon laxity and resulting in weight-bearing on the palmar surface of the proximal phalanges ("bear's paw"). Therefore, the polydactyly of mini-pigs has a pronounced negative selection effect. A visual survey of the livestock was conducted, and a description of the detected anomaly was compiled. The polydactyly in mini-pigs is a stand-alone trait and is not part of any syndromes. Individuals with polydactyly may have extra digits either on pectoral or on pectoral and pelvic limbs. On thoracic limbs, there may be either one lateral digit or a lateral digit and a medially located rudimentary hoof let. On pelvic limbs, only lateral extra digits can occur. Anatomical and morphological analyses showed that the lateral extra digit is an anatomically complete ("mature") structure, whereas the medial rudimentary digit consists of only a hoof let without other structures characteristic of normal digits. Cytological examination revealed no specif ic karyotypic features, except for Robertsonian translocation Rb 16;17 previously reported for the mini-pigs of the same livestock. Cytological f indings indicated that the polydactyly and Robertsonian translocation are not linked genetically. Genealogical analysis and results of crosses are consistent with a working hypothesis of recessive inheritance of the trait. Overall, the study shows that this type of polydactyly is anatomically and morphologically unique and not typical of Sus scrofa. In this species, only polydactyly types with medial accessory toes have been described and are usually inherited as a dominant trait with incomplete penetrance. In our case, the results of test crosses indicate recessive inheritance of the trait with varying expression and incomplete penetrance, because of which poorly expressed phenotypes are not visually detectable.

Mitochondrial DNA analysis of ancient sheep from Altai.

A comparative analysis of the genetic diversity of ancient and modern sheep can shed light on the origin of these animals and their distribution as well as help to evaluate the role of humans at each formation stage of different sheep breeds. Here we isolated ancient DNA and performed sequencing of the mitochondrial DNA D-loop from 17 sheep bone remains (~4000-1000 years old) found in the archaeological complexes in the south of Altai (Western Siberia). The length of the sequences obtained ranged between 318 and 586 bp. The haplotype diversity and nucleotide diversity were 0.801 ± 0.081 and 0.0096 ± 0.0014 respectively. The average number of nucleotide differences was ~3.1. Nucleotide sequence analysis revealed that 15 specimens were nested within previously described A,B,C,D and E lineages and that two specimens had a basal position relative to the rest of the analyzed samples. A relatively high diversity of sheep haplotypes, including the presence of two basal haplotypes, indicates that the Altai region may have been a transport route of human migration. Further ancient DNA analysis of other specimens and deeper genome sequencing of samples with novel haplotypes is needed to better understand the demographic history of sheep in Southern Siberia.

The origin of B chromosomes in yellow-necked mice (Apodemus flavicollis)-Break rules but keep playing the game.

B chromosomes (Bs) are known for more than hundred years but their origin, structure and pattern of evolution are not well understood. In the past few years new methodological approaches, involving isolation of Bs followed by whole DNA amplification, DNA probe generation, and fluorescent in situ hybridization (FISH) or the B chromosome DNA sequencing, has allowed detailed analysis of their origin and molecular structure in different species. In this study we explored the origin of Bs in the yellow-necked wood mouse, Apodemus flavicollis, using generation of microdissected DNA probes followed by FISH on metaphase chromosomes. Bs of A. flavicollis were successfully isolated and DNA was used as the template for B-specific probes for the first time. We revealed homology of DNA derived from the analyzed B chromosomes to the pericentromeric region (PR) of sex chromosomes and subtelomeric region of two pairs of small autosomes, but lower homology to the rest of the Y chromosome. Moreover, all analysed Bs had the same structure regardless of their number per individual or the great geographic distance between examined populations from the Balkan Peninsula (Serbia) and Eastern Europe (south region of Russia and central Belarus). Therefore, it was suggested that B chromosomes in A. flavicollis have a unique common origin from the PR of sex chromosomes, and/or similar evolutionary pattern.

New insights into sex chromosome evolution in anole lizards (Reptilia, Dactyloidae).

Anoles are a clade of iguanian lizards that underwent an extensive radiation between 125 and 65 million years ago. Their karyotypes show wide variation in diploid number spanning from 26 (Anolis evermanni) to 44 (A. insolitus). This chromosomal variation involves their sex chromosomes, ranging from simple systems (XX/XY), with heterochromosomes represented by either micro- or macrochromosomes, to multiple systems (X1X1X2X2/X1X2Y). Here, for the first time, the homology relationships of sex chromosomes have been investigated in nine anole lizards at the whole chromosome level. Cross-species chromosome painting using sex chromosome paints from A. carolinensis, Ctenonotus pogus and Norops sagrei and gene mapping of X-linked genes demonstrated that the anole ancestral sex chromosome system constituted by microchromosomes is retained in all the species with the ancestral karyotype (2n = 36, 12 macro- and 24 microchromosomes). On the contrary, species with a derived karyotype, namely those belonging to genera Ctenonotus and Norops, show a series of rearrangements (fusions/fissions) involving autosomes/microchromosomes that led to the formation of their current sex chromosome systems. These results demonstrate that different autosomes were involved in translocations with sex chromosomes in closely related lineages of anole lizards and that several sequential microautosome/sex chromosome fusions lead to a remarkable increase in size of Norops sagrei sex chromosomes.

