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Dna fragmentation factor 45 mutant mice exhibit resistance to kainic acid-induced neuronal cell death.

Excitotoxicity is a process where glutamate or other excitatory amino acids induce neuronal cell death. Emerging evidence suggests that apoptosis plays a key part in excitotoxic neurodegeneration. The DNA fragmentation factor 45 (DFF45 or ICAD) is a subunit of a heterodimeric DNase complex crucial for DNA fragmentation during apoptosis. Using a DFF45 mutant mouse model, we previously found that DFF45 deficient cells are more resistant to apoptosis than normal control cells. To investigate whether the lack of DFF45 may attenuate neuronal cell death induced by excitotoxicity, we compared kainic acid-induced seizure behavior and neuronal cell death in DFF45 mutant and wild-type control mice. We found that the mutant mice exhibit similar kainic acid-induced seizure severity compared to control mice. However, DFF45 mutant mice are more resistant than control mice to kainic acid-induced CA3 neuronal cell death. Interestingly, residual DNA degradation can be detected in the hippocampus of DFF45 mutant mice that exhibit KA-induced lesions. Our results suggest that a lack of DFF45 can lead to neuronal resistance to excessive activity-induced toxicity.

Animals↗

Stepwise capillary electrophoretic separation of DNA fragments using poly(ethylene oxide) solutions in the presence of electroosmotic flow.

Single-base resolution in the separation of DNA markers V and VI was achieved in the presence of electroosmotic flow (EOF), using poly(ethylene oxide) (PEO) solutions containing ethidium bromide (EtB) under isocratic conditions. Furthermore, a new approach called stepwise capillary electrophoresis (SCE) has been developed for DNA analysis, including stepwise changes in PEO concentration, EtB concentration as well as both PEO and EtB concentrations, wherein the EOF was used to introduce different PEO solutions into the capillary during the separation. DNA fragments smaller than 80 bp were both detected under isocratic conditions using 20 micrograms/ml EtB, and SCE using 1 and 20 micrograms/ml EtB, but not under isocratic conditions using 1 microgram/ml EtB. Resolution and speed of the DNA separation in SCE were different from those obtained from isocratic means, indicating that DNA underwent different concentrations of PEO and EtB in SCE. For example, DNA fragments with 458 and 504 base pairs (bp) were partially resolved in SCE, but not under isocratic conditions. The results further suggest that it is worth developing gradient techniques for widening the separation range and enhancing resolution in DNA analysis.

Buffers↗

Caspase-3-like protease influences but is not essential for DNA fragmentation in Blastocystis undergoing apoptosis.

Blastocystis hominis undergo apoptosis after treatment with a cytotoxic monoclonal antibody (MAb), 1D5, by mechanisms that are not fully understood, although our previous study demonstrated that caspase-3-like protease activity is involved. To elucidate the mechanism of MAb 1D5-induced apoptosis, we inhibited Blastocystis caspase-3-like protease to investigate if there would be a concomitant decrease in in situ DNA fragmentation. However, MAb 1D5-induced apoptosis, evidenced by DNA fragmentation, was not completely blocked by pretreating with specific caspase-3 inhibitor, Ac-DEVD-CHO, indicating that caspase-independent apoptotic pathways might also be involved. Our results also revealed that the treatment with MAb 1D5 resulted in the loss of mitochondrial membrane potential (deltapsim), independent of Ac-DEVD-CHO pretreatment. In conclusion, this study demonstrates that MAb 1D5-induced apoptosis in B. hominis is not wholly dependent on caspase-3-like protease activity and is associated with mitochondrial dysregulation. This is the first report showing evidence for complex apoptotic pathways in a unicellular parasite.

Animals↗

Measurement of apoptosis by DNA fragmentation.

Classical apoptotic cell death can be defined by certain morphological and biochemical characteristics that distinguish it from other forms of cell death. One such feature, which is a hallmark of apoptosis, is DNA fragmentation. In dying cells, DNA is cleaved by an endonuclease that fragments the chromatin into nucleosomal units, which are multiples of about 180-bp oligomers and appear as a DNA ladder when run on an agarose gel. Here, we present commonly used methods such as conventional agarose gel electrophoresis to analyze fragmented nuclei in cells. The various methods used are dependent on the extent of fragmentation or the amount of fragmented nuclei in a sample. Determining whether a cell exhibits DNA fragmentation can provide information about the type of cell death occurring and the pathways activated in the dying cell.

Apoptosis↗

Isolation of DNA fragments from chromosome 13.

