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Apoptosis and DNA fragmentation as induced by tertiary butylhydroperoxide in the brain.

In this study, the effect of intracerebroventricular administration of the free radical generator, tertiary butylhydroperoxide, on DNA, was quantitated. Previous studies had established DNA as a very important site of free radical attack. The purpose of the study was to detect whether DNA was one of the primary targets of the toxin as well as to detect any apoptosis that may have been induced by the toxin. The DNA fragmentation assay clearly showed DNA damage within 20 min of administration of 109.7 mg/kg t-BuOOH almost in all brain regions in both 2-month and 8-month-old C57BL/6 mice. In Situ Apoptosis Detection assay, where brain sections were stained with Apoptag, demonstrated that t-BuOOH induces apoptosis in many brain regions. Electron microscopy was done to show nuclear damage and DNA fragments appearing in the cytoplasm. Cresyl violet staining was done to show that while low dose (21.9 mg/kg) t-BuOOH induces apoptosis, it may also induce necrosis in other cells of the same brain region. Thus, from this study we can conclude that DNA may be one of the primary target sites of free radical attack in the brain, and results in both necrosis and apoptosis. This can have a profound effect on neurodegeneration.

Animals↗

Cloning and characterization of a Chlamydia trachomatis L3 DNA fragment that codes for an antigenic region of the major outer membrane protein and specifically hybridizes to the C- and C-related-complex serovars.

Chlamydia trachomatis L3 DNA was cloned and expressed in lambda gt11. A recombinant plaque that expressed an antigen that reacted with rabbit polyclonal antichlamydial L3 serum and with two monoclonal antibodies specific for serovars L3 and I was selected from this Chlamydia genomic library. The beta-galactosidase Chlamydia fusion protein was purified by immunoaffinity chromatography and injected into mice to produce monoclonal antibodies. These monoclonal antibodies reacted by Western (immuno-) blot with both the fusion protein and the major outer membrane protein from purified L3 elementary bodies. The chlamydial DNA fragment was shown by DNA sequence analysis to be 168 base pairs in length and to correspond to the constant regions 1 and 2 and the variable segment 1 of the major outer membrane protein gene. The recombinant chlamydial DNA fragment hybridized under stringent conditions by Southern and dot blot analysis exclusively with the DNA from the C- and C-related-complex C. trachomatis serovars.

Amino Acid Sequence↗

The characterization of a new size-sieving polymeric matrix for the separation of DNA fragments using capillary electrophoresis.

A low-viscosity, polysaccharide matrix (TreviSol-CE [TS-CE], Trevigen, Inc., Gaithersburg, MD, U.S.A.) has been characterized experimentally in capillary electrophoresis for the separation of DNA fragments. The mass fraction (%) of the matrix in buffer solution and the applied field strength may be varied according to the size of DNA fragments to be separated. The use of tris-phosphate-EDTA (TPE) buffer at pH 7, instead of the more commonly used tris-borate-EDTA (TBE) and tris-acetate-EDTA (TAE) buffers at pH 8.3, provides higher separation efficiency in conjunction with this matrix and simultaneously preserves the internal coating of the capillary for high run-to-run reproducibility. In comparison with other commercially available DNA separation matrices for CE, TS-CE provides enhanced separation ability of DNA fragments greater than 600 base pairs (bp) in length and lower UV absorbance background for enhanced detectability.

Base Sequence↗

Human granzyme B is essential for DNA fragmentation of susceptible target cells.

We have partially characterized the granules of the human NK cell line, YT-INDY, and assessed granule-mediated lysis and DNA fragmentation of assorted targets. Biochemical studies demonstrated significant quantities of granzyme B (asp-ase) and a heretofore undescribed chymase but no tryptase (i.e., granzyme A or 3) or distinct met-ase. YT-INDY expressed mRNA for granzyme B, perforin and CCPX. The existence of perforin was confirmed by immunoblot. The granules lysed both human and murine NK-sensitive and NK-resistant targets. YT-INDY and NK3.3, two human cytotoxic cells, were also lysed. EGTA reduced lysis by only 50%, suggesting that a perforin-independent lytic pathway is associated with the granules. In addition, 4-(2-aminoethyl) benzenesulfonylfluoride hydrochloride (AEBSF), an inhibitor that selectively blocked the chymase and 3,4-dichloroisocoumarin (DCI), an inhibitor that inactivated both chymase and asp-ase activities, marginally affected lysis. By gel electrophoresis and 125I-labeled deoxyuridine release assay, only murine cells (SP2/0 and YAC-1) underwent DNA fragmentation, and cleavage was completely inhibited by DCI, whereas EGTA, AEBSF and aurintricarboxylic acid (ATA) had no effect. The results, therefore, underscore the central role of granzyme B in granule-mediated DNA fragmentation, emphasize that the protease acts via an ATA-resistant endonuclease pathway and stress that nucleolysis does not invariably accompany granule-mediated cytolysis. Finally, ATA inhibited the asp-ase activity of isolated but not granule-associated granzyme B. ATA, therefore, is not a specific endonuclease inhibitor and results obtained with ATA should be viewed cautiously.

