Biomedical subjects

G N Chelomina

Publications and source records attributed to G N Chelomina.

18 recordsLinked to original sources

PubMed2006

[Ancient DNA].

The review is devoted to molecular genetic studies of ancient DNA. The problems of DNA preservation and modification after cell death, as well as techniques of working with ancient DNA, including its retrieval, removal of inhibitors, PCR amplification, and phylogenetic analysis, are discussed in detail. The possibilities are considered of using ancient DNA in resolving issues of systematics and evolution of various animal taxa, population genetics of humans and rare species, taxonomic identification and paleontological reconstructions, geographic origin of populations, microbiological analysis of paleontological and archeological finds, as well as some humanitarian aspects of its use.

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PubMed2006

[Genetic evidence of hybridization between paletailed Spermophilus pallidicauda Satunin, 1903 and alashanic S. alaschanicus Buchner, 1888 ground squirrels in Mongolia].

Analysis of Spermophilus pallidicauda Satunin, 1903 from three localities in Mongolia using cytogenetic characteristics (chromosome number and morphology, as well as the number and localization of nucleolus organizer regions) revealed the presence of a first-generation (F1) hybrid animal (2n = 36), of the paletailed S. pallidicauda (2n = 34) and alashanic S. alaschanicus (2n = 38) ground squirrels in the contact zone of their ranges. Analysis of nuclear DNA from ten ground squirrels (from a set of karyologically examined animals) by RAPD-PCR with eight oligonucleotide primers (OPA10, OPA12, OPC02, OPC5, OPC08, OPC09, OPC12, and OPD05) revealed four hybrids in two sites. with one of the hybrid being F1. The position of the hybrids in phylogenetic reconstructions made for the subgenera Citellus and Colobotis species varied depending on the method used. In the UPGMA dendrogram of genetic similarity hybrids formed their own subcluster with high bootstrap index (949) within the cluster of Citellus species. In the NJ phylogenetic tree, hybrids also clustered with high boot-strap index (886). But in this case they were located between the Colobotis and Citellus species clusters. The mtDNA haplotypes of the three hybrids examined were highly similar to the Colobotis ground squirrels, albeit in phylogenetic reconstructions they were placed between Colobotis and Citellus. The sites of the hybrid animals identification were located more than 200 km apart. Hence, the contact zone between the S. pallidicauda and S. alaschanicus can encompass a large territory in Mongolia.

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PubMed2006

[Genetic evidence of extensive introgression of short-tailed ground squirrel genes in a hybridization zone of Spermophilus major and S. erythrogenys, inferred from sequencing of the mtDNA cytochrome b gene].

We have completely sequenced the mtDNA cytochrome b gene of ground squirrels from the zone of overlapping ranges of Spermophilus major and S. erythrogenys in the Tobol-Ishim interfluve, which is a putative hybridization zone of these species. The results of the sequencing showed extensive introgression of mtDNA genes of the short-tailed ground squirrel S. e. brevicauda, whose haplotype had fully replaced the S. major haplotype. All of the ground squirrels from the Tobol-Ishim interfluve had a variant of the S. e. brevicauda mtDNA haplotype that was specific for this zone. On average, 119 substitutions (10.44%) were found between S. major from Ul'yanovsk oblast and S. e. brevicauda from the northern Kazakhstan, the mean genetic distance (D) between them being 0.115, which conforms to the corresponding parameters for the S. e. brevicauda-S. pygmaeus pair (122 substitutions, D = 118). Insignificant differences (seven substitutions, D = 0.043) were found between the S. major and S. pygmaeus haplotypes, which suggest that these species have similar mitochondrial haplotypes. Five to ten nucleotide substitutions (0.44--0.88%) were detected between the animals from the Tobol--Ishim interfluve and S. e. brevicauda. The mtDNA haplotype divergence D within the genus Spermophilus (ten species) for all codon positions ranged from 0.035 to 0.158. Phylogenetic reconstructions (MP, ML, and NJ trees) showed two well-differentiated clusters with high bootstrap support. However, there was different branching topology within the cluster and their species composition varied. The maximum likelihood tree, ML, differentiating the species into two subgenera, Citellus and Colobotis, most reliably reflected taxonomic relationships of the species from the genus Spermophilus, inferred from morphological and genetic biochemical data. The morphologically pure S. major (subgenus Colobotis) animals, used in the analysis, proved to carry the haplotype of another species, S. pygmaeus (subgenus Citellus). This poses a question on the existence of the specific haplotype of S. major, the reason of its replacement by haplotype of other species, and possible consequences of this phenomenon for survival of the species.

