Analysis of DNA synthesis rate of cultured cells from flow cytometric data

The rate of DNA synthesis along S phase is estimated from flow cytometric histograms on the basis of a mathematical model of a cell population. In the absence of loss, the model expresses the population kinetics in terms of DNA synthesis rate, S-phase influx, and population size. A single histogram is sufficient to determine the DNA synthesis rate when the population is in balanced exponential growth. Two suitably chosen histograms are necessary if the S-phase influx is exponential in a time interval longer than the S-phase duration. The analysis procedure was tested on published autoradiographic data and applied to three cultured cell lines (CM-S, 3LL, and M14 cells) that show various patterns of DNA distribution. In each case the cell-cycle fractions, the DNA synthesis rate, and the S-phase duration were obtained.     

Mitochondrial DNA polymorphism in Tuvinian population of reindeer Rangifer tarandus L

Mitochondrial DNA variation was examined in one of the southern most populations of domestic reindeer, inhabiting Tyva Republic (Tuva). In Tuvinian population sequence polymorphism of the mitochondrial DNA D loop region was demonstrated. In a sample of 29 individuals 7 mitotypes were distinguished, pointing to the preservation of rather high level of genetic diversity in this population.     

In vitro evolution of intrinsically bent DNA.

DNA fragments which are intrinsically bent or curved migrate anomalously during electrophoresis through polyacrylamide gels. Starting with an initial population of approximately 10(12) unique DNA sequences, DNA which exhibited the kind of anomalous mobility associated with DNA bending was selected and enriched using a variation of the SELEX procedure. After seven rounds of selection and amplification, the vast majority of the remaining population of DNA fragments migrated as bent DNA. Cloning and sequencing of 30 individual sequences from this population has yielded information regarding the relationship between DNA sequence and bending. Some of the previous conclusions on DNA bending have been confirmed while others have been modified, by the results presented here. In addition, the dinucleotide base step CA/TG, which had not been thought to be a major factor in DNA bending, appears to be important.     

微卫星DNA标记及其在鱼类遗传多样性研究中的应用

微卫星DNA作为第二代分子遗传标记是高等真核生物基因组中种类多、分布广、具有高度的多态性和杂合度的分子标记,由于其具有多态性检出率高、信息含量大、共显性标记、实验操作简单、结果稳定可靠等优点,已经成为种群遗传学研究中被广泛应用的分子遗传标记。微卫星DNA标记技术在鱼类的群体遗传结构的分析、物种遗传多样性的鉴定以及遗传基因连锁图谱的构建等方面已初步得到应用。该文就微卫星技术的原理方法,在鱼类遗传多样性研究中的应用概况以及应用范围和注意事项等方面进行综述。为微卫星技术在鱼类遗传多样性研究中应用提供了理论参考。     

Using eggshell membranes as a DNA source for population genetic research

In the context of population genetic research, a faster and less invasive method of DNA sampling would allow large-scale assessments of genetic diversity and genetic differentiation with the help of volunteer observers. The aim of this study was to investigate the usefulness of eggshell membranes as a DNA source for population genetic research, by addressing eggshell membrane DNA quality, degeneration and cross-contamination. To this end, a comparison was made with blood-derived DNA samples. We have demonstrated 100% successful DNA extraction from post-hatched Black-tailed Godwit (Limosa limosa) eggshell membranes as well as from blood samples. Using 11 microsatellite loci, DNA amplification success was 99.1% for eggshell membranes and 97.7% for blood samples. Genetic information within eggshell membrane DNA in comparison to blood DNA was not affected (F _ST = −0.01735, P = 0.999) by degeneration or possible cross-contamination. Furthermore, neither degeneration nor cross-contamination was apparent in total genotypic comparison of eggshell membrane DNA and blood sample DNA. Our research clearly illustrates that eggshell membranes can be used for population genetic research.     