Animals↗

Improved resolution of DNA fragments in polysaccharide-supplemented agarose gels.

The electrophoretic separation of nucleic acids, including small DNA fragments in the range 50-1000 bp, is presently carried out in polyacrylamide gels or in gels containing high concentrations of agarose. We have developed an alternative gel matrix composition which is inexpensive, nontoxic, easy to prepare, and highly transparent to visible and uv light. The composition combines a soluble nonionic polysaccharide such as hydroxyethylcellulose, methylcellulose, or galactomannan with a minimum but sufficient concentration of agarose to form a gel which immobilizes the "liquid phase sieve." These mixtures do not replace polyacrylamide for resolving fragments smaller than approximately 75 nucleotides. However, the new gels show DNA fragment resolution (band separation versus distance traveled) and optical clarity superior to those of conventional agarose.

Carbohydrates↗

Cloning of large DNA fragments, which hybridize with actinorhodin biosynthesis genes, from kalafungin and nanaomycin A methyl ester producers and identification of genes for kalafungin biosynthesis of the kalafungin producer.

Large actI, III-homologous DNA fragments were isolated from genomic libraries of the strains that produce the benzoisochromanequinone antibiotics kalafungin and nanaomycin A methyl ester, Streptomyces tanashiensis strain Kala and Streptomyces sp. OM-173, respectively. These libraries were prepared in Escherichia coli JM108 by using a novel Streptomyces-E. coli bifunctional cosmid, pKU205, and screened with polyketide synthase genes (actI and III) for actinorhodin biosynthesis from Streptomyces coelicolor A3(2) as probes. The cloned DNA fragments (28 and 42 kb) were analyzed by hybridization with DNA containing actinorhodin biosynthetic genes (actI, II, III, IV, VA, VB, VI and VII). Both fragments hybridized with the actI, III, VA and VI regions, but not with the actII, IV, VB and VII regions. The cloned fragment of S. tanashiensis DNA was analyzed by complementation tests with kalafungin-nonproducing mutants. Seven genes (kalI approximately VII), which correspond to seven steps in kalafungin biosynthesis, were found to be located on a 14 kb continuous DNA fragment. Five of the genes were located on the regions homologous to the genes for actinorhodin biosynthesis, but the other two genes were not. Although kalafungin is an intermediate or shunt product in actinorhodin biosynthesis in S. coelicolor A3(2), the genes for kalafungin biosynthesis in S. tanashiensis are not identical with those in S. coelicolor A3(2).

Anthraquinones↗

Rescue of infectious virus from permissive monkey cells containing simian virus 40 DNA fragments.

Permissive TC7 cells were separately transfected with simian virus 40 (SV40) EcoRI/Hap II A (74% genome) DNA fragments and EcoRI/Hap II B (26% genome) DNA fragments in the presence of DEAE-dextran. Fusion of the progeny of recipient cells receiving the A fragment, TC7 (SV40/74) cells, with TC7 (SV40/26) cells, which had received the B fragment, resulted in SV40 rescue. TC7 (SV40/74 + 26) cells, which had simultaneously received both complementary subgenomes, either spontaneously produced SV40 upon subculture or yielded virus upon treatment with iododeoxyuridine. In addition, fusion of rat cells containing the EcoRI/Hap II A fragment with TC7 (SV40/26) cells resulted in SV40 rescue. Cytopathology, V-antigen production, neutralization, and electron microscopy were parameters used to verify that the rescued virus was SV40. No infectious virus was produced when the combinations of cells fused did not total a complete SV40 genome equivalent.

Antigens, Neoplasm↗

Treatment with the non-ionic surfactant poloxamer P188 reduces DNA fragmentation in cells from bovine chondral explants exposed to injurious unconfined compression.