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PubMed2005

[RAPD-PCR analysis of ground squirrels from the Tobol-Ishim interfluve: evidence for interspecific hybridization between ground squirrel species Spermophilus major and S. erythrogenys].

Populations of two ground squirrel species, Spermophilus major and S. erythrogenys, from the interfluvial area of the Tobol and Ishim rivers, where their ranges overlap, have been examined using RAPD-PCR. We have identified 253 loci, which included taxon-specific markers for S. major and S. erythrogenys as well as markers for geographic populations. Estimation of genetic diversity and construction of phylogenetic relationships were performed using software programs POPGENE, TEPGA, and TREECON. In all, based on morphological traits, animals from the Tobol-Ishim interfluve were assigned to the two parental morphotypes and showed similar levels of genetic variability (H, n(a), n(e)). However, the total polymorphism level proved to be higher in ground squirrels with the major morphotype (P = 40.32%, P95 = 27.27%) than in animals with the erythrogenys morphotype (P = 32%, P95 = 22.13%). Nevertheless, the number of rare alleles was high in both cases, constituting about 70% of the total number. By contrast, interpopulation differentiation was considerably higher in S. major (6 = 0.50) than in S. erythrogenys (delta = 0.41). The genetic differentiation between local samples from the Tobol-Ishim interfluvial area was lower than that between the parental species. A significant part of the genetic diversity of the species examined and animals from the zone of overlapping ranges was accounted for by intrapopulation variability. Animals from the northern and southern parts of the Tobol-Ishim interfluve were characterized by the core traits of S. major and S. erythrogenys, respectively, falling into two distinct clusters in the UPGMA and NJ reconstructions. In addition to three hybrid individuals, identified by the bioacoustic method, three hybrid animals were distinguished using RAPD analysis. These animals earlier were thought to be "pure" species and formed their own clusters in phylogenetic reconstructions. Thus, the RAPD-PCR results directly showed the existence of stable hybridization (20% genetic hybrids) between S. major and S. erythrogenys in the Tobol-Ishim interfluvial area, which is more extensive than inferred previously from morphological and bioacoustic data.

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PubMed2004

[Genetic and taxonomic diversity of the house mouse Mus musculus from the asian part of the former Soviet Union].

Genetic diversity of the house mouse Mus musculus from 12 local populations (n = 65) of the central and eastern parts of the former Soviet Union was examined using RAPD-PCR. About 400 loci were identified, encompassing approximately 500 kb of the mouse genome. Genetic diversity was assessed using NTSYS, POPGENE, TFPGA, and TREECON software programs. In general, the house mouse sample from the regions examined was characterized by moderate genetic variation: polymorphism P = 95.6%, P99 = 60.7%, P95 = 24.2%; heterozygosity H = 0.089; the mean observed number of alleles n(a) = 1.97; effective number of alleles n = 1.13; intrapopulation differentiation deltaS = 0.387; gene diversity h = 0.09. Individual local populations displayed different levels of genetic isolation: the genetic subdivision index G(st) varied from 0.086 to 0.324 at gene flow Nm varying from 5.3 to 1.05, while the interpopulation genetic distance D(N) ranged from 0.059 to 0.186. Most of the genetic diversity of the total sample resided within the local populations: H(S) = 0.6, total gene diversity H(T) = 0.09. The exact test for differentiation, however, did not confirm the affiliation of all the mice examined to one population: chi2 = 1446, d.f. = 724, P = 0.000. Molecular markers specific to four subspecies (musculus, castaneus, gansuensis, and wagneri) were identified. Moreover, in some cases the populations and individual animals exhibited traits of different subspecies, suggesting their introgressive hybridization. It was demonstrated that the house mouse fauna on the territories investigated was characterized by the prevalence of musculus-specific markers, while gansuensis-specific markers ranked second. The castaneus-specific markers were highly frequent in the Far East, but almost absent in Central Asia, where wagneri-specific markers were detected. It was suggested that house mice from Turkmenistan could belong to one of the southern subspecies, which had not deeply penetrated into the Asian fauna of the former Soviet Union. In phenogenetic (UPGMA) and phylogenetic (NJ) reconstructions this form with the high bootstrap support was placed at the tree base, while the isolation of other clusters was not statistically significant. It is thus likely that the house mice from Turkmenistan are closest to the ancestral form of the genus Mus on the territory of the former Soviet Union.