A number of patients with retinoblastoma have a deletion of chromosome 13. Comparison of the deleted segments from different individuals reveals that all deletions involve chromosome band 13q14. This observation has lead to the hypothesis that in this region is a gene of genes important in the etiology of retinoblastoma. As a first step toward understanding those genes, the authors successfully isolated five DNA fragments from chromosome 13 using recombinant DNA techniques. The DNA fragments from chromosome 13 will be useful in identifying DNA polymorphic sites that are linked to the retinoblastoma locus tentatively assigned to 13q14. Such DNA polymorphisms will be important in the genetic counselling of families with retinoblastoma. These chromosome 13q14 fragments also may be useful in searching for microdeletions of 13q14.

Animals↗

DNA fragmentation pattern induced in thymocytes by sulphur mustard.

Sulphur mustard (HD) is a blister agent for which no specific therapy exists. The mechanism of cell injury caused by HD is not well understood. This study examined DNA damage in thymocytes exposed to a range of HD concentrations over a time course of 1-24 h. Thymocytes incubated with HD showed an increase in the production of DNA fragments of the type frequently associated with apoptosis, namely, initial formation of large fragments of 30-50, 200-300 and > 700 kilobase pairs (kbp), followed by further degradation to produce an internucleosomal 'ladder' of oligomers of approximately 180 base pairs (bp). Pulsed field electrophoresis analysis of thymocytes incubated with HD detected breakdown of the chromatin up to 3 h before a corresponding increase in the low molecular weight (MW) oligonucleosomal fragments could be seen on conventional agarose gels. These results suggest that cells damaged by HD poisoning may be irretrievably committed to cell death sooner after exposure than previous studies suggested. The nature of the DNA fragments produced suggested that apoptosis may represent a component of the pathway of cell death induced by HD. These aspects may have implications for the search for specific therapeutic reagents effective in the prevention or treatment of HD poisoning.

Animals↗

EcoRI-generated reiterated components of the rat genome. I. Sequence of two (92 and 93 bp) related DNA fragments.

The sequence of the 92 and 93 bp long, highly repetitive DNA fragments, isolated from EcoRI digested rat liver DNA, were determined. These fragments, designated 92 and 93, are found in equal abundance, 6.5 x 10(5) copies per haploid genome. J92 and J93 can be distinguished by their differential sensitivity to cleavage by HaeIII and HindIII, respectively, which cut the fragments at 75 and 57 bp from their mutually homologous 5'-ends. J92 and J93 are 38% and 35.4% G + C, respectively, and contain a disproportionate number of triplets complementary to stop codons in all reading frames. Three methylated sites were found in J92 while none could be detected in J93. The sequences around the m5C sites were 5'-Py-Py-m5C-G-Pu-Pu, except for one case where the second Py was replaced by an A. This site appeared to be hemimethylated. When J92 and J93 are placed in register from their mutually homologous 5'-ends, homology is 73% for the first 30 bp region and 63.5% for the total molecule. Thermal melting studies indicate sequence heterogeneity within J92 and J93 from substantial internal base mismatches. The sequences derived are therefore composite averages for the whole molecules. The Cot1/2 for the sequence was measured spectrophotometrically to be 2 x 10(-2) M/s on a DNA phosphorus basis and 2.15 x 10(-4) M/s on a mole fragment basis.

Animals↗

[Solid phase ligation of synthetic DNA fragments].

A synthetic oligodeoxyribonucleotide (oligo) covalently bound by an internucleotide linkage to the succinylated Sephacryl S-500 support through 1.9-diaminononane spacer was used as starting compound to assemble the E. coli rec A promoter DNA fragment from synthetic oligos by means of T4 DNA ligase. The solid-phase assembly of the designed DNA was performed by two ways: stepwise ligation of two pairs of oligos (2 dyads) or simultaneous ligation of four oligos (tetrad). Both ways gave equal results with some preference in the tetrad case. The reliability of E. coli promoter DNA fragment assembly was demonstrated by cloning it in a plasmid vector and sequencing the cloned DNA by the solid-phase Maxam--Gilbert technique.

Base Sequence↗

Selective enrichment of a large size genomic DNA fragment by affinity capture: an approach for genome mapping.

A method to enrich large size DNA fragments obtained by digestion with rare cutting restriction endonucleases was developed and applied for the isolation of a 150 kb SfiI fragment containing the beta-globin gene cluster. The digested DNA is rendered single stranded at the ends by diffusing a strand specific exonuclease into an agarose plug containing DNA. The plug is melted and solution hybridization is then performed with a bridge RNA containing specific sequences from the end of a desired fragment linked to a common probe sequence. The common probe sequence is annealed to a biotinylated RNA and the resulting tripartite hybrid is retained onto a solid matrix containing avidin and specifically released by ribonuclease action. Enrichments of greater than 350 fold have been achieved consistently. Such directed purification of large DNA fragments without cloning can considerably expedite mapping and gene localization in a complex genome and facilitate the construction of sublibraries from defined regions of the genome.

