Showing papers on "Nuclear DNA published in 1987"

Restriction fragment polymorphisms in biological species of armillaria mellea

Abstract: This study used restriction fragment polymorphisms in nuclear and mitochondrial DNA to confirm what had been surmised from the studies of mating interactions among isolates of Armillaria mellea (broad sense): that the "biological species" are distinct entities among which genetic divergence has occurred. We examined the DNAs of 16 isolates representing 8 biological species. Three different types of DNA were used as probes in Southern hybridizations with EcoRI-digested, whole-cell or nuclear DNAs: i) total mitochondrial DNA from a strain of biological species I, ii) ten bacterial plasmid clones carrying random EcoRI fragments of nuclear DNA from a strain of biological species I, and iii) a plasmid clone carrying the entire rDNA repeat from Schizophyllum commune. Most of the restriction fragments identified were variable in the sample and most of the variability was between, rather than within, biological species.

Evolution of the genus Leishmania as revealed by comparisons of nuclear DNA restriction fragment patterns

Abstract: Restriction endonuclease DNA fragment patterns have been used to examine the relationships among 28 isolates of Leishmania as well as Crithidia, Endotrypanum, and Trypanosoma cruzi. Fragments of nuclear DNA were generated with six restriction enzymes, and blots were hybridized with probes from three loci. Among the major lineages the fragment patterns are essentially completely different, while within the major lineages various degrees of divergence are found. Molecular evolutionary trees were constructed using the method of Nei and Li to estimate the percent nucleotide sequence divergence among strains from the fraction of fragments shared. Defined groups, such as species or subspecies within the major lineages, are also grouped by nuclear DNA comparisons. Within the donovani complex, we find Leishmania donovani chagasi and Leishmania donovani infantum to be as similar as strains within Leishmania donovani donovani, consistent with the proposal by other workers that New World visceral leishmaniasis originated quite recently.

Nuclear DNA changes, genome differentiation and evolution in Nicotiana ( Solanaceae )

Abstract: A survey of 51 species fromNicotiana subgg.Tabacum, Rustica andPetunioides has shown that evolution was accompanied by a five-fold variation in nuclear DNA amounts. This variation, however, was not directly correlated with the changes in chromosome number. Drastic rearrangement of karyotypes is characteristic for the evolution ofNicotiana spp. Significant gain or loss in nuclear DNA has often accompanied such changes, but DNA variation has also occurred without significant changes in karyotype arrangements.—The distribution of nuclear DNA is discontinuous inNicotiana, species cluster into DNA groups with consistently regular increments in the mean DNA amounts. The discontinuities are viewed as “steady states” in terms of genomic balance and biological fitness.—Changes in the amount of nuclear DNA and in the heterochromatin are compared with the morphological, chromosomal and adaptive changes which accompanied speciation in 14 subgeneric sections. The evolutionary significance of DNA variation is discussed.

Inter and intraspecific variation in nuclear DNA content in Aedes mosquitoes

Abstract: Haploid nuclear DNA of 23 species of Aedes, as determined by Feulgen cytophotometry, was found to vary 3-fold. This was accompanied by a 2-fold variation in total chromosomal length. There was a significant correlation (r = 0·765, P<0·001) between these two parameters. Genome size varied from 0·87 pg to 1·3 pg among 10 strains of Aedes albopictus, from wide geographic regions. Large scale differences in chromosomal DNA amounts have accompanied speciation and evolution in aedine mosquitoes.

Nuclear DNA variation in the genus Allium L. (Liliaceae)

Abstract: 4C nuclear DNA contents were determined for 42 Allium species, selected from all major taxonomic sections in the genus. Estimates of nuclear volumes were also made. A range of 4C DNA values from 41·19 pg to 142·78 pg was found, largely unrelated to basic chromosome number, polyploidy or taxonomic group, but correlated with flowering time. The results are discussed in relation to distribution of DNA values in the genus, proportions of chromosome C-banding, breeding systems and climatic adaptation.