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PubMed2003

[Low genetic differentiation and close evolutionary connection between Anas platyrhynchos and Anas poecilorhyncha: data from RAPD-PCR analysis].

Using RAPD-PCR, we examined genetic diversity and phylogenetic relationships in two groups of river ducks: Anas platyrhynchos, A. poecilorhyncha, A. strepera and A. crecca, A. formosa, A. querquedula. Molecular taxon-specific markers were found for teals (A. crecca, A. formosa, A. querquedula) and gadwall (A. strepera). Each of the species examined was shown to exhibit high genetic diversity. The mean levels of intraspecific genetic polymorphism in the groups of mallards (P = 77%) and teals (P = 74.5%) were approximately equal whereas the mean interspecific genetic distances in teals were significantly higher than in mallards (D = 0.432 and D = 0.336, respectively). The levels of interspecific genetic differentiation in the species groups were also different. The genetic distances between the teal species and between gadwall and mallards were equal to 0.668-0.971 while the genetic distance between mallard A. platyrhynchos and spot-billed duck A. poecilorhyncha was 0.401, which slightly exceeds the intraspecific values for mallards (0.356-0.377). The RAPD patterns for this species pair showed high variability and a lack of fixed differences. This was adequately reflected on both intra- and interspecific differences and on phylogenetic constructions in which the morphological species did not form their own clusters but were intermixed. In contrast to mallards, the other species, which showed high genetic variability, were reliably separated in phenogenetic and phylogenetic reconstructions. The possible explanations of the low genetic differentiation of A. platyrhynchos and A. poecilorhyncha are discussed.

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PubMed2003

[Genetic diversity of carrion and jungle crows from RAPD-PCR analysis data].

RAPD-PCR analysis of the genetic diversity of the carrion crow (Corvus corone) and jungle crow (C. macrorhynchos) living in the continental parts of their species ranges and on some Russian and Japanese Far Eastern islands has been performed. Taxon-specific molecular markers have been found for each species. The genetic diversity of the carrion crow is considerably less than that of the jungle crow at the same genetic distance (P95 = 68.2%, DN = 0.27 and P95 = 88.4%, DN = 0.24, respectively). In both species, the genetic polymorphism of island samples is almost two times greater than that of continental samples (62 and 31.8%, respectively, for C. corone and 81.5 and 47.2%, respectively, for C. macrorhynchos). In addition, differences in genetic diversity between males and females (P95 = 55.1 and P95 = 72.1, respectively) has been found in the carrion crow but not in the jungle crow. The gene diversity of C. macrorhynchos is greater than that of C. corone: the mean numbers of alleles per locus are 2 and 1.81, effective numbers of alleles are 1.62 and 1.43, and the mean expected heterozygosities are 0.39 and 0.30, respectively. The phenograms and phylograms significantly segregate the clusters of the carrion and jungle crows. The clustering patterns of carrion crows corresponds to the intraspecies taxonomic and geographic differentiation: subspecies C. c. corone and C.c. orientalis living in the western and eastern parts of the species range, respectively, form different subclusters. The cluster of the jungle crow does not exhibit differentiation into subspecies C. m. mandshuricus and C. m. japonensis; molecular genetic differences between them are small.

