Variability at 15 autosomal microsatellite DNA loci in Russian population

The paper presents allele frequencies at 15 STR loci (D3S1358, vWA, FGA, TH01, TPOX, CSFIPO, D5S818, D13S317, D7S820, D16S539, D2Sl338, D8S1179, D21S1l, D18S51, D19S433), used in forensic medicine, in Russian sample (n = 176) representing population of the European part of the Russian Federation. The combined power of discrimination (PD) and the combined power of exclusion (PE) for the 15 STR loci were 0.999 999 999 999 999 986 and 0.999 999 331 310 171 000, respectively. The data obtained for allele and genotype frequencies conformed to Hardy-Weinberg expectations. According to the presented data, loci D2S1338, D18S51, D21Sll and FGA are the most informative markers for Russians. The data obtained may be used as reference database for forensic medicine laboratories in Russian Federation.     

A comparison of mutation induction at the tk and hprt loci in human lymphoblastoid cells; quantitative differences are due to an additional class of mutations at the autosomal tk locus

X-Rays, ethyl methanesulfonate and ICR-191 induced 2 classes of trifluorothymidine-resistant mutants at the autosomal tk locus in human lymphoblastoid cells. These classes were differentiated by their growth rates; some mutants grew with a normal doubling time of 14-18 h (tk-NG), while others grew much more slowly, with doubling times of 21-44 h (tk-SG). Only mutants with normal growth rates were observed at the X-linked hprt locus; the frequencies of mutations induced at hprt were equal to those induced for tk-NG mutants. Thus, more mutations overall (by up to a factor of 6) were induced at tk than at hprt. These results are discussed in relation to recent studies in rodent cells, in which much greater mutation frequencies were observed at autosomal loci.     

Genetic variation at 9 autosomal microsatellite loci in Asian and Pacific populations.

Genetic variation at 9 autosomal microsatellite loci (CFS1R, TH01, PLA2A, F13A1, CYP19, LPL, D20S481, D20S473, and D20S604) has been characterized in 16 Asian and Oceanic populations, mostly from mainland and insular Southeast Asia. The neighbor-joining tree and the principal coordinates analysis of the genetic relationships of these populations show a clear separation of Papua New Guinea Highlanders and, to a lesser extent, Malayan aborigines (Orang Asli or Semai) from the rest of the populations. Although the number of markers used in this study appears to be inadequate for clarifying the patterns of genetic relationships among the studied populations, in the principal coordinates analysis a geographic trend is observed in the mainland and insular Southeast Asian populations. Furthermore, in an attempt to contrast the extent of variation between autosomal and Y-chromosome-specific microsatellite loci and to reveal potential differences in the patterns of male and female migrations, we have also compared genetic variation at these 9 autosomal loci with variation observed at 5 Y-chromosome-specific microsatellites in a common set of 14 Asian populations.     

The TP53 dependence of radiation-induced chromosome instability in human lymphoblastoid cells

The dose and TP53 dependence for the induction of chromosome instability were examined in cells of three human lymphoblastoid cell lines derived from WIL2 cells: TK6, a TP53-normal cell line, NH32, a TP53-knockout created from TK6, and WTK1, a WIL2-derived cell line that spontaneously developed a TP53 mutation. Cells of each cell line were exposed to (137)Cs gamma rays, and then surviving clones were isolated and expanded in culture for approximately 35 generations before the frequency and characteristics of the instability were analyzed. The presence of dicentric chromosomes, formed by end-to-end fusions, served as a marker of chromosomal instability. Unexposed TK6 cells had low levels of chromosomal instability (0.002 +/- 0.001 dicentrics/cell). Exposure of TK6 cells to doses as low as 5 cGy gamma rays increased chromosome instability levels nearly 10-fold to 0.019 +/- 0.008 dicentrics/cell. There was no further increase in instability levels beyond 5 cGy. In contrast to TK6 cells, unexposed cultures of WTK1 and NH32 cells had much higher levels of chromosome instability of 0.034 +/- 0.007 and 0.041 +/- 0.009, respectively, but showed little if any effect of radiation on levels of chromosome instability. The results suggest that radiation exposure alters the normal TP53-dependent cell cycle checkpoint controls that recognize alterations in telomere structure and activate apoptosis.     