The Solution to the Cytological Paradox of Isomorphy

Abstract: Cells with polyploid nuclei are generally larger than cells of the same organism or species with nonpolyploid nuclei. However, no such change of cell size with ploidy level is observed in those red algae which alternate isomorphic haploid with diploid generations. The results of this investigation reveal the explanation. Nuclear DNA content and other parameters were measured in cells of the filamentous red alga Griffithsia pacifica. Nuclei of the diploid generation contain twice the DNA content of those of the haploid generation. However, all cells except newly formed reproductive cells are multinucleate. The nuclei are arranged in a nearly perfect hexagonal array just beneath the cell surface. When homologous cells of the two generations are compared, although the cell size is nearly identical, each nucleus of the diploid cell is surrounded by a region of cytoplasm (a "domain") nearly twice that surrounding a haploid nucleus. Cytoplasmic domains associated with a diploid nucleus contain twice the number of plastids, and consequently twice the amount of plastid DNA, than is associated with the domain of a haploid nucleus. Thus, doubling of ploidy is reflected in doubling of the size and organelle content of the domain associated with each nucleus. However, cell size does not differ between homologous cells of the two generations, because total nuclear DNA (sum of the DNA in all nuclei in a cell) per cell does not differ. This is the solution to the cytological paradox of isomorphy.

Relationship between nuclear DNA synthesis and centrosome reproduction in sea urchin eggs.

Abstract: The importance of nuclear DNA synthesis for the doubling, or reproduction, of centrosomes in cells that are not growth-limited, such as sea urchin eggs, has not been clearly defined. Studies of enucleated, fertilized eggs show that nuclear activities are not required at each cell cycle for the normal reproduction of the complete centrosome. However, other studies report that the inhibition of nuclear DNA synthesis in intact eggs by the drug aphidicolin prevents centrosome reproduction and entry into mitosis as seen by nuclear envelope breakdown. To resolve this paradox, we systematically characterized the effect of aphidicolin on cell division in eggs from three species of sea urchins. Eggs were continuously treated with 5 or 10 micrograms/ml aphidicolin starting 5 min after fertilization. This blocked total incorporation of 3H-thymidine into DNA by at least 90%, as previously reported. We found that the sperm aster always doubles prior to first mitosis. Over a period of several hours, the centrosomes reproduce in the normal 2-4-8-16 fashion, with a period that is longer and more variable than normal. In every culture, a variable percentage of the eggs undergoes nuclear envelope breakdown. Once broken down, the nuclear envelope never visibly reforms even though centrosomes continue to double. Fluorescent labeling of DNA revealed that the chromatin does not condense into discrete chromosomes. Whether or not the nuclear envelope breaks down, the chromatin appears as an amorphous mass of fibers stretched between first two and then four asters. Later, the nuclear envelope/chromatin loses its association with some or all centrosomes. Our results were the same for all eggs at both drug concentrations. Thus, nuclear DNA synthesis is not required for centrosome reproduction in sea urchin eggs.

Nuclear DNA amplification in cultured cells of Oryza sativa L.

Abstract: Highly repeated nuclear DNA sequences from suspension cultured cells of Oryza sativa L. cv. ‘Roncarolo’ have been cloned in pBR322. Ten clones with specific digestion patterns have been randomly selected. Nine sequences appear to be organized in a clustered tandem array while one is interpersed in the rice genome. The clones have been used to gather information on: (a) their modulation in cultured cells as compared to whole plant and (b) their distribution in different rice cultivars belonging to the Japonica or Indica subspecies of Oryza sativa L. Hybridization with nuclear DNA isolated either from suspension or from seedlings of the ‘Roncarolo’ cultivar revealed extensive quantitative variations, with most cloned sequences showing amplification (up to 75-fold) in cultured cells. Hybridization with nuclear DNA isolated from seedlings or suspension cultured cells from different cultivars belonging to the Japonica or to the Indica sub-species of O. sativa have shown that (a) amplification also occurs in a similar pattern in the case of DNA from the other tested suspension cultured cell types but not in the case of DNA from seedlings; (b) in some cases the tested sequences show minor but significant variations in different rice accessions.

DNA in Tree Species

Abstract: The DNA quantity and quality of the haploid chromosome complement is commonly termed genome, and the size of the genome and its organization is an important area of research in biology. The quantity or haploid nuclear DNA content (C-value) is given in picograms (10−12g) or daltons; the quality is characterized by the base sequence, the number of different nucleotide sequences (or complexity) and their frequency (or reiteration). The genomes of tree species are typical eukaryote genomes that differ from prokaryotes by their larger size, increased information content, excess of non-coding (repetitious) DNA, association of the DNA with acidic and basic proteins, and separation from the cytoplasm by a nuclear envelope.

Polyploid polymorphism in Andropogon gerardii

Abstract: The relationship between nuclear DNA content and chromosome number was investigated in Andropogon gerardii. The distribution of cytotypes in a natural population of this grass was also examined. Nuclear DNA content was determined using flow cytometry rather than the traditional method of Feulgen microphotometry. Our results demonstrate the increased accuracy and speed of this new method in the detection and study of polyploidy. Nuclear DNA content is strongly correlated to chromosome number in Andropogon gerardii (r = 0.971, P <0.01). The natural population of this grass was found to consist of plants with 2N = 60 chromosomes (hexaploid cytotype) and 2N = 80 chromosomes (octoploid cytotype), in equal proportions. Intermediate cytotypes were lacking in the natural population, although three progeny plants grown in the greenhouse from wild-collected seed show intermediate values of nuclear DNA content and have 2N = 70 chromosomes. The two coexisting cytotypes are intermingled and show no difference in micro...

