DNA measurements of mitotic chromosomes of the rabbit (Orytolagus cuniculus)

DNA cytophotometry was used to obtain the relative DNA content of mitotic chromosomes of Orytolagus cuniculus. DNA ranking of the rabbit chromosomes is presented, and related to the quinacrine and Giemsa-banded karyotype. In addition, the relative DNA content of the short and long arms of each chromosome was calculated and the DNA-based centromeric index, (i.e., the ratio of long-arm DNA to total chromosomal DNA) determined. The Y chromosome is clearly a submetacentric chromosome on the basis of the DNA measurements.     

Rapid detection of aneuploidy in <Emphasis Type="Italic">Musa</Emphasis> using flow cytometry

We report a procedure for the rapid and convenient detection of aneuploidy in triploid Musa using DNA flow cytometry. From a population of plants derived from gamma-irradiated shoot tips, plants were selected based on aberrant morphology and their chromosome numbers were counted. Aneuploids plants with chromosome numbers 2n=31 or 32 were found as well as the expected triploid plants (2n=3x=33). At the same time, the nuclear DNA content of all plants was measured using flow cytometry. The flow cytometric assay involved the use of nuclei isolated from chicken red blood cells (CRBC), which served as an internal reference standard. The relative DNA content of individual plants was expressed as a ratio of DNA content of CRBC and Musa (DNA index). In order to estimate the chromosome number using flow cytometry, the relative DNA content of plants with unknown ploidy was expressed as a percentage of the DNA content of triploid plants. The classification based on flow cytometry fully agreed with the results obtained by chromosome counting. The results indicated that flow cytometry is a convenient and rapid method for the detection of aneuploidy in Musa.     

Analysis of a model of cell cycle in eukaryotes

A dynamic model of the cell cycle for eukaryotic cells, which takes into account the rates of ribosome and protein synthesis and the discontinuous events of DNA replication and cell division, is analyzed. It is shown that, by changing the values of the parameters, three different cell cycle regimens are possible, which are similar to cell cycle patterns experimentally observed and which show the action of different control mechanisms. The model allows the determination of the macromolecular levels as a function of the cycle time. Taking into consideration the age distribution function of the cells in an ideal exponentially growing population, mathematical relations are calculated that link the levels of macromolecular components (protein, ribosomes and DNA) to the temporal parameters of the cell cycle, such as the relative duration of the S phase. It is also shown that the relative length of all cell cycle phases may be determined if the labelling index and the relative DNA content of the cell population are known. All these relations suggest new and convenient procedures to determine cell cycle parameters.     

Centromeric index versus DNA content flow karyotypes of human chromosomes measured by means of slit-scan flow cytometry

We have applied slit-scan flow cytometry (SSFCM) to classify human chromosomes according to their centromeric index (CI) and relative DNA content. The resulting bivariate--CI vs. DNA content--distributions shows 14 peaks for normal human chromosomes. Distinct peaks are produced by chromosomes 1, 2, 3, 4 + 5, 6 + 7 + X, 8, 13 + 14 + 15, 16, 17 + 18, 19 + 20, and 21 + 22 + Y. In addition, chromosomes 9 through 12 are resolved into three peaks. The identity of the chromosomes comprising each peak was determined by comparing CI vs. DNA content distributions measured for normal human chromosomes by means of SSFCM with CI and DNA content values measured for human chromosomes with image analysis. The accuracy of CI measurement by SSFCM was verified by measuring CIs for human chromosomes isolated from human/rodent hybrid cell lines containing only a few known human chromosomes. These studies showed CIs measured for human chromosomes 1-19 and 21 to be in close agreement with the CIs calculated by means of image analysis. We further confirmed the chromosome assignments for each peak by showing that the relative volumes of the peaks in the CI vs. DNA content distributions for chromosomes from normal cells are similar to the relative frequencies of chromosomes expected for these peaks based on the peak assignments.     