Excessive mechanical loading to a joint has been linked with the development of post-traumatic osteoarthritis (OA). Among the suspected links between impact trauma to a joint and associated degeneration of articular cartilage is an acute reduction in chondrocyte viability. Recently, the non-ionic surfactant poloxamer 188 (P188) has been shown to reduce by approximately 50% the percentage of non-viable chondrocytes 24 h post-injury in chondral explants exposed to 25 MPa of unconfined compression. There is a question whether these acutely 'saved' chondrocytes will continue to degrade over time, as P188 is only thought to act by acute repair of damaged cell membranes. In order to investigate the degradation of traumatized chondrocytes in the longer term, the current study utilized TUNEL staining to document the percentage of cells suffering DNA fragmentation with and without an immediate 24 h period of exposure of the explants to P188 surfactant. In the current study, as in the previous study by this laboratory, chondral explants were excised from bovine metacarpophalangeal joints and subjected to 25 MPa of unconfined compression. TUNEL staining was performed at 1 h, 4 days, and 7 days post-impact. The current study found that P188 was effective in reducing the percentage of cells with DNA fragmentation in impacted explants by approximately 45% at 4 and 7 days post-impact. These data suggest that early P188 intervention was effective in preventing DNA fragmentation of injured chondrocytes. The current hypothesis is that this process was mitigated by the acute repair of damaged plasma membranes by the non-ionic surfactant P188, and that most repaired cells did not continue to degrade as measured by the fragmentation of their DNA.

Animals↗

Effect of highly fragmented DNA on PCR.

We characterized the behavior of polymerase chain reactions (PCR) using degraded DNA as a template. We first demonstrated that fragments larger than the initial template fragments can be amplified if overlapping fragments are allowed to anneal and extend prior to routine PCR. Amplification products increase when degraded genomic DNA is pretreated by polymerization in the absence of specific primers. Secondly, we measured nucleotide uptake as a function of template DNA degradation. dNTP incorporation initially increases with increasing DNA fragmentation and then declines when the DNA becomes highly degraded. We demonstrated that dNTP uptake continues for >10 polymerization cycles and is affected by the quality and quantity of template DNA and by the amount of substrate dNTP. These results suggest that although reconstruction of degraded DNA may allow amplification of large fragments, reconstructive polymerization and amplification polymerization may compete. This was confirmed in PCR where the addition of degraded DNA reduced the resultant product. Because terminal deoxynucleotidyl transferase activity of Taq polymerase may inhibit 3' annealing and restrict the length of template reconstruction, we suggest modified PCR techniques which separate reconstructive and amplification polymerization reactions.

DNA↗

Dissociation of DNA fragmentation from other hallmarks of apoptosis in nitric oxide-treated neutrophils: differences between individual nitric oxide donor drugs.

The events of apoptotic cell death can be experimentally dissociated from each other in certain cell types. Here we demonstrate the ability of structurally diverse nitric oxide (NO) donating compounds to delay or enhance neutrophil apoptosis and to differentially influence distinct parameters of programmed cell death. We provide evidence that high concentrations of the NO donors GEA 3162, SPER/NO, and DEA/NO induce morphological and biochemical markers of neutrophil apoptosis, but that only DEA/NO causes a concomitant increase in DNA fragmentation as evidenced by nuclear propidium iodide intercalation and the classical laddering pattern of electrophoresed DNA. In contrast, both GEA 3162 and SPER/NO inhibit DNA cleavage in a time- and concentration-dependent manner. We are the first to show that DNA fragmentation can be dissociated from other changes of apoptosis in NO-treated neutrophils and that it may therefore be inappropriate to assess NO-induced apoptosis solely by measuring DNA fragmentation in this cell type.

Annexin A5↗

Macromolecular crowding accelerates the cohesion of DNA fragments with complementary termini.

Macromolecular crowding increases the rate of nonenzymatic cohesion of the complementary ends of lambda DNA. Both lambda DNA and DNA fragments bearing the cohesive ends of lambda DNA are similarly affected. High concentrations of plasma albumin or Ficoll 70 increase the rate of cohesion by ca. 100-fold whereas high concentrations of polyethylene glycol 8000 cause greater than 2000-fold stimulation in this rate. These results have implications for the mechanism of polymer-stimulated enzymatic ligation of DNA or RNA. In addition, these crowding effects may help to explain the rapid cohesion of lambda DNA observed in vivo. An improved procedure for the recovery of DNA fragments separated by agarose gel electrophoresis is also described.

