Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “nuclear DNA”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2Linked to original sources
PubMed1976

[Isolation of mitochondrial DNA, purified of nuclear DNA, from animal tissues (degree of methylation and level of pyrimidine nucleotide clustering--criteria of purity)].

A method of preparation of mitochondria free of nuclear DNA and its fragments by treatment of mitochondria with DEAE-cellulose has been developed. This method is based on binding nuclear nucleic acids and nucleoproteins to DEAE-cellulose particles in the media used for isolation of mitochondria. Treatment with DEAE-cellulose under the conditions described does not induce any visible degradation of mitochondria and mitochondrial DNA. The mitochondrial DNA preparations obtained from beef and rat liver are represented with closed circular molecules of contour length about 5.5 mu. The 5-methylcytosine content in beef and rat mitochondrial DNA (3.03 and 2.0 mole %, respectively) is twice as much as in corresponding nuclear DNA. Besides, mitochondrial DNA strongly differs from nuclear ones by a lower degree of pyrimidine clustering: the amount of mono- and dipyrimidine fragments (about 32 mole %) in mitochondrial DNA is 1.5 times as large and the content of long pyrimidine clusters (hexa- and others) is 2--4 times as low as those in nuclear DNA. The methylation level and the pyrimidine clustering degree may be used as criteria for the purity of mitochondrial DNA from nuclear DNA.

Animals↗
PubMed2000

Neuronal nuclear DNA fragmentation in the aged canine brain: apoptosis or nuclear DNA fragility?

Neuronal DNA fragmentation, as revealed with the method of in situ end-labeling of nuclear DNA fragmentation (TUNEL), has been reported in both the canine and human brains in normal ageing, and in some human age-related neurodegenerative diseases. These results have suggested that apoptosis plays an important role in age-related neuronal loss. It is not clear, however, whether the TUNEL method is highly specific for apoptosis, as DNA fragmentation also occurs in the late stages o necrosis. In this study we have examined 27 dogs aged from 8 to 18 years, to investigate the occurrence of nuclear DNA fragmentation. An autolysis index based on current histological criteria was assigned to each animal to evaluate the effects of autolysis on nuclear DNA integrity. Our results have shown that neuronal nuclear DNA fragmentation is frequent in aged dogs, although it is not accompanied by apoptotic morphology. Yet, a positive relation between TUNEL labelling and the degree of tissue autolysis was observed. In contrast, no TUNEL labelling was detected in young control dogs despite autolysis indices being similar to those in aged dogs. Taken together, these results suggest that neuronal nuclear DNA fragmentation is an age-related phenomenon, not due to apoptosis, whenever other factors render neuronal DNA more susceptible to autolytic fragmentation. We confirm the effect of autolysis in a subpopulation of neurons in the aged canine brain, inducing nuclear DNA fragmentation.

Aging↗
PubMed1995

[The objective comparison of nuclear DNA content with nuclear grade in breast cancer].

Relationship between nuclear DNA contents and nuclear grade was investigated objectively in 76 invasive ductal breast cancer patients. DNA ploidy and S-phase fraction (SPF) were determined by flow cytometry in fresh frozen specimens. Nuclear grade was evaluated objectively as nuclear area (NA) or coefficiency variant of NA (NA.CV) calculated from morphmeter on H-E stained imprint preparation and needle aspiration smear preparation. NA and NA.CV on each preparation of aneuploid tumors (38) were significantly higher than those of diploid tumors (36). No correlation between NA and SPF was found in both diploid and aneuploid tumors. SPF was related to NA.CV on each preparation only in aneuploid tumors. NA and NA.CV on needle aspiration smear preparation had good relationship to those on H-E stained imprint preparation. These results demonstrated that NA and NA.CV on each preparation reflect DNA contents more objectively and suggested that needle aspiration smear might be useful to estimate the biological malignancies for selection of operative method and decision of neoadjuvant therapy.

Adult↗
PubMed1993

Eliminating mitochondrial DNA competition for nuclear DNA primers.