Base Sequence↗

A simple and efficient method for the separation and detection of small DNA fragments by electrophoresis in formamide containing agarose gels and Southern blotting to DBM-paper.

We show in this report that DNA fragments smaller than 300 bp are separated with high resolution by electrophoresis in concentrated (up to 7%) agarose gels containing 50% formamide. The separated DNA fragments can subsequently be quantitatively transferred to DBM-paper [Alwine, J.C. et al., Proc. Natl. Acad. Sci. USA (1977) 74, 5350-54] using the Southern technique [Southern, E.M., J. Mol. Biol. (1975) 98, 503-517], while preserving the sharpness of the original gel pattern. Since thin (0.2-0.4 mm) and thick (up to 5 mm) agarose slab gels can be easily handled in vertical or horizontal apparatus, this method should prove to be a very useful extention of the Southern technique, applicable to a variety of analytical and preparative purposes.

Base Composition↗

Sequence-specific photomodification of single-stranded and double-stranded DNA fragments by oligonucleotide perfluoroarylazide derivative.

A highly efficient, sequence-specific photomodification of single-stranded (ss) and double-stranded (ds) DNA fragments was carried out with a hexadecathymidilate derivative, R approximately p(T)16 (R-perfluoroarylazido group), using 27-base pair DNA fragments as a target [table: see text] The main points of modification were G7 and G24 of the A-rich strand of the ss target and G7 and G22 of the A-rich and T-rich strands, respectively, for the ds target. The extent of photomodification was 60%-77% for ss DNA and 10%-53% for ds DNA depending on the reaction conditions. Photomodification increased in buffer with a high ionic strength (1.0 M) and at low temperature (4 degrees C) when presumably the triplexes were more stable.

Azides↗

Overexpression of AP endonuclease protects Leishmania major cells against methotrexate induced DNA fragmentation and hydrogen peroxide.

Generation of abasic (AP) sites is one of the main anomalies to arise in cellular DNA. These lesions are highly mutagenic, and need to be repaired by the base-excision repair (BER) system. Oxidative stress and misincorporation of dUTP are important sources of mutation load trough generation of AP sites. Kinetoplastid protozoa are able to survive in a highly oxidative environment within the host macrophages and between the different strategies used for survival, active DNA repair mechanisms must exist. In order to assess the role of BER in protecting parasites against DNA damage, we have overexpressed one enzyme of the pathway, AP endonuclease, in Leishmania major. Parasites overproducing AP endonuclease of L. major (APLM) showed an increased resistance to hydrogen peroxide, a mutagen that produces oxidative stress, and also to methotrexate (MTX), an inhibitor of thymidylate biosynthesis which causes a massive incorporation of dUTP into DNA, when compared to control cells. Moreover, DNA fragmentation caused by MTX was prevented in cells overexpressing APLM. Our results suggest that APLM is a key enzyme in mediating repair of AP sites in these pathogens.

Animals↗

Characterization of a plant scaffold attachment region in a DNA fragment that normalizes transgene expression in tobacco.

Using a low-salt extraction procedure, we isolated nuclear scaffolds from tobacco that bind specific plant DNA fragments in vitro. One of these fragments was characterized in more detail; this characterization showed that it contains sequences with structural properties analogous to animal scaffold attachment regions (SARs). We showed that scaffold attachment is evolutionarily conserved between plants and animals, although different SARs have different binding affinities. Furthermore, we demonstrated that flanking a chimeric transgene with the characterized SAR-containing fragment reduces significantly the variation in expression in series of transformants with an active insertion, whereas a SAR fragment from the human beta-globin locus does not. Moreover, the frequency distribution patterns of transgene activities showed that most of the transformants containing the plant SAR fragment had expression levels clustered around the mean. These data suggest that the particular plant DNA fragment can insulate the reporter gene from expression-influencing effects exerted from the host chromatin.

Animals↗

Use of buccal epithelial cells for PCR amplification of large DNA fragments.

The analysis of human DNA is widely employed in the genetic studies of families and populations, and in most cases is performed with samples obtained from peripheral blood. The use of buccal epithelial cells as a source of DNA for PCR amplifications has several advantages over blood sampling but has only been used to amplify small fragments of DNA. Its use in forensic analysis has been limited to cases where the sampling of peripheral blood is not feasible. In the present study we show that buccal epithelial cells are a reliable source of DNA for the PCR amplification of high molecular mass fragments, which could be used in large-scale population sampling. Since most PCR gender-typing systems rely on the amplification and electrophoretic separation of the amelogenin gene, our results show that buccal epithelial cells may be the preferred source of DNA for gender-typing analysis.