Organization of nucleotide sequences in the chicken genome

The four major components of chicken DNA were prepared by density gradient centrifugation and characterized in several basic properties: relative amounts, dG + dC content, buoyant densities, compositional heterogeneity, and reassociation kinetics. While the relative amounts and the compositions of the major components of chicken DNA were similar to those found in mammalian genomes, their compositional heterogeneities were found to be narrower. The relative amounts of interspersed repeated and unique sequences were strikingly different in different components and also different from those found in the corresponding major components of mouse and human DNAs. If one takes into consideration that major DNA components (a) account for practically all of main-band DNA and (b) derive by preparative breakage from very long DNA segments of fairly homogeneous composition, the isochores, our findings indicate that the distribution of interspersed repeats is different in different chromosomal regions and is species-specific.     

Flow cytometric sexing of mammalian sperm

This review reexamines parameters needed for optimization of flow cytometric sexing mammalian sperm and updates the current status of sperm sexing for various species where this technology is currently being applied. Differences in DNA content have provided both a method to differentiate between these sex-determining gametes and a method to sort them that can be used for predetermining sex in mammals. Although the DNA content of all cells for each mammalian species is highly conserved, slight but measurable DNA content differences of sperm occur within species even among cattle breeds due to different sizes of Y-chromosomes. Most mammals produce flattened, oval-headed sperm that can be oriented within a sorter using hydrodynamic forces. Multiplying the percentage the difference in DNA content of the X- or Y-chromosome bearing sperm times the area of the flat profile of the sperm head gives a simple sorting index that suggests that bull and boar sperm are well suited for separation in a flow sorter. Successful sperm sexing of various species must take into account the relative susceptibilities of gametes to the stresses that occur during sexing. Sorting conditions must be optimized for each species to achieve acceptable sperm sexing efficiency, usually at 90% accuracy. In the commercial application of sperm sexing to cattle, fertility of sex-sorted bull sperm at 2 x 10(6)/dose remains at 70-80% of unsexed sperm at normal doses of 10 to 20 x 10(6) sperm. DNA content measurements have been used to identify the sex-chromosome bearing sperm populations with good accuracy in semen from at least 23 mammalian species, and normal-appearing offspring have been produced from sexed sperm of at least seven species.     

Changes in cellularity induced by radiation in a solid tumour.

The growth, and cellular responses of Morris hepatoma 3924 A to a locally-administered dose of 3750 R X-rays were studied using the following parameters; (1) relative tumour volume changes; (2) tritiated thymidine (3H-TdR) incorporation into DNA; (3) tumour DNA content and (4) cellular analysis, including 3H-TdR labelling index, mitotic index, aberrant mitotic frequency and relative cell density. Before depression of tumour growth, cell proliferation is temporarily interuppted. As proliferation is reinitiated, a short-lived synhcrony and prolongation of cell-cycle traverse are reflected in (a) the labelling index and mitotic index, (b) the relative cell density, and (c) the rate of incorporation of 3H-TdR into DNA. Within 4 days after radiation, cell proliferation and 3H-TdR incorporation are significantly depressed. Simultaneously there are reductions in both the relative cell density and tumour DNA contents, and these remain depressed as the tumours initiate regression. From these studies, it is apparent that the cellular responses to radiation insult occur well in advance of measurable volume changes and are observed both in tumours that continue to regress and in those that initiate regrowth.     

Fetal dexamethasone exposure impairs cellular development in neonatal rat heart and kidney: effects on DNA and protein in whole tissues

Fetal glucocorticoid exposure causes postnatal growth retardation. To examine the mechanisms underlying effects on specific organ systems, we administered 0.2 or 0.8 mg/kg of dexamethasone to pregnant rats on gestational days 17, 18, and 19 and assessed three biochemical markers of cell development in heart and kidney of the offspring: DNA content per organ as an index of total cell numbers, DNA per g tissue as an index of cell packing density, and protein/DNA ratio as an index of relative cell size. In both tissues, DNA content became markedly subnormal during the first postnatal week, the ontogenetic period of rapid cell division. Partial recovery occurred by the end of the first postnatal month. In the heart, cell packing density was subnormal initially and the cells were significantly enlarged. In contrast, packing density was slightly elevated in the kidney; protein/DNA was increased by the low dose of dexamethasone, but markedly decreased by the high dose. These results suggest that tissue growth impairment caused by prenatal dexamethasone treatment reflects primary deficits in cell proliferation that extend to a variety of different cell types; however, consequent effects on cell packing density and cell size are dose-specific, possibly reflecting actions of glucocorticoids selective for certain cell types or phases of cell development.     