Random-fragment hybridization analysis of evolution in the genus neurospora: the status of four-spored strains.

Abstract: A random-fragment hybridization method employing nuclear DNA has been developed to explore phylogenetic relationships in the genus Neurospora. Four cloned fragments and repetitive rDNA sequences were examined for restriction-fragment polymorphisms among 14 strains representing four species. The findings demonstrate that variation among randomly selected nuclear fragments can be employed to group related taxa with a higher degree of resolution than has been obtained with other DNA hybridization methods, isozyme electrophoresis, or restriction analysis of repetitive DNA. Based on our analysis of cloned fragments, we conclude that four-spored, secondarily-homothallic strains collected worldwide represent a monophyletic group. Trees constructed on the basis of restriction-fragment cataloging and coarse-structure restriction-site maps are for the most part consistent with the present mating-based species concept. We are encouraged that this method will provide an additional important experimental tool for evolutionary studies.

Genome size variation in North American minnows (Cyprinidae). II. Variation among 20 species.

Abstract: Genome sizes (nuclear DNA contents) from 200 individuals representing 20 species of North American cyprinid fishes (minnows) were examined spectrophotometrically. The distributions of DNA values of individuals within populations of the 20 species were essentially continuous and normal; the distribution of DNA values among species was continuous and overlapping. These observations suggest that changes in DNA quantity in cyprinids are small in amount, involve both gains and losses of DNA, and are cumulative and independent in effect. Significant heterogeneity in mean genome size occurs both between individuals within populations of species and among species. The former averages maximally around 6% of the cyprinid genome and is nearly the same as the amount of DNA theoretically needed for the entire cyprinid structural gene component. The majority of the DNA content variation among the 20 species is distributed above the level of individuals within populations. Comparisons of average genome size difference or distance between individuals drawn from different levels of taxonomic organization indicate that considerably greater divergence in genome size has occurred in the extremely speciose cyprinid genus Notropis as compared with other North American cyprinid genera. This may suggest that genome size change is concentrated in speciation episodes. Finally, no associations were found between interspecific variation in genome size and five life-history characters. This suggests that much of the variation in genome size within and among the 20 species may be phenotypically inconsequential.

Leiomyosarcomas and Benign Smooth Muscle Tumors of the Stomach: Nuclear DNA Patterns Studied by Flow Cytometry

Abstract: Paraffin-embedded archival tissue samples were used for determination of DNA ploidy by flow cytometry on 117 surgically resected gastric smooth muscle tumors (44 leiomyosarcomas, 53 leiomyomas, and 20 benign leiomyoblastomas). The technique of Hedley was used for preparation of paraffin-embedded tissue into single dissociated nuclei, and the method of Vindelov was used for staining with propidium iodide. Among the 53 leiomyomas, the DNA ploidy pattern was diploid in most tumors (87%), except for 2 DNA tetraploid/polyploid and 5 DNA aneuploid samples. In comparison, the 20 benign leiomyoblastomas had more frequent abnormal DNA histograms: DNA tetraploidy/polyploidy in 5 (25%) and DNA aneuploidy in 2 (10%). The DNA histograms of the 44 leiomyosarcomas (including 4 epithelioid leiomyosarcomas) were classified as follows: 20 cases (45%) exhibited a DNA diploid pattern, 14 cases (32%) had a DNA tetraploid/polyploid pattern, and 10 cases (23%) had DNA aneuploid peaks. For the patients with leiomyosarcomas, the DNA ploidy pattern was significantly correlated with survival (P

Tomato protoplast DNA transformation : physical linkage and recombination of exogenous DNA sequences

Abstract: Tomato protoplasts have been transformed with plasmid DNA's, containing a chimeric kanamycin resistance gene and putative tomato origins of replication. A calcium phosphate-DNA mediated transformation procedure was employed in combination with either polyethylene glycol or polyvinyl alcohol. There were no indications that the tomato DNA inserts conferred autonomous replication on the plasmids. Instead, Southern blot hybridization analysis of seven kanamycin resistant calli revealed the presence of at least one kanamycin resistance locus per transformant integrated in the tomato nuclear DNA. Generally one to three truncated plasmid copies were found integrated into the tomato nuclear DNA, often physically linked to each other. For one transformant we have been able to use the bacterial ampicillin resistance marker of the vector plasmid pUC9 to 'rescue' a recombinant plasmid from the tomato genome. Analysis of the foreign sequences included in the rescued plasmid showed that integration had occurred in a non-repetitive DNA region. Calf-thymus DNA, used as a carrier in transformation procedure, was found to be covalently linked to plasmid DNA sequences in the genomic DNA of one transformant. A model is presented describing the fate of exogenously added DNA during the transformation of a plant cell. The results are discussed in reference to the possibility of isolating DNA sequences responsible for autonomous replication in tomato.