Bacteriophage lambda↗

Effect of caspase inhibitors on myocardial infarct size and myocyte DNA fragmentation in the ischemia-reperfused rat heart.

OBJECTIVE: Caspase family proteases are recognized as key mediators of apoptosis. However, the role of caspases in the ischemia-reperfused heart remains uncertain. We evaluated the effect of caspase inhibitors on myocardial infarct size and the myocyte DNA fragmentation in the ischemia-reperfused rat hearts. METHODS: Three groups of Sprague-Dawley rats (n = 7, each) were subjected to 30 min of ischemia followed by 6 h of reperfusion. One of the following drugs: (1) YVAD-aldehyde, a caspase-1-like protease inhibitor (3.5 mg/kg; YVAD), (2) DEVD-aldehyde, a caspase-3-like protease inhibitor (3.5 mg/kg, DEVD), (3) vehicle (140 microliters/kg) was administered intravenously 5 min prior to the ischemia in each group. Myocardial infarct size was defined by triphenyltetrazolium chloride (TTC) staining. Immunohistochemical staining by in situ nick end labeling (TUNEL) of cardiomyocytes and DNA electrophoresis were used for detecting DNA fragmentation. Ultrastructural analysis was done by electron microscopy. The caspase activity was measured in the myocardium of both groups. RESULTS: The percentage of TUNEL-positive myocyte nuclei (%AP) was quantified by microscopy. A ladder pattern was detected by electrophoresis of DNA from the risk area and TUNEL-positive myocytes were seen in the risk area. The %AP was significantly reduced from 20 +/- 1% to 12 +/- 3% by YVAD and to 10 +/- 3% by DEVD (both P < 0.01). However, caspase inhibitors did not significantly change the infarct size. Electronmicrograph showed similar salcolemmal and mitochondrial damage in both group. The caspase activity was blocked by DEVD at 4 h after reperfusion. CONCLUSION: Myocyte DNA fragmentation and caspase activation was inhibited by caspase inhibitors without reduction of the infarct size in ischemia-reperfused rat hearts.

Analysis of Variance↗

Accumulation of DNA fragments in aging Paramecium tetraurelia in axenic and nonaxenic media.

The accumulation of DNA fragments in aging Paramecium tetraurelia after 15 days (or approximately 60 generations) of clonal growth in both axenic and nonaxenic media was assayed by alkaline elution assay. This sensitive technique permits measurement of single-strand breaks in double-stranded DNA. The results obtained indicate that P. tetraurelia aged in axenic medium accumulate more apurinic/apyrimidinic lesions, strand breaks, or single-strand gaps than do P. tetraurelia aged in nonaxenic medium. This implies that cells grown in axenic medium have a shorter lifespan than do cells grown in nonaxenic medium. The accumulation of DNA fragments may be the basic mechanism of aging in P. tetraurelia.

Carbon Radioisotopes↗

Relationship between DNA fragmentation and nuclear status of in vitro-matured porcine oocytes: role of cumulus cells.

The present study was conducted to investigate the effects of the attachment of cumulus cells to oocytes and coculture with cumulus cells during maturation culture on the nuclear status and DNA fragmentation of porcine denuded oocytes (DOs). In the first experiment, cumulus cells were removed from cumulus-oocyte complexes (COCs) at 0, 8, 16, 24 or 32 h after the onset of maturation culture and the DOs were then cultured in their original droplets until 42 h of culture was reached. In the second experiment, all COCs were denuded before the onset of culture and the DOs were cocultured with their removed cumulus cells. The DOs were transferred into fresh medium at 0, 8, 16, 24 or 32 h after the onset of coculture with cumulus cells and then cultured until 42 h of culture was reached. After culture, DNA fragmentation and the nuclear status of oocytes were examined using the terminal deoxyribonucleotidyl transferase-mediated dUTP-digoxigenin nick end-labelling (TUNEL) method. When the DOs were returned to the same droplets after removal of the cumulus cells, the removal of the cumulus cells after 16 h of culture significantly decreased the proportion of oocytes remaining at the germinal vesicle (GV) stage. However, coculture treatment of DOs in the presence of their removed cumulus cells had no significant effects on the GV breakdown (GVBD) of oocytes. There were no significant differences in the proportion maturing to MII oocytes among the groups following removal of cumulus cells after the onset of maturation culture; however, DOs cocultured with cumulus cells until the end of maturation culture exhibited an increased maturation rate compared with DOs cocultured for 8 and 16 h. The total proportion of TUNEL-positive oocytes of oocytes remaining at the GV stage was higher than that of oocytes reaching other stages, irrespective of the removal of cumulus cells and coculture treatments. However, coculture for more than 16 h decreased the total proportion of TUNEL-positive oocytes. Our results indicate that the attachment of cumulus cells to oocytes may have a critical role for oocytes undergoing GVBD and that coculture with cumulus cells promotes the ability of oocytes to complete maturation. Moreover, coculture with cumulus cells may assist the oocyte to avoid undergoing DNA fragmentation.