Genetic variation at twentythree microsatellite loci in sixteen human populations

We have analysed genetic variation at 23 microsatellite loci in a global sample of 16 ethnically and geographically diverse human populations. On the basis of their ancestral heritage and geographic locations, the studied populations can be divided into five major groups, viz. African, Caucasian, Asian Mongoloid, American Indian and Pacific Islander. With respect to the distribution of alleles at the 23 loci, large variability exists among the examined populations. However, with the exception of the American Indians and the Pacific Islanders, populations within a continental group show a greater degree of similarity. Phylogenetic analyses based on allele frequencies at the examined loci show that the first split of the present-day human populations had occurred between the Africans and all of the non-African populations, lending support to an African origin of modern human populations. Gene diversity analyses show that the coefficient of gene diversity estimated from the 23 loci is, in general, larger for populations that have remained isolated and probably of smaller effective sizes, such as the American Indians and the Pacific Islanders. These analyses also demonstrate that the component of total gene diversity, which is attributed to variation between groups of populations, is significantly larger than that among populations within each group. The empirical data presented in this work and their analyses reaffirm that evolutionary histories and the extent of genetic variation among human populations can be studied using microsatellite loci.     

Variation of 15 autosomal microsatellite DNA loci in the Russian population

The allele frequencies of 15 autosomal STR loci (D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317, D7S820, D16S539, D2S1338, D8S1179, D21S11, D18S51, and D19S433) used in forensic medicine were determined for the Russian population of European Russia (N = 176). The power of discrimination (PD) and power of exclusion (PE) of the system of the 15 STR loci were 0.999 999 999 999 999 986 and 0.999 999 331 310 171 000, respectively. The allele and genotype frequency distributions in the Russian population corresponded to the Hardy-Weinberg equilibrium. The D2S1338, D18S51, D21S11, and FGA loci were identified as the most informative markers for the Russian population and proposed as a reference for forensic studies in the Russian Federation.     

Evidence for heterozygote instability in microsatellite loci in house wrens

Microsatellite loci have high mutation rates and high levels of allelic variation, but the factors influencing their mutation rate are not well understood. The proposal that heterozygosity may increase mutation rates has profound implications for understanding the evolution of microsatellite loci, but currently has limited empirical support. We examined 20 microsatellite mutations identified in an analysis of 12 260 meiotic events across three loci in two populations of a songbird, the house wren (Troglodytes aedon). We found that for an allele of a given length, mutation was significantly more likely when there was a relatively large difference in size between the allele and its homologue (i.e. a large ‘allele span’). Our results support the proposal of heterozygote instability at microsatellite loci.     

Effects of oxidative and alkylating damage on microsatellite instability in nontumorigenic human cells

Microsatellite instability is a phenomenon that is well characterized in mismatch repair-deficient tumor cell lines, including the potential etiological role of endogenous DNA damage. However, our understanding of microsatellite mutational mechanisms in repair-proficient, nontumorigenic cells is limited. We determined microsatellite mutation frequencies for human lymphoblastoid cells using an episomal DNA shuttle vector in which a (TTCC/AAGG)(9) microsatellite is inserted in-frame within the herpes simplex virus thymidine kinase (HSV-tk) gene. The responses of plasmid-bearing cells to reactive oxygen species or alkylating agents were compared after treatment with hydrogen peroxide (H(2)O(2)) and N-ethyl-N-nitrosourea (ENU). H(2)O(2) treatment induced a statistically significant increase in overall HSV-tk mutation frequency relative to controls, with catalase reducing the effect. H(2)O(2) treatment increased the mutation frequency within the microsatellite and the HSV-tk coding region to a similar extent (five and six-fold, respectively, relative to the control). Mutational specificity analyses demonstrated that the proportion of mutations within the microsatellite is not statistically different among the H(2)O(2), catalase, and PBS treatment groups. In contrast, treatment of cells bearing the microsatellite vector with ENU altered the mutational spectrum, relative to solvent control. ENU induced the expected base substitutions within the HSV-tk coding region, but did not increase the microsatellite mutation frequency. The low level of microsatellite mutagenesis observed after reactive oxygen species (ROS) insult likely reflects the normal repair processes of these nontumorigenic, repair-competent cells. Our ex vivo experiments demonstrate the manner in which repetitive DNA in normal human cells might respond to endogenous mutagens.     