Reduced Levels of DNA Polymorphism and Fixed between-Population Differences in the Centromeric Region of Drosophila Ananassae

We have estimated DNA sequence variation within and between two populations of Drosophila ananassae, using six-cutter restriction site variation at vermilion (v) and furrowed (fw). These two gene regions are located close to the centromere on the left and right X chromosome arms, respectively. In the fw region, no DNA polymorphism was detected within each population. In the v region, average heterozygosity per nucleotide was very low in both populations (pi = 0.0005 in the Burma population, and 0.0009 in the India population). These estimates are significantly lower than those from loci in more distal gene regions. The distribution of DNA polymorphisms between both populations was also striking. At fw, three fixed differences between the Burma and India populations were detected (two restriction site differences and one insertion/deletion of approximately 2 kb). At v, each DNA polymorphism in high frequency in the total sample was nearly fixed in one or the other population, although none of them reached complete fixation. The observed pattern of reduced variation within populations and fixed differences between populations appears to correlate with recombination rate. We conclude that recent hitchhiking associated with directional selection is the best explanation for this pattern. The data indicate that different selective sweeps have occurred in the two populations. The possible role of genetic hitchhiking in rapid population differentiation in gene regions of restricted recombination is discussed.     

黑龙江省完达山东部林区马鹿种群遗传多样性的微卫星分析

黑龙江省完达山东部林区是东北马鹿(Cervus elaphus xanthopygus)种群密度较高的分布区之一,本文对2年冬季采集的167份马鹿粪便进行了7个微卫星座位的个体识别,评价了马鹿种群遗传多样性,并分析近期马鹿数量的急剧下降对种群遗传结构的影响。结果表明:167份粪便DNA分属66只个体;种群平均等位基因数9.00±2.77;平均有效等位基因数3.97±0.99;平均多态信息含量0.69±0.09;平均期望杂合度0.74±0.08;平均观察杂合度0.69±0.08。整个种群显著偏离Hardy-Weinberg平衡,但种群固定系数Fis为0.060,没有显著偏离零。可见,完达山东部林区马鹿种群遗传多样性较高,数量的急剧下降近期还没有表现在种群遗传结构上。     

Effect of sonication on paraffin-embedded tissue preparation for DNA flow cytometry

Since the publication of paraffin block extraction procedures, flow cytometric analysis of DNA ploidy and S-phase of tumor specimens has been widely applied. DNA aneuploidy, DNA tetraploid (elevated G2/M), and elevated S-phase are clinically significant in some tumor systems. True DNA tetraploid cell lines will contain a large 4c population and perhaps an 8c population; samples with cell aggregates will also contain a 6c population. Microscopic examination of samples having a 6c peak revealed nuclei with adhering debris and doublets, triplets, and larger nuclear aggregates. After sonication, a uniform suspension of single nuclei without adherent debris was seen. In addition to reducing the percent of G2/M cells, sonication also reduced S-phase percent such that it was closer to the bromodeoxyuridine labeling index. The DNA ploidy classification of specimens was also compared pre- and post-sonication. Four of 96 breast cancer samples changed classification; all were specimens in which the histogram became cleaner and a small DNA aneuploid peak became apparent after sonication.     

DNA double-strand damage and repair following gamma-irradiation in isolated spermatogenic cells

Various cell types in spermatogenesis exhibit differential sensitivity to radiation-induced DNA damage. The investigation of DNA radiosensitivity in vitro is complicated by the heterogeneous population of male germ cells (MGC) present in isolated single-cell suspensions. In the present investigation, the neutral elution technique was used to assess gamma-irradiation-induced DNA double-strand damage (DSD) in spermatogonia and preleptotene spermatocytes (SG/PL), pachytene spermatocytes and spermatid spermatocytes, as well as in MGC. In addition, the capability of these cell types to repair DNA double-strand damage was investigated. Based on the well established timing of the rat spermatogenic cycle, the DNA of specific cell populations was labeled using tritiated thymidine. DNA from labeled cells was determined isotopically, whereas total DNA was quantitated using a fluorometric method. DSD was induced in a dose-dependent manner in the heterogeneous population as well as in the labeled cell populations. SG/PL were more sensitive to gamma-irradiation-induced DSD than either the heterogeneous MGC population, pachytene or spermatid spermatocytes. Each cell type exhibited a similar capability to repair DSD following exposure to 3000 rad; repair was rapid (maximal within 45 min) and incomplete (less than 40%). Only pachytene spermatocytes exhibited significant repair following exposure to 6000 rad. Since a difference in sensitivity to radiation-induced DSD was demonstrated, the capability of each cell type to repair a similar initial frequency of strand damage was investigated. SG/PL, pachytene and spermatid spermatocytes differed in their capability to repair similar levels of strand damage. However, the difference in dose required to achieve equal damage may have contributed to other cellular effects, thus altering repair. In summary, a model is described that permits the evaluation of genotoxic responses in specific populations of spermatogenic cells within a heterogeneous cell suspension. The ability of specific cell types to repair gamma-irradiation-induced DNA double-strand damage is demonstrated.     