Mitochondrial DNA (mtDNA) sequences were synthesized with nuclear DNA (nucDNA) sequence-tagged site (STS) primers by mismatch priming in three independent studies of the human nuclear genome. Mismatch primer binding sites on the mtDNA were identified with from 6- to 10-bp identity at the 3' ends of the primers. In two of three cases, single-stranded mtDNA copies were gel-isolated with intended nucDNA PCR products. During routine screening of the STSs, the radiolabeled gel-isolated products hybridized to polymorphic mtDNA restriction fragments. Intense signals after overnight exposure of radiolabeled PCR probes on Southern blots suggest contaminating mtDNA PCR products. The theoretical annealing temperatures of the mismatches were well below the annealing temperatures of the PCR primers, demonstrating annealing reactions driven by the molar surplus of the primers, that is, mass action. The probability that two primers (either one of a pair or both), designed to amplify nucDNA, will bind to and amplify mtDNA may be as high as 1 in 64, assuming that an identical match with only the 3' hexanucleotide is sufficient for amplification. To circumvent this problem we have developed OLIGFIND, a program that has identified the 104 of 4096 possible hexamers that are not present in human mtDNA. Our results suggest that time could be saved by designing STS primers with one of these 104 hexamers at the 3' end. OLIGFIND can also evaluate primer 3' ends for potential PCR products from mtDNA.

Base Sequence↗
PubMed2004

DNA-dependent protein kinase (DNA-PK) phosphorylates nuclear DNA helicase II/RNA helicase A and hnRNP proteins in an RNA-dependent manner.

An RNA-dependent association of Ku antigen with nuclear DNA helicase II (NDH II), alternatively named RNA helicase A (RHA), was found in nuclear extracts of HeLa cells by immunoprecipitation and by gel filtration chromatography. Both Ku antigen and NDH II were associated with hnRNP complexes. Two-dimensional gel electrophoresis showed that Ku antigen was most abundantly associated with hnRNP C, K, J, H and F, but apparently not with others, such as hnRNP A1. Unexpectedly, DNA-dependent protein kinase (DNA-PK), which comprises Ku antigen as the DNA binding subunit, phosphorylated hnRNP proteins in an RNA-dependent manner. DNA-PK also phosphorylated recombinant NDH II in the presence of RNA. RNA binding assays displayed a preference of DNA-PK for poly(rG), but not for poly(rA), poly(rC) or poly(rU). This RNA binding affinity of DNA-PK can be ascribed to its Ku86 subunit. Consistently, poly(rG) most strongly stimulated the DNA-PK-catalyzed phosphorylation of NDH II. RNA interference studies revealed that a suppressed expression of NDH II altered the nuclear distribution of hnRNP C, while silencing DNA-PK changed the subnuclear distribution of NDH II and hnRNP C. These results support the view that DNA-PK can also function as an RNA-dependent protein kinase to regulate some aspects of RNA metabolism, such as RNA processing and transport.

Adenosine Triphosphatases↗
PubMed1987

The application of microspectrocytofluorometric measurement of Feulgen nuclear DNA content to experimental tumors of rat submandibular gland. 1. Pathogensis and nuclear DNA content.

Pellets containing 9,10-dimethyl-1,2-benzanthracene (DMBA) were inserted into the submandibular glands of 65 male Fischer rats to determine the nuclear DNA content of both metaplastic epithelium during the process of development of squamous metaplasia (noted at 1, 2, 5, 7, 9, 10, 11, 13 and 15 weeks after insertion) and tumor cells of squamous cell carcinoma 24 weeks after insertion. From the second week of insertion onward, squamous metaplasia was found in excretory duct remaining epithelium in the tissues around the pellet. Dysplasia or a lining of metaplastic epithelium with atypia adjacent to pellets (i.e., formation of an epidermal cyst) was observed 5 weeks after insertion. Coincident with this dysplasia or metaplastic epithelium with atypia, variation in the nuclear DNA content was observed, showing the emergence of octaploids and a widespread histogram pattern with many peaks. Between 7 and 15 weeks, 25%-66% of the lining metaplastic epithelium showed variation in the nuclear DNA content due to shift of a peak (major mode) to a triploid as well as a vague major mode with the appearance of octaploids, etc. Tumors of the submandibular gland were recognized at 24 weeks in 11 (55%) of 20 rats. Nine were keratinized squamous cell carcinomas and the remaining 2 were carcinosarcomas. Marked abnormalities in the nuclear DNA content were observed in 5 of the 11 rats (45.5%), 3 with keratinizing squamous cell carcinoma and 2 with carcinosarcomas. In contrast, no marked variation in the nuclear DNA content was found in 5 rats in which the tumor was associated with cysts.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed1994

[Flow cytometric analysis of nuclear DNA content of lung cancer--correlation between nuclear DNA content and tumor doubling time].