Estimating recent growth in the cuttlefish Sepia officinalis: are nucleic acid-based indicators for growth and condition the method of choice?

A laboratory calibration study was undertaken with juvenile Sepia officinalis (80-85 g initial wet weight) to investigate the effects of different food rations and different starving intervals on RNA/dry weight (DW) ratios and RNA/DNA ratios in cephalopod mantle muscle at two different temperatures. The digestive gland index was also used as an additional indicator of recent growth. High food rations and low temperature went along with high RNA/DW ratios and high RNA/DNA ratios. Starving resulted in a linear decline in growth performance and a concomitant decrease in RNA/DW and RNA/DNA ratio, with RNA/DNA ratios representing the growth data better. RNA/DNA ratios decreased faster at higher temperatures. A fluorimetric assay for nucleic acid analysis was optimized for cephalopod mantle tissues and yielded reproducible RNA/DNA ratios with a relative variance below 10%. Thus, it may be possible to use this estimator of recently encountered feeding regime for the evaluation of mortality rates of early teuthid paralarvae to eventually support stock management. Also, log relative digestive gland weight showed a strong relationship with starving time, but, surprisingly, not with temperature. Data from the two temperatures analyzed could be combined to form a common regression line of relative digestive gland index with starving time. This indicator for recent growth might be especially suitable for large specimens with a well-developed digestive gland.     

Coordinate Variation in Lengths of Deoxyribonucleic Acid Molecules and Head Lengths in Morphological Variants of Bacteriophage T4

We have investigated three classes of small bacteriophage T4 particles which differ from normal T4 particles in length of their deoxyribonucleic acid (DNA), in head length, in protein content, and in density. The different particles contain DNA molecules measuring 0.90, 0.77, or 0.67, respectively, of the normal T4 length. An additional class of viable particles contains DNA molecules of 1.1 unit length. These discrete differences in DNA length correspond to discrete differences in length (but not width) of the respective heads and are roughly proportional to the resulting differences in head volumes. The measured relative dimensions of the different heads fit best the relative dimensions predicted by a quasi-icosahedral model in which the smallest T4 head corresponds to an icosahedron with a triangulation number T = 21. The mid-portion of this structure is thought to be elongated by adding successive rows of gene 23 protein hexamers, the normal T4 head having three added rows. Different mutants produce small particles of the three classes in varying proportions, but no mutant produces exclusively particles of a single class. Particles of each class, with indistinguishable DNA content, show additional minor differences in protein content, as measured by differences in buoyant density and in the relative ratio of (32)P to (35)S.     

Direct measurement of femtogram amounts of DNA in cells and chloroplasts by quantitative microspectrofluorometry

Absolute DNA amounts of individual chloroplasts were determined by measuring the fluorescence intensity of chloroplasts stained with 4',6-diamidino-2-phenylindole (DAPI) relative to that of the bacterium Pediococcus damnosus (cerevisiae) smeared on the same slide. An absolute DNA content of 7.7 X 10(15) g for a standard P. damnosus cell type was calculated by comparing the relative fluorescence values and frequency of each stage of cellular development in a culture to the average DNA content of all cell types determined by chemical methods. Chlorophyll was extracted from the chloroplasts during fixation so that chlorophyll autofluorescence was not present when DAPI fluorescence was measured. Absolute amounts of DNA could then be determined for single chloroplasts, either within cells that were individually selected from a mixed cell population or in small preparations of isolated chloroplasts. The DNA amounts of chloroplasts from mesophyll cells determined in this way were similar to the values previously determined by bulk averaging methods. Chloroplast DNA amounts from different cell types of the leaf could be measured by microspectrofluorometry, and it was found that chloroplasts from spinach epidermal cells contained about half as much DNA as chloroplasts from adjacent mesophyll cells.     

DNA stainability in aneuploid breast tumors: comparison of four DNA fluorochromes differing in binding properties.