CONTROL OF MITOCHONDRIAL TURNOVER UNDER THE INFLUENCE OF THYROID HORMONE

The effect of thyroid hormone on the turnover of mitochondrial DNA and protein was studied in rat heart and liver. Changes in turnover were observed in both thyroidectomized and normal rats following administration of thyroid hormone. In heart and liver the turnover of mitochondrial DNA and protein was slower in thyroidectomized rats than in normal rats. The turnover of mitochondrial DNA and protein was affected similarly following the administration of thyroid hormone, suggesting that mechanisms which control turnover of mitochondrial constituents may be predicated upon a major part of the mitochondrion. In heart a decreased rate of degradation contributes to the increase in total mitochondrial protein. Mitochondrial DNA, labeled before administration of thyroid hormone, turns over, after the start of thyroid hormone administration, at a different rate from that in newly synthesized DNA. The different turnover rates suggest that in liver the pre-existing population of mitochondria is being replaced by another population synthesized under new physiological conditions.     

Variability of allozyme and cpSSR markers in the populations of Siberian spruce

The variability of 21 allozyme and three microsatellite loci of chloroplast DNA (cpDNA) was studied in the populations of Siberian spruce (Picea obovata Ledeb.) from Irkutsk oblast, Magadan oblast, Buryatia, and Mongolia. It was demonstrated that the highest level of genetic diversity among the examined populations at both allozyme and microsatellite loci was observed in the Tulyushka population from Irkutsk oblast. The lowest level of genetic diversity was observed in marginal isolated populations of Bogd Uul and Magadan. In the relict spruce population from Olkhon Island, differing from the other populations in the lowest allelic diversity of both types of markers, no expected decline of expected heterozygosity and haplotype diversity was observed. In this population, the variability parameters mentioned were close to the population mean. The obtained intrapopulation and intraspecific variability parameters of allozyme and microsatellite loci of chloroplast DNA and the data on the population differentiation at these loci indicate that the given markers can be used for the analysis of the population structure of Siberian spruce.     

Quantitation of total DNA per cell in an exponentially growing population using the diphenylamine reaction and flow cytometry

The diphenylamine assay used to estimate the absolute mass of DNA/cell as well as absolute differences in DNA content between cell populations is based upon the assumption that all of the cells are in the G0 or G1 phase of the DNA synthetic cycle. However, if cells are in exponential growth and synthesizing DNA, portions of the population will be in S or G2 phases and the diphenylamine assay will overestimate the total mass of DNA/cell. Conversely, flow cytometry (FCM) can estimate relative differences in total DNA/cell and the proportions of an exponentially growing population in G1, S, and G2 but cannot estimate absolute mass or differences in DNA/cell. In this report, we describe a methodology of combined diphenylamine and FCM assays of total DNA/cell which is applicable to any eukaryotic cell population. The method involves using the two assay methods concurrently and correcting the diphenylamine data for the FCM-derived distribution of the cells within the DNA synthetic cycle. The methodology was tested on single-cell-derived stocks of the obligate intracellular protozoan parasite Trypanosoma cruzi which displays marked but stable intraspecific heterogeneity.     