Variability of fifteen autosomal microsatellite DNA loci in five populations of aboriginal South Siberians

The allele distributions for 15 STR loci included in the AmpFISTR SGM Plus and AmpFISTR Profiler Plus kits ("Applied Biosystems", USA) were determined in 261 healthy unrelated individuals belonging to five indigenous populations of South Siberia: in Buryats, Altaians, Tofalars, Sojots and Khakassians. No significant differences in allele frequencies were found between populations studied. Combined power of discrimination (PD) for the STR loci investigated were estimated for the populations under study.     

Genetic variation at microsatellite loci in Spanish sheep

Genetic variation at 18 microsatellite loci was analysed in six indigenous Spanish sheep: Churra; Latxa; Manchega; Rasa-Aragonesa; Castellana and Merino. Merinos had frequently the highest number of alleles per locus, whereas Latxas showed the lowest one at many loci. Markers ordered decreasingly according to the number of variants differentiated in the whole population were: MAF70; TGLA13; CSSM66; BM143, BM6444; MAF36; MAF64; CSSM6; TGLA53; OarFCB11; MAF33; BM4621; MAF48; MAF65; BM1258; ILSTS002; ADCYC and OarCP34. Parameters of variability such as effective number of alleles and gene diversities corroborated the high level of variation frequently displayed by microsatellite markers. Comparison of allele distributions among populations and loci did not reveal consistent shapes. Distributions were centralised in some cases, whereas in others some kind of skewness was evident. Breed-specific alleles were detected at most loci, being frequent in Merinos and rare in Churras.     

Analysis of genetic diversity of population of Northern Eurasia from autosomal microsatellite loci

The paper presents the results of analysis of the gene pools of several North Eurasian ethnic groups (Buryats, Evenks, Altaians, Russians, Kyrgyzes, Tuvinians, Tatars, and Ukrainians) examined using a panel of autosomal microsatellite markers (D4S397, D5S393, D7S640, D8S514, D9S161, D10S197, D11S1358, D12S364, and D13S173) mapped on different chromosomes and represented by the (CA)n dinucleotide repeats. In the group of populations examined the proportion of genetic variability at microsatellite loci explained by interpopulation differences was about 2.5%, while genetic differences between the individuals within a population accounted for 97.5% of this variability. Analysis of genetic relationships among the populations revealed substantial differences between the populations belonging to the Indo-European and Altaic linguistic families in gene diversity at microsatellite loci.     

The variation of 15 autosomal microsatellite DNA loci in five indigenous populations of South Siberia

The allele frequencies of 15 autosomal STR loci (D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317, D7S820, D16S539, D2S1338, D8S1179, D21S11, D18S51, and D19S433) included into the AmpFlSTR SGM Plus and AmpFlSTR Profiler Plus kits (Applied Biosystems, United States) were determined for five indigenous populations of South Siberia: Buryats, Altaians, Tofalars, Sojots, and Khakassians (N = 261). No significant differences in allele frequencies were found between the populations. The combined power of discrimination of the STR loci was determined for every population.     