A total of 65 resected cases with primary lung cancer were examined on correlation between nuclear DNA content by flow cytometry and other prognostic factors, including tumor doubling time (DT). 1) DNA diploidy was found in 18 cases (28%) and DNA aneuploidy in 47 cases (72%). Percent aneuploidy was 79.5% in cases with adenocarcinoma, which tended to be higher than that in cases with squamous cell carcinoma (57.1%). 2) Percent aneuploidy in cases with advanced carcinomas tended to be higher than that in cases with earlier carcinomas, and percent aneuploidy in cases with rapid growing carcinomas tended to be higher than that in cases with slow growing carcinomas. 3) The geometric mean of DT of DNA aneuploid tumor was 130.0 day, which tended to be shorter than that of DNA diploid tumor (171.9 days), but the difference was not significant. There was not a significant correlation between DT and DNA Index. 4) The five-year survival rate of 47 patients with DNA aneuploid tumor was 45%, which was significantly lower than that of 18 patients with DNA diploid tumor (78%).

Cell Division↗
PubMed1993

Paragangliomas. Static cytometric studies of nuclear DNA patterns.

BACKGROUND: The biologic behavior of most paragangliomas cannot be predicted from their histologic appearance. Recently, cytometric studies have found an association between an aggressive clinical behavior and the presence of a hyperdiploid or tetraploid range in the DNA nuclear content. METHODS: The authors have studied morphometric (nuclear area and nuclear form factor) and DNA densitometric (integral optical density and DNA ploidy) features of 23 cases of paraganglioma by means of slide cytophotometry with the microTICAS system (University of Chicago, Chicago, IL). The samples were selected from paraffin-embedded tissue, and representative sections were stained with the Feulgen technique. The differences between groups (cervical versus extracervical paragangliomas) were investigated with the Mann-Whitney test and Fisher discriminant linear function. RESULTS: The densitometric study showed aneuploid cell lines in 15 of 16 noncervical paragangliomas (with a DNA index within the tetraploid range), whereas 3 of 7 cervical paragangliomas were aneuploid and only 1 case did not have not a diploid cell line (with a DNA index within the peridiploid range). Mean ploidy (4.33 arbitrary units [AU] and 2.72 AU, respectively), nuclear area (58.74 microns 2 and 32.08 microns 2, respectively), the minor and major DNA indices (1.09-1.24 and 1.83-1.96, respectively), and DNA content variability (2c deviation indices [2cDI] of 8.62 and 1.88 AU, respectively) were higher in noncervical paragangliomas. With Fisher linear discriminant function, mean nuclear area (P = 0.0008), 2cDI (P = 0.0030), and the minor DNA index of each cell proliferation were correlated with location. None of the variables established statistically significant differences in comparisons of malignant and benign paragangliomas. CONCLUSIONS: Karyometric and DNA densitometric parameters have limited value in determining the prognosis of paragangliomas, although they are correlated with tumoral location, which is still an indicator in establishing the prognosis of these neoplasms.

Adolescent↗
PubMed1988

Degree of malignancy of thymic epithelial tumors in terms of nuclear DNA content and nuclear area. An analysis of 39 cases.

For determination of the degree of malignancy among thymic epithelial tumors, the DNA content and area of nuclei in 13 cases each of noninvasive thymoma, invasive thymoma, and thymic carcinoma were investigated by cytofluorometry and morphometry. The nuclear DNA content was determined in terms of the mean nuclear DNA content, DNA histogram pattern, and the occurrence of the aneuploid stem cell line. The mean nuclear DNA content of the thymic carcinoma was significantly higher than that of both subgroups of thymoma (P less than 0.01), but there was no significant difference between noninvasive and invasive thymomas. The aneuploid stem cell line appeared in 92.3% of thymic carcinomas, one case (7.7%) of invasive thymomas, and none of noninvasive thymomas. Abnormal DNA histogram patterns were seen in 53.8% of thymic carcinomas and none of the thymomas. The mean nuclear area increased significantly in the increasing order of noninvasive thymoma, invasive thymoma, and thymic carcinoma (P less than 0.01). The cytofluorometric and morphometric results demonstrated a significant difference in degree of malignancy between thymic carcinoma and thymoma; however, there was a trend toward an increasing degree of malignancy from noninvasive to invasive thymomas, yet there was a sizeable overlap in results between the two groups. Therefore, these two methods are not satisfactory for predicting the behavior of an individual case of noninvasive or invasive thymoma.

Adult↗
PubMed1989

Reference standards for flow cytometry and application in comparative studies of nuclear DNA content.

Nuclear DNA mass in cells from a reference species can be used to obtain high-resolution estimates of DNA mass from a target species. In our study of DNA mass in cells from 45 selected species, representing each of the major vertebrate classes, we have obtained values of from 1.5 to 110.0 pg of DNA. Because values in or near this range would be expected in the study of nuclear DNA mass in vertebrates and other organisms, the species in this report can provide a useful catalogue of references for comparative studies of DNA.