Animals↗

DNA fragmentation in cereal roots indicative of programmed root cortical cell death.

In cereals, a progressively increasing root cortical cell death (RCD) occurs from the root tip and upwards when measured with vital staining methods. In this study, nuclear DNA fragmentation was studied in seminal root segments of wheat and barley in order to investigate if the cell death resembled apoptosis. The fraction of cells with TUNEL-positive nuclei increased gradually with increasing root age in both the cortex and the stele. Southern analysis showed a typical ladder pattern, indicating nucleosomal fragmentation already in 2-day-old root segments, and this became more pronounced in older root segments. DNA fragmentation appeared to be more extensive in wheat than in barley roots. These results confirm earlier studies, where RCD has been found to be earlier initiated and to proceed at a faster rate in wheat. The characteristic DNA fragmentation found in the roots indicates programmed cell death with mechanistic similarities to apoptosis. Ultrastructural examination of nuclei in cortex cells with transmission electron microscopy revealed an increased chromatin condensation in older roots, particularly in wheat. In addition, we found nucleosomal DNA ladders in young leaf tissue from wheat but not from barley.

Journal Article↗

Increased resolution of large DNA fragments by a two dimensional pulse field gel electrophoresis.

An electrophoretic method for separating well-defined large DNA fragments from higher and lower molecular weight molecules is described. It combines in a first dimension either a contour-clamped homogeneous electric field or an orthogonal field alternation gel electrophoresis technique followed by a perpendicular field inversion gel electrophoresis (FIGE) in a second dimension. A complex migration curve after the FIGE run is obtained depending on the applied pulse time, the forward/reverse ratio being kept constant at 3. However, a part of the curve appears as a straight line where the migration is inversely proportional to the molecular weight of the DNA fragments. In this zone, DNA molecules are particularly well separated from other fragments. When the forward pulse time increases, this part is displaced toward the higher molecular weights. Moreover a simple relationship between the middle part of the straight line and the forward pulse time has been established.

DNA↗

Meta-analysis of sperm DNA fragmentation using the sperm chromatin structure assay.

Meta-analyses were conducted to investigate the relationship of sperm DNA fragmentation on pregnancy outcome using in-vivo fertilization, IUI, routine IVF and ICSI. Couples with no known infertility problems were 7.0 times (CI 3.17, 17.7) more likely to achieve a pregnancy/delivery if the DNA fragmentation index (DFI) was <30% (n = 362, P = 0.0001) using in-vivo fertilization. Infertile couples using IUI were 7.3 times (CI 2.88, 18.3) more likely to achieve a pregnancy/delivery if their DFI was <30% (n = 518, P = 0.0001). With routine IVF, infertile couples were approximately 2.0 times (CI 1.02, 2.84) more likely to become pregnant if their DFI was <30% (n = 381, P = 0.03). For ICSI and/or routine IVF, the results showed a non-significant trend where infertile couples were 1.6 times (CI 0.92, 2.94) more likely to achieve a pregnancy/delivery if the DFI was <30% (n = 323,P = 0.06). The in-vivo and IUI meta-analyses were similar, indicating that IUI infertility patients with <30% DFI have as good a statistical probability of obtaining a pregnancy/delivery as in-vivo presumably fertile couples with the same DFI. These meta-analyses show that the Sperm Chromatin Structure Assay infertility test was significantly predictive for reduced pregnancy success using in-vivo, IUI and routine IVF, and to a lesser extent ICSI fertilization.

Chromatin↗

Construction of a human BcgI DNA fragment library.

A library made up of 36bp DNA fragments generated by digestion of human DNA with the restriction endonuclease Bcg I has been constructed. It contains 2.5x106 independent clones, representing several times the total human genome which should contain about 400000 such fragments. It is proposed to make use of these BcgI fragments to clone part of the coding sequences contained in the minor H3 isochore which represents 3% of the human genomic DNA and a quarter of all genes.

Cloning, Molecular↗