Amelogenin↗

Induction of apoptosis by dietary polyunsaturated fatty acids in human leukemic cells is not associated with DNA fragmentation.

Apoptosis is important in anticancer strategy. In this study, bivariate annexin V/PI flow cytometry showed that dietary polyunsaturated fatty acids, arachidonic acid (AA) and eicosapentaenoic acid (EPA), induced apoptosis in human leukemic HL-60 but not K-562 cells. Results from DNA-PI flow cytometry and TUNEL flow cytometry illustrated that neither AA nor EPA induced DNA fragmentation in the leukemic cells. These findings suggested that the AA- and EPA-induced apoptosis might not associate with endonucleases activation, and DNA fragmentation could not be used as a sole criterion to identify apoptotic cells.

Apoptosis↗

Isolation and characterization of two male-specific DNA fragments from the bovine gene.

Two independent male-specific DNA fragments were isolated from the bovine genome by the technique of cloning by deletion enrichment. Each is represented in the order of one to five copies per haploid genome. Neither fragment was found to be polymorphic between two individuals of different breeds with 12 different restriction enzymes. A 'zoo blot' demonstrated that one fragment had a closely related sequence in the sheep genome, although no other hybridizing sequences were detected in a variety of animal DNAs tested with both probes. The DNA sequence of each fragment is presented; one fragment has a continuous open reading frame and a potential Z-DNA forming region.

Animals↗

Influence of age on hypoxia/reoxygenation-induced DNA fragmentation and bcl-2, bcl-xl, bax and fas in the rat heart and brain.

To test the hypothesis that the aging mammalian heart and brain might have increased vulnerability to acute stress, DNA fragmentation was studied after hypoxia-reoygenation in young adult (6 months) and old (22-24 months) F344 rats. Heart and brain tissue were examined at the following time points: 30, 60, or 90 min of hypoxia (H, 5% O2, 95% N2) plus 2 h of reoxygenation (R, room air, 21% O2). With increasing duration of hypoxia preceding the reoxygenation, the extent of DNA fragmentation (in situ terminal dUTP nick end labeling, TUNEL, positive cells) was progressively higher in both age groups, greater in the old compared to that of the young adult rat. The levels of the anti-apoptotic proteins bcl-2 and bcl-xL, were similar in young and old at baseline and tended to increase in both age groups after hypoxia/reoxygenation. The pro-apoptotic protein, bax, was higher at baseline in the old; it rose after hypoxia/reoxygenation in the young adult heart and brain, but was unchanged in the old heart and was decreased in the old brain. The ratios of bcl-2/bax and of bcl-xL/bax were higher in the old heart and brain compared to that in the young adult after hypoxia/reoxygenation. Thus, compared to that of the young adult, the heart and brain of the old rat have lower thresholds and are more vulnerable to injury induced by hypoxia/reoxygenation, despite rapid and heightened expression of the anti-apoptotic proteins bcl-2 and bcl-xl. This could be due partly to the age-associated increase in the basal expression of the pro-apoptotic protein bax, as well as possibly other factors.

Aging↗

In situ DNA fragmentation occurs in white matter up to 12 months after head injury in man.

Using the terminal deoxynucleotidyl transferase-mediated biotinylated deoxyuridine triphosphate nick-end labelling (TUNEL) histochemical technique, evidence for DNA fragmentation was sought in the hippocampus, cingulate gyrus and insula from 18 patients who survived for up to 12 months after head injury, and 15 matched controls. Both conventional (haematoxylin and eosin and Luxol-fast blue/cresyl violet) and immunohistochemical (glial fibrillary acidic protein, CD68) staining techniques were used to identify the cellular response and its time course in the regions of interest. Only the occasional TUNEL-positive (+) cell/unit area was seen in any area of the control brains. In contrast there were more TUNEL+ cells/unit area in the injured brains. TUNEL+ cells were present in white matter and their average numbers ranged from three to five per unit area for up to 3 months survival in the extreme capsule and the parasagittal white matter, with similar numbers in the hippocampus, and between two and three per unit area in the parasagittal white matter and hippocampus of the cases surviving up to 12 months post injury. Between one and two TUNEL+ cells/unit area were also seen in grey matter, of which most appeared as neurones. About 5% of the TUNEL+ cells in white matter had the morphological features of apoptosis: the corresponding figure in grey matter was less than 1%. In many instances the TUNEL+ cells were also CD68+ and appeared by light microscopy to be macrophages. It was concluded that, as reflected by TUNEL histochemistry, long-term DNA fragmentation is present in white matter after traumatic brain injury in man.

Adolescent↗