Step-wise progression of mammalian 10-kb DNA replication intermediates to mature chromatin

In mammalian DNA synthesis the primary replication intermediates are joined to larger intermediates. After the joining process is complete one can detect a distinct stage called the post-elongation stage. Furthermore a 10-kb DNA1 population is detected before the post-elongation stage whereas a 10-kb DNA2 population is part of this stage DNA. When cells are treated with 3-aminobenzamide, an inhibitor of poly(ADP-ribose) synthetase, an altered post-elongation-stage DNA was detected, which does not contain 10-kb fragments. The step(s) affected by 3-aminobenzamide prevents the appearance of 10-kb DNA in the post-elongation stage. The drug effect is reversible with the appearance of 10-kb DNA in the post-elongation stage when the cells are washed free of drug. Hence there is a step-wise progression from 10-kb DNA, via the post-elongation stage, to mature chromatin.     

Ploidy of endothelium in high-grade astrocytomas

To determine the ploidy and proliferative activity of the endothelium in high-grade astrocytomas, the nuclear DNA content of 11 high-grade astrocytomas, including two gliosarcomas, was measured by cytophotometry. This technique allowed comparison of the endothelial population with the astrocytic population. In all cases, the endothelium was diploid, with an average of 24.6% of cells in the S + G2M phases of the cell cycle. In contrast, the astrocytic population displayed marked DNA abnormalities. The two gliosarcomas had a marked difference in proliferative activity of the endothelium with 4% and 40% of cells, respectively, in the S + G2M phases. These data indicate that the vast majority of endothelial cells compromising the vascular hypercellularity observed in high-grade astrocytomas are in the normal cell cycle whereas in many cases the malignant astrocytes are not. The nuclear DNA content of gliosarcomas appears to be similar to other high-grade astrocytomas.     

The effect of ancient DNA damage on inferences of demographic histories

The field of ancient DNA (aDNA) is casting new light on many evolutionary questions. However, problems associated with the postmortem instability of DNA may complicate the interpretation of aDNA data. For example, in population genetic studies, the inclusion of damaged DNA may inflate estimates of diversity. In this paper, we examine the effect of DNA damage on population genetic estimates of ancestral population size. We simulate data using standard coalescent simulations that include postmortem damage and show that estimates of effective population sizes are inflated around, or right after, the sampling time of the ancestral DNA sequences. This bias leads to estimates of increasing, and then decreasing, population sizes, as observed in several recently published studies. We reanalyze a recently published data set of DNA sequences from the Bison (Bison bison/Bison priscus) and show that the signal for a change in effective population size in this data set vanishes once the effects of putative damage are removed. Our results suggest that population genetic analyses of aDNA sequences, which do not accurately account for damage, should be interpreted with great caution.     

微卫星DNA在分子遗传标记研究中的应用

随着种群遗传学的发展 ,分子遗传标记特别是微卫星标记已经成为研究种群遗传的有力工具。本文就微卫星遗传标记的研究背景、技术应用以及优势与不足等方面进行了综述。     

Jaagsiekte retrovirus is widely distributed both in T and B lymphocytes and in mononuclear phagocytes of sheep with naturally and experimentally acquired pulmonary adenomatosis