Yield of DNA-Protein Cross-Links in γ-Irradiated Chinese Hamster Cells

Abstract: γ-Irradiation of Chinese hamster V79 cells increases the percentage of nuclear DNA cross-linked to proteins. Studies were carried out to ascertain whether the radiation-induced increase in DNA-protein cross-links (DPC) is due to an increase in the number of DNA fragments which are cross-linked to protein or to an increase in the size of bound DNA fragments. Cells were prelabeled with [ 3 H]thymidine and irradiated (10-600 Gy), and DPCs were collected on nitrocellulose filters. Native gel analyses of the DNA recovered from the filters indicate that the number average molecular weight of cross-linked DNA (1.22 × 10 7 Da) is the same in unirradiated cells and in cells given up to 100 Gy. Assuming 5 pg of DNA per V79 cell, it was possible to calculate that there are approximately 6 × 10 3 DPC per unirradiated cell and that 150 DPC are formed per gray of γ-radiation for doses of 0–100 Gy. Thus, radiation increases the number of new linkages between DNA and protein. At radiation doses greater than 200 Gy the percentage of nuclear DNA cross-linked to protein approaches a plateau value. The number of DPC (>6 × 10 4 ) formed at higher doses is within the range of the estimated number of DNA attachment sites on the nuclear matrix.

Variable copy number DNA sequences in rice

Abstract: We have cloned two types of variable copy number DNA sequences from the rice embryo genome. One of these sequences, which was cloned in pRB301, was amplified about 50-fold during callus formation and diminished in copy number to the embryonic level during regeneration. The other clone, named pRB401, showed the reciprocal pattern. The copy numbers of both sequences were changed even in the early developmental stage and eliminated from nuclear DNA along with growth of the plant. Sequencing analysis of the pRB301 insert revealed some open reading frames and direct repeat structures, but corresponding sequences were not identified in the EMBL and LASL DNA databases. Sequencing of the nuclear genomic fragment cloned in pRB401 revealed the presence of the 3′rps12-rps7 region of rice chloroplast DNA. Our observations suggest that during callus formation (dedifferentiation), regeneration and the growth process the copy numbers of some DNA sequences are variable and that nuclear integrated chloroplast DNA acts as a variable copy number sequence in the rice genome. Based on data showing a common sequence in mitochondria and chloroplast DNA of maize (Stern and Lonsdale 1982) and that the rps12 gene of tobacco chloroplast DNA is a divided gene (Torazawa et al. 1986), it is suggested that the sequence on the inverted repeat structure of chloroplast DNA may have the character of a movable genetic element.

Nucleotide sequence and molecular characterization of a maize mitochondrial plasmid-like DNA.

Abstract: The mitochondrial genome of Black Mexican Sweet maize consists of the principal genome, a 2.3 kb minilinear DNA, a 1,913 by (1.9 kb) and a 1,445 bp (1.4 kb) minicircular DNA. The three extrachromosomal DNAs exhibit characteristics of autonomous replication in cell suspension culture. The complete sequence of the 1.4 kb minicircle was determined. It has 61 by of near perfect sequence homology to the 1.9 kb minicircle. Both minicircular DNAs are transcriptionally active; the longest open reading frame of the 1.4 kb minicircle was 231 bp. A putative origin of replication was identified as a high A+T sequence. These minicircles were present in some but not all of 20 maize lines surveyed. None of the lines examined carried the 1.4 kb minicircle without the 1.9 kb minicircle. Nuclear DNA of one line of the seven examined carried homology to both DNAs.

Nuclear DNA contents in the genus Ficus (Moraceae)

Abstract: Nuclear DNA contents in 15 species of large tropical hardwood genusFicus have been determined by cytophotometry. The 2 C-values are rather low and uniform, suggesting no appreciable changes during speciation. The small genome size is discussed in relation to woody habit.