Animals↗
PubMed1993

Nuclear DNA patterns in adrenal cortex proliferative lesions.

In cortical adrenal gland tumours there are discrepancies between morphological criteria for malignancy and biological behaviour. This makes it difficult to select the appropriate treatment. We have studied morphometric and DNA densitometric features of 24 adrenal proliferative lesions (hyperplasia, adenoma, and carcinoma) by means of slide cytometry. All variables have been correlated with pathological diagnosis. The samples were selected from paraffin-embedded tissue, and representative lesions were Feulgen stained. Densitometric study showed aneuploid cell lines in every carcinoma, 5 of 8 adenomas, and 5 of 10 hyperplastic lesions. Both DNA nuclear content (mean ploidy of 2.11 c, 2.41 c, and 3.05 c) mean nuclear area (average of 31.26 microns 2, 35.92 microns 2, and 42.39 microns 2) showed progressive increase from hyperplasia to adenoma, and carcinoma. Mean shape factors were lowest in adenomas (1.69) and highest in carcinomas (1.82). Those karyometric variables which showed statistically significant differences (p < 0.05) among diagnostic groups were included in a stepwise three-way discriminant analysis. Only three parameters, shape factor (p = 0.0008), mean ploidy (p = 0.0012), and adrenal weight (p = 0.0055) persisted as independent predictive factors. Using the three variables selected by discriminant analysis on our cases, 100% of the adenomas were correctly classified, 83% of the carcinomas, and 80% of the hyperplasias. Tumour weight and nuclear shape factor differentiated adrenal cortex adenoma from carcinoma, while mean ploidy distinguished adrenal cortical hyperplasia from carcinoma. Nuclear pleomorphism (shape factor) and DNA-ploidy are the most important nuclear features in predicting the biological course of proliferative adrenal cortex lesions, although by themselves they are not bona-fide discriminators.

Adenoma↗
PubMed1987

The application of microspectrocytofluorometric measurement of Feulgen nuclear DNA content in experimental tumors of rat submandibular gland, 2. The correlation between proliferative ability and nuclear DNA content of tumor tissue in autotransplanted areas.

We have reported that there is a difference in the variation of the nuclear DNA content of tumor cells among cases of squamous cell carcinoma induced by 9,10-dimethyl-1,2-benzanthracene (DMBA) in the rat submandibular gland. In the present investigation, the relationship between the nuclear DNA content of tumor cells in autotransplanted sections collected from primary lesions of DMBA-induced tumors and their proliferative ability in the subfascial area of the rat abdomen was examined. As a result of autotransplantation, proliferation in the autotransplanted area was observed in 6 of 14 (42.8%) cases of autotransplantation. Five of these had a keratinizing squamous cell carcinoma while the remaining one had a sarcomatoid tumor. The histological type of the tumor of the proliferative lesion in the transplanted area was very similar to that of the tumor tissues in the primary lesion or the transplanted section collected from the primary lesions. In the proliferative group, marked variation of the nuclear DNA content was observed in the tumor cells of the transplanted section. The proliferative index (PI) was high for these tumor cells in this group. There was no variation in the nuclear DNA content in the tumor cells of the nonproliferative group, and the PI was also low. These results were considered to suggest that there was a correlation between the nuclear DNA content of these experimental tumor cell and their proliferative ability in the autotransplanted area. Therefore, the determination of nuclear DNA content by this method can be used as an objective index of the proliferative ability of tumor tissue.

Animals↗
PubMed2003

Differences in mitochondrial and nuclear DNA status of high-density and low-density sperm fractions after density centrifugation preparation.

OBJECTIVE: To determine the mitochondrial DNA and nuclear DNA fragmentation of sperm populations separated by using discontinuous density gradient. DESIGN: Analysis of mitochondrial and nuclear DNA status of sperm from high and low density layers. SETTING: Regional fertility center. PATIENT(S): Twenty-eight men who presented for an initial infertility investigation. MAIN OUTCOME MEASURE(S): Semen was prepared by using discontinuous density gradient (90.0%:45.0%) and subjected to a modified long polymerase chain reaction to assess mitochondrial DNA deletions and to a modified single-cell alkaline gel electrophoresis assay to determine nuclear DNA fragmentation. RESULT(S): The high-density fraction displayed significantly more wild-type mitochondrial DNA (75% of samples) than did the low-density fraction (25% of samples). In the high-density fraction, the incidence of single deletions was higher than that of double or multiple deletions, and the deletions were predominantly small. A strong correlation was observed between nuclear DNA fragmentation and the number and size of mitochondrial DNA deletions. CONCLUSION(S): Density centrifugation isolates a population of sperm with high-quality mitochondrial DNA and nuclear DNA.