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PubMed2002

[RAPD-PCR analysis of genetic diversity in the Manchurian pheasant].

The genetic diversity of a local population of the Manchurian pheasant Phasianus colchicus pallasi was studied using RAPD-PCR. Based on the DNA patterns obtained in PCR with five arbitrary decanucleotide primers, we assessed genetic polymorphism of this population, estimated genetic distances between individuals, and constructed an NJ phylogenetic tree, and an UPGMA dendrogram of genetic similarity. The population was shown to exhibit high average genetic polymorphism (P = 79.4%) and genetic distances (D = 0.267). Possible reasons for the high genetic diversity of this local population are discussed.

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PubMed2000

[Isolation of DNA from museum exhibits of butterflies (Lepidoptera, Papilionidae) and PCR analysis with random and universal genes-specific primers].

The effect of the duration of storage of entomological material on DNA preservation was estimated. The results of the optimization of conditions for the analysis of random amplified polymorphic DNA in a polymerase chain reaction (RAPD-PCR) are presented as applied to the DNA of lepidopterans of the family Papilionidae. RAPD patterns are shown for the first time in Atrophaneura alcinous and four species of the genus Parnassius (sensu lata). The applicability of museum specimens of butterflies for RAPD analysis was demonstrated. The results of PCR analysis using DNA obtained from different collection specimens stored for up to five years were compared. The authenticity of DNA obtained from collection specimens was proved using PCR with universal primers, which are specific to the COI and COII cytochrome genes of mitochondrial DNA (mt DNA). The lengths of individuals gene fragments obtained by the amplification of both museum and live specimens were 800 and 1600 bp. The conservative regions of mitochondrial genome were shown to be slightly different in two A. alcinous subspecies.

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PubMed1999

[Use of RAPD-PCR-analysis of cellular DNA for the evaluation of genetic polymorphism and subspecies diagnostics of the Far Eastern leopard Panthera pardus orientalis].

Genetic polymorphism in the Far-Eastern leopard subspecies Panthera pardus orientalis was examined by RAPD-PCR analysis of total cellular DNA. Primers diagnostic for the leopard subspecies were detected. These primers can be used for differentiating wild-living animals from those kept in captivity and distinguishing different breeding lines. Genetic diversity was shown to be lower in animals from the zoo (D = 0.058) and higher in a natural population (D = 0.137). Two lines of the Persian subspecies were genetically closest (D = 0.042), and the Persian and Far-Eastern subspecies represented by wild animals, genetically most remote (D = 0.274). The level of genetic divergence of the Persian subspecies and Far-Eastern subspecies (zoo animals) was lower (D = 0.108) than between representatives of the Persian subspecies from the captive and natural population (D = 0.220). On the basis of analysis of relatedness, performed using NTSYS and PHYLIP software packages, the possibility cannot be excluded that some P. p. orientalis animals from the zoo have a hybrid origin and may be assigned to another Far-Eastern subspecies.

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PubMed1998

[Genetic differentiation of Caucasian wood mice: comparison of isozymic, chromosomal and molecular divergence].

Data on the complex genetic analysis of three sympatric species of Caucasian wood mice, Apodemus ponticus, A. fulvipectus, and A. uralensis are presented. A high degree of genetic differentiation at the isozymic, karyological and molecular (nuclear DNA) levels was revealed. The genetic distances between each pair of species varied significantly within a wide range depending on the analyzed level of the organization of genetic material. Mean values of genetic divergence from one species to another were also variable. These findings indicated that evolution of chromosomes was slower than that of isozymes, and the degree of species divergence was similar on cytogenetic and molecular levels. They also suggested that the rates of species evolution could vary in different phyletic lineages and on different levels of organization. Some phyletic lineages of Apodemus could be distinguished by different directions of evolution.

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PubMed1998

[Sequencing of the mtDNA cytochrome b gene and reconstruction of the matriarchal relationships between wood and field mice of the genus Apodemus (Muridae, Rodentia)].