DNA content polymorphism and tissue culture regeneration in Caribbean pine

Abstract: The three varieties of Caribbean pine have significantly different amounts of nuclear DNA: Pinus caribaea var. caribaea, 11.5; P. caribaea var. hondurensis, 21; and, P. caribaea var. bahamensis, 25 pg. Dormant embryos of the three varieties had more nuclear DNA than germinating seedlings, and this extra DNA was spread through several classes from 2C to 7C; however, upon germination the seedling DNA rapidly reorganizes into the 2C–4C distribution typical of diploid plants. DNA content polymorphism of the dormant embryos among the three varieties was directly correlated with the diploid amount of DNA and with needle and cotyledon diversity. Buds regenerated from dormant embryo explants in tissue culture were genetically stable; however, the roots of regenerated plants had DNA contents ranging up to nine times the haploid amount. The instability is ascribed to the auxin content of the rooting medium, but buds regenerated or growing on this medium were stable. This bud stability and the production of buds on ...

Analysis of DNA size, content and cell cycle in leaves of Napier grass (Pennisetum purpureum Schum.).

Abstract: Mesophyll cell nuclei isolated from leaves of Pennisetum purpureum were analysed by flow cytometry to determine the nuclear DNA content and the percentage of cells in different phases of the cell cycle. Samples taken from base, middle and tip regions of leaves 2 to 8 (leaf 1, which was adjacent to the meristem, was too small to sample) showed no significant differences in the amount of DNA per G1 nucleus due to either age or position. The average amount of DNA per G1 nucleus was 5.78 pg. Although the majority of cells for each sample were in G1, samples taken from older leaves had higher percentages of cells in G2 and S phases. More specifically, base and middle regions of older leaves had a higher percentage of cells in G2 than all three positions in younger leaves. Electrophoretic analysis of nuclear DNA from leaves 2 to 7 showed no evidence of degradation or difference in fragment size for any sample or position. This study was compared to previous work on the relationship between leaf age and embryogenic competence in Pennisetum purpureum. The results suggest that changes in the cell cycle, and/or a loss or fragmentation of the nuclear DNA, are not responsible for loss of embryogenic competence in mature leaf tissue.

Ploidy and proliferative activity of human brain tumors. A flow cytofluorometric study.

Abstract: Ploidy and proliferative characteristics were estimated by flow cytometry of the nuclear DNA content of 92 human brain tumors. Samples were frozen at -20 degrees C immediately after surgery and single cell suspensions were obtained with a mechanical dissociation technique. Propidium iodide was employed for nuclear DNA staining. Human normal brain tissue was used as internal diploid reference standard. 86% of benign tumors had unimodal DNA distribution with a DNA index (DNA I = modal channel of the G0/1 peak of the studied population/modal channel of the G0/1 peak of the normal brain) usually within the diploid or near-diploid range. 14.0% had aneuploidy, with an additional cell peak having a median DNA I of 1.60. Among malignant tumors, these figures were 61.2 and 38.8% (p less than 0.001). The percentage of S phase cells was higher in malignant (median = 3.6) than in benign tumors (median = 2.0, p less than 0.01), without correlation to histological tumor subtype. Flow cytometry appears to be a useful method for evaluating differences in DNA distribution in tumors of the central nervous system.

Sequence homology to the Drosophila per locus in higher plant nuclear DNA and in Acetabularia chloroplast DNA.

Abstract: In plant cells a DNA sequence was found which is homologous to the Drosophila per locus. In rape and spinach the homologous sequence occurs in the nuclear but not in the chloroplast genome while in Acetabularia it is found in the chloroplast but not in the nuclear genome. A 1.175 kb EcoRI-SalI fragment of the chloroplast genome of Acetabularia containing the homologous sequence was subcloned into pUC12 and sequenced. The core of the 1.175 kb fragment is a repetitive tandemly arranged sequence of 43 units of the hexamer GGA ACT coding for glycine and threonine.

A DNA cytophotometric and chromosome banding study in Hedera helix (Araliaceae), with reference to differential DNA replication associated with juvenile–adult phase change

Abstract: The present DNA cytophotometric and chromosome banding comparison of the juvenile and the adult developmental phase in the common ivy, Hedera helix, was undertaken as an attempt to verify or refute the asserted phase-correlated differential DNA replication in this plant. No statistically significant differences between the two developmental phases were found in genome size (as determined from mitotic nuclei), nuclear DNA content in resting meristems and somatic leaf tissues, and content of constitutive heterochromatin as measured from C-banded metaphase plates. There is no evidence for differential DNA replication in Hedera helix. Key words: Hedera helix, differential DNA replication, morphogenesis, genome size, chromosome structure.