Highly conserved Z and molecularly diverged W chromosomes in the fish genus Triportheus (Characiformes, Triportheidae).

The main objectives of this study were to test: (1) whether the W-chromosome differentiation matches to species' evolutionary divergence (phylogenetic concordance) and (2) whether sex chromosomes share a common ancestor within a congeneric group. The monophyletic genus Triportheus (Characiformes, Triportheidae) was the model group for this study. All species in this genus so far analyzed have ZW sex chromosome system, where the Z is always the largest chromosome of the karyotype, whereas the W chromosome is highly variable ranging from almost homomorphic to highly heteromorphic. We applied conventional and molecular cytogenetic approaches including C-banding, ribosomal DNA mapping, comparative genomic hybridization (CGH) and cross-species whole chromosome painting (WCP) to test our questions. We developed Z- and W-chromosome paints from T. auritus for cross-species WCP and performed CGH in a representative species (T. signatus) to decipher level of homologies and rates of differentiation of W chromosomes. Our study revealed that the ZW sex chromosome system had a common origin, showing highly conserved Z chromosomes and remarkably divergent W chromosomes. Notably, the W chromosomes have evolved to different shapes and sequence contents within ~15-25 Myr of divergence time. Such differentiation highlights a dynamic process of W-chromosome evolution within congeneric species of Triportheus.

Mitochondrial DNA D-loop haplogroup contributions to the genetic diversity of East European domestic chickens from Russia.

To elucidate geographical and historical aspects of chicken dispersal across Eastern Europe, we analysed the complete mitochondrial DNA D-loop sequence of 86 representatives from chicken breeds traditionally raised in the territory of the East European Plain (Orloff, Pavlov, Russian White, Yurlov Crower, Uzbek Game and Naked Neck). From the 1231-1232 bp D-loop sequence, 35 variable sites that defined 22 haplotypes were identified in modern chicken. All populations, except Uzbek Game, exhibited high values of haplotype and nucleotide diversity suggesting a wide variation in maternal diversity. Inclusion of mtDNA sequences from other European and Asian countries revealed representatives from this study belonging to haplogroups A, E1 and C1. We also assessed fossil chicken material dated to the 9th-18th century from archaeological sites in Northern and Eastern Europe. Three haplotypes found in the fossil specimens belonged to haplogroup E1, while one sample dated to the 18th century was assigned to the C1 haplogroup. This is the first report of the occurrence of the C1 haplogroup in European chicken populations prior to the 20th century based on the fossil material. These results provide evidence for a relatively recent introduction of all haplotypes other than E1 into the East European chicken gene pool with the significant impact of the C1 haplogroup mainly distributed in Southern China.

DIVERSITY OF SEX DETERMINING MECHANISMS IN RAY-FINNED FISHES (ACTINOPTERYGII).

Ray-finned fishes (Actinopterygii) is a very diverse and numerous clade of vertebrates. Besides the diversity of ecological niches and morphology, species of this clade have substantial differences in mechanisms of sex determination. Unfortunately, our modern knowledge about sex determining mechanisms is limited to a small number of species. Even from the modest number of published works on this topic it is obvious that evolution of sex determining system in ray-finned fishes is very plastic: in some closely related species sex systems can be significantly different, there are taxa with quite conservative systems, and the same genomic loci may play sex determination role independently in various groups. Such diversity allows considering ray-finned fishes to be used as a convenient model taxon for researching emergence and development of different sex determining systems.

[ANESTHESIA FOR AIRWAY ENDOSCOPIC RECANALISATION WITH SELFEXPANDED STENTS].