The primary sequence of a 402-bp part of the cytochrome b gene was determined in nine species of wood and field mice of the genus Apodemus. The majority of mutations were synonymous. The total number of transitions exceeded than of transversions. Among all substitutions, C-T transitions prevailed (51%); the most common substitution type in genus-specific sites was C-A transversions (42%). In interpopulation analysis, only transitions were recorded. A phylogenetic tree, constructed with the use of the neighbor-joining method, showed that the genus Apodemus is divided into three highly divergent groups: south Asian (Apodemus argenteus, A. semotus), east Asian (A. speciosus, A. agrarius), and Eurocaucasian (A. sylvaticus, A. flavicollis, A. uralensis, A. ponticus, A. flavipectis). The mean genetic distances within each group were 12.6, 11.2, and 8.8%, respectively. The species of the first group are more remote genetically and ancestrally with regard to the other groups. The interspecies divergence estimated for A. speciosus ranged from 0.25 to 3.75%. Thus, the evolutionary age of the genus Apodemus is about 6 Myr, and time of divergence of A. speciosus populations is 0.1-1.5 Myr. The phylogeny inferred from the data on the sequence of the cytochrome b gene in Apodemus mtDNA is somewhat different from similar phylogenies based on other genetic data and from the zoological taxonomy of wood and field mice. However, the above classification of species is confirmed by features of their karyotypes and segmentation of satDNA, and by the RFLP of total nDNA and isozyme polymorphism. Our results are in good agreement with the new classification of wood and field mice recently proposed by Russian zoologists.

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PubMed1998

[Molecular phylogeny of forest and field mice of the genus Apodemus (Muridae, Rodentia) based on the data on restriction analysis of total nuclear DNA].

Based on restriction-fragment length polymorphism (RFLP) of total nuclear DNA (nDNA), analyses of phylogenetic relations and genetic similarity were performed in nine species of forest and field mice of the genus Apodemus. Genetic distances calculated for different species pairs ranged from 0.24 to 12.53%; i.e., the differences were 50-fold. The estimated evolutionary age of the genus Apodemus is approximately 12 million years. In general, the obtained data on genetic similarity and phylogenetic relationship allow us to differentiate at least three groups of species: (1) southern Paleoarctic (A. argenteus), (2) eastern (A. peninsulae, A. speciosus, and A. agrarius), and (3) western (A. sylvaticus, A. flavicollis, A. ponticus, A. uralensis, and A. fulvipectus) ones. The latter two groups are related to the northern Paleoarctic. Such a division into groups corresponds to characteristic features of karyotype organization and segmentation of satellite DNA (satDNA) of these species, as well as the nature of variation in isozymes and in a fragment of the enzyme-encoding sequence of cytochrome b gene isolated from the mitochondrial genome. Species groups (1) and (3) exhibited a high probability of a monophyletic origin (70 and 99%, respectively). Group (2) is unlikely to be monophyletic, and the genetic distances in it are significantly greater than those in group 3. A. argenteus is the most diverged, both phenogenetically and phylogenetically. The data are consistent with a new zoological classification, which assumes the division of the unified genus Apodemus into two taxa of generic rank and suggest that the southern Paleoarctic forest mouse should be regarded as a separate taxon of at least subgeneric rank.

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PubMed1996

[DNA restriction polymorphism in European and Asiatic species of wood mice of the genus Apodemus].

Comparative restriction analysis of genomic DNA from six wood mice species of the genus Apodemus as well as from the house mouse Mus musculus and a Norway rat Rattus norvegicus was conducted by means of AluI, TagI, Csp6I, and BglII endonucleases. The data from RFLP and UPG analyses allowed division of all the forms studied into two groups, evolutionarily young and old, including European (sylvaticus, flavicollis, and microps) and Asiatic (peninsulae, speciosis, and agrarius, together with the striped field mouse) wood mice species, respectively. The first group is characterized by low interspecies and intragenomic RFLPs of the repeated DNA sequences, while these indices were higher in the second group. The interspecies genetic distances averaged around 1.2% within the first group, around 5.88% within the second group, and around 9.49% between the groups. The divergence of A. agrarius from the Asiatic species of wood mice was 5.33%, twofold lower than divergence from the European species (9.17%).