The aim of this study was to evaluate whether or not the differences in chromatin structure between diploid stromal cells or lymphocytes, which are often used as DNA ploidy standard, and aneuploid breast tumor cells can significantly affect the estimates of the DNA index of these tumors. To this end, the DNA content estimates of 34 aneuploid breast tumors, differing in size, degree of differentiation, and presence or absence of estrogen and progesterone receptors and metastases, were compared using four common DNA fluorochromes: DAPI, Hoechst 33342, propidium iodide, and acridine orange. These dyes differ in their mode of interaction with DNA (binding to minor groove or intercalation) and for each of them binding to DNA is restricted to a different degree by nuclear proteins. It was expected, therefore, that if differences in chromatin structure play a role in DNA content estimates, the DNA index of the measured tumors may vary depending on the dye. The cell nuclei were isolated from the tumors using a detergent-based procedure and stained with each of the dyes and the DNA index was estimated using peripheral blood lymphocytes as a DNA content standard. For each of the tumors, the DNA index estimates with all four dyes correlated very well. When the results obtained with individual dyes were compared in pairs, the correlation coefficients (r) of DNA indices were all above 0.96 (correlation at p less than 0.001). The best concordance was seen between specimens stained with Hoechst 33342 and DAPI (r = 0.99), and the least between those stained with Hoechst 33342 and propidium iodide (r = 0.96). The data indicate that DNA content analysis of unfixed nuclei, utilizing the above fluorochromes, is not significantly biased by differences in chromatin structure of the measured cells.     

基于非线性方法的DNA序列分析

以人类DNA序列为原始数据,对其进行数字编码。在利用功率谱分析编码DNA序列的基础上,利用Hurst指数进一步分析序列的自相似性。从分析结果看出,DNA序列中的确存在长程相关现象,而且这种长程相关现象与DNA的组成结构有关,表现为它的结构基团的Hurst指数大于其功能基团的Hurst指数。同时,从内含子含量的角度分析序列的长程相关程度,结果表明,同一序列中,内含子含量与不同的化学基团具有不同的关系。这表明不同的化学结构对DNA序列特征具有不同的贡献。这些结论从非线性方法的角度对DNA序列的分析提供了新的思路。     

Evolutionary importance of the relationship between cytogeography and climate: New insights on creosote bushes from North and South America

Relationships between genome size and environmental variables suggest that DNA content might be adaptive and of evolutionary importance in plants. The genus Larrea provides an interesting system to test this hypothesis, since it shows both intra- and interspecific variation in genome size. Larrea has an amphitropical distribution in North and South American deserts, where it is most speciose. Larrea tridentata in North America shows a gradient of increasing autopolyploidy; while three of the four studied South American species are diploids, Larrea divaricata, Larrea nitida, Larrea ameghinoi, and the fourth is an allopolyploid, Larrea cuneifolia. We downloaded available focal species’ georeferenced records from seven data reservoirs. We used these records to extract biologically relevant environmental variables from WorldClim at 30 arc seconds scale, to have a broad characterization of the variable climatic conditions of both regions, and a climatic envelope for each species. We estimated relative DNA content index and relative monoploid genome values, by flow cytometry, of four most abundant Larrea species throughout their respective ranges. Then we winnow the bioclimatic dataset down to uncorrelated variables and sampled locales, to analyse the degree of association between both intra- and interspecific relative DNA content and climatic variables that are functionally relevant in arid environments using Pearson correlations, general linear and mixed effects models. Within the genus Larrea, relative DNA content increases with rising temperature and decreases with rising precipitation. At the intraspecific level, all four species show relative DNA content variation across climatic conditions. Larrea is a genus that shows genome size variation correlated with climate. Our results are also consistent with the hypothesis that extreme environmental pressures may have facilitated repeated whole genome duplication events in North America, while in South America, reticulate evolution, as allopolyploidization, and speciation might have been climate-dependent since the Oligocene.     