UNLABELLED: Tracheal and bronchial endoscopic stenting can give a quick therapeutic result or delay surgiCal treatment of patients with stenosis. It also can improve quality of life, create conditions for palliative therapy and increase survival of incur- able oncological patients. This paper contains description of our experience in anesthesia for tracheal stenting with re- spiratory support. MATERIALS AND METHODS: 23 patients were investigated retrospectively (15 males, 8females). They had 28 interventions under general anesthesia. 14 patients had malignant and 9 had non-malignant lesions. Complicated somatic status, stenosis extention and localization, type of laryngoscope. unprotected airways determined choice of in- travenous anesthesia with high-frequency ventilation and muscle relaxation. RESULTS: Improvement (dyspnea decreasing) was mentioned in 78,3% (18/23) cases after stenting, in 8,7% (2/23) cases improvement was slight; in 4,3% (1/23) cases - no change; in 8,7% (2/23) cases patients died complications after stenting occurred in 10 cases (43,5%). In 4 cases (17,4%) - stent displacement; in 2 cases (8,7%) - purulent tracheobronchitis; in 1 case (4,35%) - paroxysmal cough with pain. In 1 case loss of stent during paroxysmal cough and vocal cords edema occurred. In 2 cases (8,7%) operation was failed and patients died due to the lesion progression and respiratory insufficiency. CONCLUSIONS: Anesthetic pro- tection is an important component at endoscopic recanalization with selfexpanded stents. Management is difficult due to complicated somatic status, and unprotected airways. Significant health enhancement, dyspnea decreasing even by exercise stress justified high anesthetics risks.

[Ancient DNA: Results and Prospects (the 30th Anniversary)].

Evolutionary genetics has reached a new level of research thanks to the opportunity to study the genomes of not only present-day but also of ancient organisms. The obtaining of reliable data when working with ancient DNA is possible only in the case of interdisciplinary collaboration between archaeologists, paleontologists, molecular geneticists, and bioinformaticians. Despite laborious and high-cost technologies, the results never cease to amaze and can not only fill the gaps in the knowledge of the evolutionary history of different species but can also review the existing ideas on population development and dynamics. In this review, we discuss the history of the development of investigative techniques in ancient DNA research and the most striking results of these studies, including the most recent achievements.

[DYNAMICS OF APOPTOTIC MARKERS (INTERLEUKIN-2 AND TNF-α) IN THE BLOOD SERUM OF CHILDREN WITH CHRONIC GASTRODUODENITES].

UNLABELLED: The aim was to investigate apoptotic dynamics by IL-2 and TNF-α levels in the blood serum of children with chronic gastroduodenites. MATERIALS AND METHODS: There were examined 90 children with chronic gastroduodenitis. Cytokine level in the serum was studied at admission and in dynamics. RESULTS: Chronic gastroduodenitis is accompanied by the increase of IL-2 and TNF-α concentration thus reflecting the activity of apoptotic processes. The decrease of the markers' (IL-2 and TNF-α) levels after 10-11 days, 3 and 9 months after treatment indicates the decrease of apoptotic activity. In hyperplastic and atrophic gastritis there has been registered the highest and the lowest concentration of the markers, respectively. H. pylori contributes to the TNF-α production mainly.

[The program of accelerated rehabilitation after esophagoplasty (fast track surgery) in esophageal cancer surgery].

Esophagectomy with simultaneous plasty in patient with esophageal cancer is still associated with a high incidence of postoperative complications and long-stay patient in the clinic. The purpose of our report is to inform the use of the program of accelerated rehabilitation after esophagectomy in a prospective study of 13 patients during the period from 2010 to 2011 year and the role of the anesthesiologist in its implementation. Methods aimed at the preoperative examination, minimally invasive surgery, thoracic epidural anesthesia/analgesia with local anesthetics as a component of anesthesia and postoperative analgesia, early extubation and mobilization of the patient with the implementation of breathing exercises, early enteral feeding, and the planned short postoperative stay in resuscitation and hospital were used. Postoperative complications were observed in 3 (23/1%) patients: one patient (7/7%) had right-side pneumonia, two patients (15/4%) had right-side pneumothorax requiring emergency re drainage. The average intensive care stay was 2 (1-4) days, postoperative hospital stay--9 (7-12) days. Further monitoring of the patients did not show any long-term complications. The results confirm that it is possible to optimize the healing perioperative process in patients after esophagectomy with simultaneous plasty by using of accelerated rehabilitation program without the risk of increasing the frequency of postoperative complications. it will provide the reduction of length of hospital stay. In view of multifaceted and controversial issue the following researches in this direction are necessary.

Independent sex chromosome evolution in lower vertebrates: a molecular cytogenetic overview in the Erythrinidae fish family.

The Erythrinidae fish family is an excellent model for analyzing the evolution of sex chromosomes. Different stages of sex chromosome differentiation from homomorphic to highly differentiated ones can be found among the species of this family. Here, whole chromosome painting, together with the cytogenetic mapping of repetitive DNAs, highlighted the evolutionary relationships of the sex chromosomes among different erythrinid species and genera. It was demonstrated that the sex chromosomes can follow distinct evolutionary pathways inside this family. Reciprocal hybridizations with whole sex chromosome probes revealed that different autosomal pairs have evolved as the sex pair, even among closely related species. In addition, distinct origins and different patterns of differentiation were found for the same type of sex chromosome system. These features expose the high plasticity of the sex chromosome evolution in lower vertebrates, in contrast to that occurring in higher ones. A possible role of this sex chromosome turnover in the speciation processes is also discussed.