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PubMed1995

[Molecular-genetic typing of three representatives of the transpalearctic species of forest and field mice (Apodemus, Muridae, Rodentia)].

The genomes of three species of wood mouse (Apodemus falzfeini and A. ponticus from the Caucasus and A. argenteus from Japan) were compared by means of restriction analysis of nuclear DNA. The species are differentiated from each other and from previously studies species. Each species has its species-specific features. Within the genus Apodemus, A. ponticus is most closely related to the European species A. sylvaticus and A. flavicollis. A. falzfeini has a peculiar type of restriction with EcoR I (specific for dispersed repeats) and Hind III (specific for satDNA). The genome of this species contains three families of EcoR I repeats previously found in various species (European and Asian) of wood mouse and Hind III components characteristic of both wood and field mice. A. argenteus differs from all other forms of Apodemus, the genome of which contains the 375-bp Hind III satellite, by the presence of a EcoR I satDNA fraction consisting of 240-bp repeating units.

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PubMed1993

Divergence of two families of repeated DNA in wood and field mice of the genus Apodemus (Muridae, Rodentia).

The nDNA of six species of a wood and field mice of the genus Apodemus (2n = 48): peninsulae, sylvaticus, flavicollis, microps, speciosus, agrarius, grey rat Rattus norvegicus as well, and house mouse Mus musculus were studied using EcoRI and HindIII restriction endonucleases with an agarose and polyacrylamide gel electrophoresis and a microdensitometry. It is shown for dispersed sequences that a quarter of 1.85 kb EcoRI genus specific family of repeated DNA is constant but a quarter of 1.35 kb EcoRI repeats, which are specific for more large taxon unit, is variable. The HindIII satDNA of the various species differs in the length of monomer, size of more representative multimer and digestion of the monomers by the same endonuclease of restriction; HindIII satDNA quantity correlates with 1.35 kb EcoRI repeat content. Some nonidentified components are found in Apodemus genomes. The possible ways evaluation of the repetitive DNA are briefly discussed. It was supposed that the evolutionary age of the wood mice is directly proportional to the length of HindIII multimer and inversely proportional to the amount of HIndIII satDNA with a 1.35 kb EcoRI repeats.

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PubMed1993

[Differentiation of GC-rich restriction sites in the highly repeated DNA in Apodemus (Muridae, Rodentia].

nDNAs of six species of wood and field mice of the genus Apodemus (peninsulae, flavicolis, microps, speciosus, and agrarius), grey rat Rattus norvegicus as well, and house mouse Mus musculus were digested with restriction endonucleases (MspI (CCGG), BspRI (GGCC) and MvaI (CCA/TGG). Two highly representative satellites are found in A.peninsulae (8%) and M.musculus (20%) genomes using BspRI and MvaI. The length of restriction fragments of these components are equal to n x 30 and n x 230 nb, respectively. Based on the results of PDRF of nDNA in rodent interspecies, genetic distances are estimated and phylogenetic tree reconstructed. Among wood mice examined A.sylvaticus and A.flavicollos are most closely related, A.peninsulae is more diverged. Field mouse has approx. equal differences from the european and asian species of wood mice. A middle value of genetic distances is about 7.12% in Apodemus genus, 12.69 and 13.2% between Apodemus with M.musculus and R.norvegicus, respectively.

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PubMed1990

[Repetitive DNA, chromosome polymorphism and speciation of gerbils].

Restriction analysis of DNA and differential staining of chromosomes in three species of the genus Meriones: M. tristrami. M. meridianus. M. inguiculatus was carried out. High extent of homology of the genomes under study was found at the molecular and chromosomal levels. Speciation of M. tristrami followed by numerous fissions of metacentric chromosomes is assumed to be connected with appearance of the short BspRI sequence. Possible mechanisms of the mammal genome evolution are discussed.

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