Adult↗
PubMed1992

[Comparison between nuclear DNA and histologic grade of prostatic carcinoma].

DNA nuclear ploidy determined by flow cytometry was evaluated from prostate tissue in 51 patients with prostatic cancer who had undergone radical prostatectomy. DNA ploidy pattern was diploid in 46% and aneuploid in 54% of tumors. DNA ploidy was compared to histological tumor grading. 92 Aneuploidy was found in 0% of the tumors with Gleason score between 2 and 4 in 62% between 5 and 7 and in 50% between 8 and 10. Our results suggest there is no relationship between the two parameters.

Aged↗
PubMed1978

Evidence that the amount of chloroplast DNA exceeds that of nuclear DNA in mature leaves.

Cell-free homogenates containing intact chloroplasts and nuclei were allowed to settle for up to 1 h before the top 2 ml of the 5-ml homogenate was withdrawn. Whereas less than 18% of the chloroplasts moved from the top to the bottom portions, the ratio of nuclei to chloroplasts in the top portion changed from approximately 1/200 to 1/900. The total numbers of chloroplasts and nuclei were counted in the homogenate before settling and in the top 2 ml and bottom 3 m1 after settling. The total DNA content of the homogenate and the top and bottom portions after settling was determined by the diphenylamine colorimetric assay. By simultaneous equations, the absolute amount of DNA in chloroplasts and nuclei was determined. The results are consistent with previous observations of chloroplast DNA by fluorescence microscopy which indicated that the amount of chloroplast DNA per chloroplast is a function of chloroplast size. In addition, the results show that the amount of chloroplast DNA per average chloroplast in large leaves is 0.14 times 10(-12) g, a magnitude higher than previous reports in the literature, and that large leaves contain about twice as much chloroplast DNA as nuclear DNA.

Cell Fractionation↗
PubMed1992

Evaluation of DNA nuclear pattern as a prognostic determinant in resected pancreatic ductal adenocarcinoma.

From a cohort of 72 patients who underwent radical resection for ductal adenocarcinoma of the pancreas between 1951 and 1980, 62 paraffin-embedded specimens were analyzed by flow cytometry. Patients were divided into two groups according to the length of survival: long-term survivors (19 patients who survived 3 or more years after operation) and short-term survivors (43 patients who died within 12 months after resection). In 30 specimens (48%), the nuclear DNA pattern was diploid, whereas 32 were nondiploid (two tetraploid and 30 aneuploid). There were no significant differences in the number of diploid/nondiploid patterns, the fraction of cells in DNA synthetic (S) phase, or the DNA index between the two groups. These data suggest that there is no difference in the DNA content analysis of patients with pancreatic ductal adenocarcinoma when comparing long-term with short-term survivors following resection.

Carcinoma, Intraductal, Noninfiltrating↗
PubMed1995

Flow cytometric nuclear DNA content analysis of renal tumors in children: prognostic significance of nuclear DNA ploidy.

We studied, by flow cytometry, the DNA contents of paraffin-embedded tumor specimens from 90 infants and children with kidney tumors, and analyzed the relationship of DNA ploidy with histological types and prognosis. Data of adequate quality were obtained from 90 cases: 65 tumors with favorable histology, 5 congenital mesoblastic nephromas and 20 tumors with unfavorable histology. The 90 cases had nuclear DNA histogram patterns that were classified as DNA diploid in 64 tumors, aneuploid in 19 and tetraploid in 7. There were no significant correlations between DNA ploidy and histological types or clinical stages. Survival rates for patients with diploidy were 80 and 70% at 2 and 5 years, respectively, and those of patients with aneuploidy were 72 and 61% at 2 and 5 years, respectively. On the other hand, patients with a DNA tetraploid pattern had significantly worse survival rates of 43 and 29% at 2 and 5 years, respectively. Among patients with aneuploidy or tetraploidy, the S-phase fractions in those who died (mean +/- SD: 10.3 +/- 4.1 and 22.1 +/- 11.6%, respectively) appear to be greater than those in their surviving counterparts (8.8 +/- 4.0 and 12.1 +/- 2.8%). Hence, although the differences between diploid and aneuploid DNA patterns were not correlated with differential prognosis in children with kidney tumors, a tetraploid pattern clearly indicates a poor prognosis, especially in combination with histological types and clinical stages.

Adolescent↗