Infrared studies of deoxyribonucleic acids, their consituents and analogues. II. Deoxyribonucleic acids with different base composition

The base composition of DNA from microorganisms varies over a wide range of guanine + cytosine (G-C) content. We have examined the infrared spectra of a number of DNA samples isolated from different microorganisms and have found marked differences in their infrared spectra. These differences have been related to the G-C content of the investigated DNA samples. A comparison between the infrared spectra of nucleosides, synthetic polynucleotides, apurinic acid, and apyrimidinic acid has permitted a more extensive assignment of infrared bands to distinct base residues. The relative intensity of the absorption bands at 1485 and 1505 cm.^?1 depends on the G-C content of the deuterated DNA sample. On the basis of these results a new method for the determination of the G-C content in DNA has been developed from the results. Its advantage is that the measurement is rapid and the DNA samples are not changed by the procedure.     

High resolution DNA content measurements of mammalian sperm

The high condensation and flat shape of the mammalian sperm nucleus present unique difficulties to flow cytometric measurement of DNA content. Chromatin compactness makes quantitative fluorescent staining for DNA difficult and causes a high index of refraction. The refractive index makes optical measurements sensitive to sperm head orientation. We demonstrate that the optical problems can be overcome using the commercial ICP22 epiillumination flow cytometer (Ortho Instruments, Westwood, MA) or a specially built cell orientating flow cytometer (OFCM). The design and operation of the OFCM are described. Measurements of the angular dependence of fluorescence from acriflavine stained rabbit sperm show that it is capable of orienting flat sperm with a tolerance of +/- 7 degrees. Differences in the angular dependence for the similarly shaped bull and rabbit sperm allow discrimination of these cells. We show that DNA staining with 4-6 diamidino-2-phenylindole (DAPI) or an ethidium bromide mithramycin combination allows resolution of the X and Y populations in mouse sperm. They have also been successful with sperm from the bull, ram, rabbit, and boar. Reliable results with human sperm are not obtained. The accuracy of the staining and measurement techniques are verified by the correct determination of the relative DNA content of these two populations in sperm from normal mice and those with the Cattanach [7 to X] translocation. Among the potential uses of these techniques are measurement of DNA content errors induced in sperm due to mutagen exposure, and assessment of the fractions of X and Y sperm in semen that may have one population artifically enriched.     

正常人及不育者精子核DNA的定量研究

用流式细胞术,Feulgen显微分光光度法,荧光显微分光光度法测定正常人精子核DNA相对含量:结果表明,上述方法所测得的精子核DNA相对含量稳定,变化范围小。同时用Feulgen显微分光光度法测定不育者精子核DNA相对含量。显示不育者精子核DNA相对含量高于正常人,提示精子核DNA核蛋白复合物异常可能是某些男性不育症的原因。此项研究为诊断男性不育症提供了新方法,在男性学精子核分子研究方面提供了依据。     

NMR study of the structural transition in the DNA-bound water system in the interval of physiological temperatures

Temperature dependence of spin-spin proton relaxation times of DNA and bound water and the content of bound water in the samples of DNA, saturated with water in the atmosphere with different relative humidities from 0 to 100% were studied by means of pulsed NMR. It is shown that the temperature transition in the system of DNA-bound water in the interval 18-35 degrees is observed only when the relative humidity is more than 70% and the double-stranded structure of DNA exists. The transition of DNA from one conformation into another passes through some intermediate state more labile and probably less ordered. This transition is accompanied by changes in the structure of the hydration shell. In the case when relative humidity is greater than 80%, the partial dehydration of DNA stimulated by the transition is observed. This dehydration increases with the increase of relative humidity.     

Development of a spot reliability evaluation score for DNA microarrays

We developed a reliability index named SRED (Spot Reliability Evaluation Score for DNA microarrays) that represents the probability that the calibrated gene expression level from a DNA microarray would be less than a factor of 2 different from that of quantitative real-time polymerase chain reaction assays whose dynamic quantification range is treated statistically to be similar to that of the DNA microarray. To define the SRED score, two parameters, the reproducibility of measurement value and the relative expression value were selected from nine candidate parameters. The SRED score supplies the probability that the expression level in each spot of a microarray is less than a certain-fold different compared to other expression profiling data, such as QRT-PCR. This score was applied to 1,500,000 points of the expression profile in the RIKEN Expression Array Database.