[Clinical case of amyotrophic lateral sclerosis management and treatment in the non-core clinic].

The article points out the problems of amyotrophic lateral sclerosis (ALS) diagnostics, management and treatment in the non-core clinic (oncological dispensary intensive care unit). There is no legislative base for medical and social protection of patients with ALS in Russia. Article stresses the need to attract the attention of Ministry of healthcare of Russia to this problem.

[Genomic structure and sex determination in squamate reptiles].

Squamata is the largest reptilian order including snakes and lizards which occupies a key position in phylogeny of amniotes. A variety of sex determination modes in lizards is one of the most interesting parts of the biology of this order. These mechanisms are genomic sex determination (both XY and ZW systems) and temperature-dependent sex determination. Studies of squamata sex chromosomes are pivotal for understanding evolution of other vertebrate sex chromosomes. Unfortunately, this clade has long been neglected by molecular geneticists. In this paper, we describe recent data on molecular cytogenetics and genomics of squamates, evolution of their sex chromosomes and sex determination mechanisms.

Murine multicolor banding.

Multicolor banding approach, first introduced for human chromosomes only, was established as an optimal approach for karyotyping of murine chromosomes. Here we present the established mcb probe sets for all murine autosomes and the X-chromosome and review their potential application.

[The ruptures of the trachea with the intubation tube in patients with esophagus cancer].

Postintubation tracheal ruptures is a rare but serious complication with high risk for the patient's life. The preliminary diagnosis is usually made after occurrence of subcutaneous emphysema, blood spitting, respiratory insufficiency, pneumothorax and/or pneumomediastinum. The suspected rupture of the trachea should be verified by fiber-optic bronchoscopy. The decision about necessity of surgical or conservative treatment is based on the compilation of clinical, radiologic and endoscopic data. We present 9 cases (7 women and 2 men) of postintubation tracheal ruptures, occurred during the esophageal (6), lung (2) and mammary gland (1) surgery.

Chromosome evolution in Perissodactyla.

Comparative painting has provided a wealth of useful information and helped to reconstruct the pathways of karyotype evolution within major eutherian phylogenetic clades. New data have come from gene localizations, BAC mapping and high throughout sequencing projects that enrich and provide new details of genome evolution. Extensive research on perissodactyl genomes has revealed not only increased rates of chromosomal rearrangements, but also an exceptionally high number of centromere repositioning events in equids. Here were combined new physical mapping, comparative painting and genome sequencing data to refine the putative ancestral karyotype maps and to revise the previously proposed scenario of perissodactyl karyotype evolution.

Chromosomal evolution in Rodentia.

Rodentia is the most species-rich mammalian order and includes several important laboratory model species. The amount of new information on karyotypic and phylogenetic relations within and among rodent taxa is rapidly increasing, but a synthesis of these data is currently lacking. Here, we have integrated information drawn from conventional banding studies, recent comparative painting investigations and molecular phylogenetic reconstructions of different rodent taxa. This permitted a revision of several ancestral karyotypic reconstructions, and a more accurate depiction of rodent chromosomal evolution.

Karyotype evolution of eulipotyphla (insectivora): the genome homology of seven sorex species revealed by comparative chromosome painting and banding data.

The genus Sorex is one of the most successful genera of Eulipotyphla. Species of this genus are characterized by a striking chromosome variability including XY1Y2 sex chromosome systems and exceptional chromosomal polymorphisms within and between populations. To study chromosomal evolution of the genus in detail, we performed cross-species chromosome painting of 7 Sorex species with S. granarius and S. araneus whole-chromosome probes and found that the tundra shrew S. tundrensis has the most rearranged karyotype among these. We reconstructed robust phylogeny of the genus Sorex based on revealed conserved chromosomal segments and syntenic associations. About 16 rearrangements led to formation of 2 major Palearctic groups after their divergence from the common ancestor: the S. araneus group (10 fusions and 1 fission) and the S. minutus group (5 fusions). Further chromosomal evolution of the 12 species inside the groups, including 5 previously investigated species, was accompanied by multiple reshuffling events: 39 fusions, 20 centromere shifts and 10 fissions. The rate of chromosomal exchanges upon formation of the genus was close to the average rate for eutherians, but increased during recent (about 6-3 million years ago) speciation within Sorex. We propose that a plausible ancestral Sorex karyotype consists of 56 elements. It underwent 20 chromosome rearrangements from the boreoeutherian ancestor, with 14 chromosomes retaining the conserved state. The set of genus-specific chromosome signatures was drawn from the human (HSA)-shrew comparative map (HSA3/12/22, 8/19/3/21, 2/13, 3/18, 11/17, 12/15 and 1/12/22). The syntenic association HSA4/20, that was previously proposed as a common trait of all Eulipotyphla species, is shown here to be an apomorphic trait of S. araneus.