Jaagsiekte sheep retrovirus (JSRV) is a type D retrovirus specifically associated with a contagious lung tumor of sheep, sheep pulmonary adenomatosis (SPA). JSRV replicates actively in the transformed epithelial cells of the lung, and JSRV DNA and RNA have been detected in lymphoid tissues of naturally affected animals. To determine the lymphoid target cells of JSRV, CD4(+) T cells, CD8(+) T cells, B lymphocytes, and adherent cell (macrophage/monocyte) populations were isolated from the mediastinal lymph nodes of naturally affected sheep and lambs inoculated with JSRV. Cells were enriched to high purity and then analyzed for JSRV proviral DNA by heminested PCR, and the proviral burden was quantitated by limiting dilution analysis. JSRV proviral DNA was found in all subsets examined but not in appropriate negative controls. In sheep naturally affected with SPA, JSRV proviral burden was greatest in the adherent cell population. In the nonadherent lymphocyte population, surface immunoglobulin-positive B cells contained the greatest proviral burden, while CD4(+) and CD8(+) T cells contained the lowest levels of JSRV proviral DNA. In most of the cases (5 of 8), provirus also could be detected in the peripheral blood mononuclear cell (PBMC) population. A kinetic study of JSRV infection in the mediastinal lymphocyte population of newborn lambs inoculated with JSRV found that JSRV proviral DNA could be detected as early as 7 days postinoculation before the onset of pulmonary adenomatosis, although the proviral burden was greatly reduced compared to adult natural cases. This was reflected in the levels found in PBMC since proviral DNA was detected in 2 of 13 animals. At the early time points studied (7 to 28 days postinoculation) no one subset was preferentially infected. These data indicate that JSRV can infect lymphoid and phagocytic mononuclear cells of sheep and that dissemination precedes tumor formation. Infection of lymphoid tissue, therefore, may play an important role in the pathogenesis of SPA.     

Mitochondrial COI gene transfers to the nuclear genome of Dendroctonus valens and its implications

Mitochondrial gene transfer to the nuclear genome could affect the accuracy of results in population genetics and evolutionary studies using mitochondrial gene markers. In a population genetics study of the red turpentine beetle (Dendroctonus valens), an invasive species in China, we found numerous ambiguous sites existing in the Cytochrome Oxidase I (COI) gene sequences obtained directly from polymerase chain reaction (PCR) products amplified from total genomic DNA using universal primers. By comparing the profiles of restriction endonuclease digestions and the sequences of PCR products amplified from mitochondrial DNA and nuclear DNA of the same individuals, we confirmed it was a phenomenon of mitochondrial gene transfer to the nuclear genome. Large numbers of COI pseudogenes were detected in this species. According to different levels of condon position bias and phylogenetic analysis, these should have originated from independent integration events. The impact of nuclear mitochondrial DNA sequences on population genetics analyses was discussed.     

Assessing populations of a disease suppressive microorganism and a plant pathogen using DNA arrays

Understanding the relationships between disease suppressive microbial populations and plant pathogens is essential to develop procedures for effective and consistent disease control. Currently, DNA array technology is the most suitable technique to simultaneously detect multiple microorganisms. Although this technology has been successfully applied for diagnostic purposes, its utility to assess different microbial populations, as a basis for further study of population dynamics and their potential interactions, has not yet been investigated. In this study, a DNA macroarray with multiple levels of phylogenetic specificity was developed to measure population densities of a specific disease suppressive microorganism, Trichoderma hamatum isolate 382, and the plant pathogen Rhizoctonia solani. Amongst others, the DNA array contained genus-, species- and isolate-specific detector oligonucleotides and was optimized for sensitive detection and reliable quantification of the target organisms in potting mix samples. Furthermore, this DNA array was used to quantify disease severity as well as incidence of severe disease based on pathogen population densities in the growing medium. Taking into account the unlimited expanding possibilities of DNA arrays to include detector oligonucleotides for other and more microorganisms, this technique has the potential for studying the population dynamics and ecology of several target populations in a single assay.     

Exonuclease I hydrolyzes DNA with a distribution of rates

We report heterogeneity in the time necessary for Exonuclease I to hydrolyze identical DNA fragments. A real-time fluorescence method measured the time required by molecules of Exonuclease I to hydrolyze single-stranded DNA that was synthesized to have two fluorescently labeled nucleotides. One fluorescently labeled nucleotide was located near the 3′ end of the DNA and the other near the 5′ end. Heterogeneity in the hydrolysis rate of the exonuclease population was inferred from the distribution of times necessary to cleave these DNA fragments. In particular, we found simple first-order kinetics, using a single hydrolysis rate, did not result in a good fit to the data. Better fits to the data were obtained if one assumed a distribution of hydrolysis rates for the exonuclease population. Under our experimental conditions, this broad distribution of rates was centered near 100 nt/s.