Dnmt1 deficiency leads to enhanced microsatellite instability in mouse embryonic stem cells

DNA hypomethylation is frequently seen in cancer and imparts genomic instability in mouse models and some tissue culture systems. However, the effects of genomic DNA hypomethylation on mutation rates are still elusive. We have developed a model system to analyze the effects of DNA methyltransferase 1 (Dnmt1) deficiency on DNA mismatch repair (MMR) in mouse embryonic stem (ES) cells. We generated sibling ES cell clones with and without functional Dnmt1 expression, containing a stable reporter gene that allowed us to measure the slippage rate at a mononucleotide repeat. We found that Dnmt1 deficiency led to a 7-fold increase in the microsatellite slippage rate. Interestingly, the region flanking the mononucleotide repeat was unmethylated regardless of Dnmt1 status, suggesting that it is not the local levels of DNA methylation that direct the increase in microsatellite instability (MSI). The enhanced MSI was associated with higher levels of histone H3 acetylation and lower MeCP2 binding at regions near the assayed microsatellite, suggesting that Dnmt1 loss may decrease MMR efficiency by modifying chromatin structure.     

Adaptive response induction and variation in human lymphoblastoid cell lines

Adaptive response is a term used to describe the ability of a low, priming dose of ionizing radiation to modify the effects of a subsequent higher, challenge dose, but it has been observed to be highly variable in both presence and magnitude. To examine this variability, 10 human lymphoblastoid cell lines were screened for adaptability to 137Cs radiation by determining the frequency of micronuclei in binucleated cells. Of these, six adapted, three did not adapt and one was synergistic. The assay was then repeated on each of the cell lines to test for reproducibility. Five cell lines showed the same result both times; four of these adapted and one did not.To determine whether fluctuations in the cell cycle distribution in the irradiated population of cells could alter the adaptive response, and therefore explain some of the observed variability, two of the cell lines were tested for adaptation after enriching the population, by synchronization, for a given cell cycle stage. In both cell lines, the direction of the response was altered when the distribution of cells within the cell cycle was changed, suggesting that the adaptive response can be affected by cell cycle stage at the time of irradiation.     

Allelic losses in mutations at the aprt locus of human lymphoblastoid cells.

We analyzed the nature of mutations at the autosomal locus coding for adenine phosphoribosyltransferase (aprt) in human cells to elucidate the process(es) governing mutagenesis at autosomal loci. A human lymphoblastoid cell line, WR10, was found to be heterozygous for mutated allele at the aprt locus, and was used for mutation analyses. By the use of a restriction fragment length polymorphism associated with the aprt locus in WR10 cells, the molecular characteristics of mutations arising spontaneously or induced by gamma-rays were investigated. Eighty-five percent (22/26) of the spontaneous mutant clones and 93% (64/69) of the gamma-ray-induced mutant clones resulted from loss of one of the two aprt alleles. Determination of the dosage of aprt genes in those mutants with allelic losses revealed that approximately half of them retained two copies of the mutated allele. These data suggest that the mutational events leading to APRT deficiency are analogous to those reported for tumor suppressor genes in malignancies.     

Interferon production in human T lymphoblastoid cells

Human T lymphoblastoid cell (RPMI 8402 cell) produced interferon (IFN) through the induction by Sendai virus. The priming effect on the interferon production in the RPMI 8402 cell could be found by the pretreatment of human leukocyte IFN (Hu IFN-alpha), but not by that of the IFN produced in the RPMI 8402 cell (T-IFN). The superinduction by the irradiation of ultraviolet rays or the treatment of antimetabolites (actinomycin D and cycloheximide) or 5-bromodeoxyuridine was not found. The T-IFN was completely neutralized by the anti-Hu IFN-beta serum, but not by the anti-Hu IFN-alpha serum at all. In conclusion, it was confirmed that the IFN produced in the RPMI 8402 cell through the induction by Sendai virus was antigenically identical to Hu IFN-beta.