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PubMed2000

Tissue transglutaminase in the small intestine of the mouse as a marker for apoptotic cells. Colocalization with DNA fragmentation.

Besides the morphological changes in cells undergoing apoptosis, such as chromatin condensation and cell shrinkage, histological demonstration of DNA fragmentation by in situ end labeling (ISEL) has been widely used for the demonstration of apoptotic cells in tissue sections. Although DNA fragmentation can be demonstrated in apoptotic cells and apoptotic bodies in most cases, there is no clear correlation of ISEL staining with apoptosis. It has often been demonstrated that, in many morphologically intact cells, nuclei with fragmented DNA can be found. Thus staining with ISEL for the detection of apoptosis is useful only in connection with other markers for apoptosis as, for example, characteristic morphological changes. Here we show that tissue transglutaminase protein is unequivocally expressed in apoptotic enterocytes as shown by DNA fragmentation and morphology. Tissue transglutaminase is not expressed in enterocytes with healthy morphology, although DNA fragmentation can be demonstrated in these cells. Thus the immunohistochemical demonstration of tissue transglutaminase may serve as a simple marker for apoptotic epithelial cells in tissue sections.

Animals↗

PubMed1996

Involvement of histone hyperacetylation in triggering DNA fragmentation of rat thymocytes undergoing apoptosis.

The treatment of rat thymocytes with trichostatin A and sodium butyrate, which are inhibitors of histone deacetylase, resulted in an increase in DNA fragmentation in a concentration-dependent manner. A significant increase in DNA fragmentation induced by these compounds was observed after a lag time of 2 h. Analysis of the fragmented DNA revealed the production of approximately 50 kb DNA fragments and DNA ladders, the biochemical hallmarks of apoptotic cell death. Judging from a laser scanning microscopic analysis, the inhibitors of histone deacetylase induced nuclear condensation, the morphological feature of apoptosis. Biochemical and morphological analyses demonstrated that trichostatin A and sodium butyrate induced thymocyte apoptosis. Furthermore, hyperacetylation of nuclear histones was observed in thymocytes treated with the inhibitors of histone deacetylase. These effects of sodium butyrate and trichostatin A were seen 0.5 and 1 h, respectively, after incubation of the cells. These results thus indicate that hyperacetylation of nucleosomal histones precedes DNA fragmentation in thymocytes undergoing apoptosis induced by trichostatin A and sodium butyrate.

Acetylation↗

PubMed1997

Arachidonic acid induces DNA-fragmentation in human polymorphonuclear neutrophil granulocytes.

We analyzed DNA-fragmentation in human polymorphonuclear neutrophil granulocytes (PMNs) from healthy donors after addition of exogenous arachidonic acid (AA) and eicosapentaenoic acid (EPA) by flow cytometry (propidium iodide staining of DNA and DNA strand break detection). The PMNs were incubated from 30 min up to 48 hours in RPMI 1640 which was supplemented with different concentrations of AA or EPA (5-40 microM). In contrast to EPA the addition of AA led to a significant increase in apoptosis up to 67.8% compared to the RPMI-control whereas the addition of EPA led to an inhibition of DNA-fragmentation. When the cells were incubated with MK 886 (1 microM, inhibitor of leukotriene biosynthesis) an increase in DNA-fragmentation (up to 63.3%) was observed. Conversely, in the presence of indomethacin (1 microM, inhibitor of prostanoid synthesis) an inhibition in DNA-fragmentation (up to 60.9%) occurred. Furthermore, preincubation of PMNs with pentoxifylline (1mM, phosphodiesterase inhibitor) reduced AA-stimulated DNA-fragmentation up to 43.4%. These data provide evidence for the involvement of AA and distinct AA metabolites in the regulation of apoptosis in human PMNs.

Apoptosis↗

PubMed1994

Molecular characterization and determination of the coding capacity of the genome of equine herpesvirus type 2 between the genome coordinates 0.235 and 0.258 (the EcoRI DNA fragment N; 4.2 kbp).

The complete DNA nucleotide sequence of the EcoRI DNA fragment N (0.235 to 0.258 viral map units) of equine herpes virus type 2 (EHV-2) strain T400/3 was determined. This DNA fragment comprises 4237 bp with a base composition of 55.23% G+C and 44.77% A+T. Nineteen open reading frames (ORFs) of 50-287 amino acid (aa) residues were detected. ORF number 10 is located between the nucleotide position 2220 and 2756 coding for a protein of 179 amino acid residues. This protein shows significant homology to the cytokine synthesis inhibitory factor (CSIF; interleukin 10) of human (76.4%) and mouse (68.5%), and to the Epstein-Barr virus (EBV) protein BCRF1 (70.6%). The existence of an interleukin 10 (IL-10) analogous gene within the genome of the EHV-2 was confirmed by screening the genome of nine EHV-2 strains using specific oligonucleotide primers corresponding to the 5' and 3' region of this particular gene by polymerase chain reaction. In all experiments an 870 bp DNA product was amplified. The specifity of the amplified DNA fragments obtained from individual EHV-2 strains was confirmed by DNA-DNA hybridization experiments. The DNA sequence analysis of the amplified DNA products of the EHV-2 strain LK was carried out. This analysis revealed the identity of the corresponding IL-10 gene (540 bp) of this strain to the IL-10 gene of EHV-2 strain T400/3. The presented data indicate that the EHV-2 genome harbors a viral interleukin 10-like gene. This is further evidence that the IL-10 gene can be present in the genomes of members of the Herpesviridae family.

Amino Acid Sequence↗

PubMed2004

An analytical system based on a compact flow cytometer for DNA fragment sizing and single-molecule detection.

BACKGROUND: Previous reports have demonstrated accurate DNA fragment sizing of linear DNA fragments, from 564 to approximately 4 x 10(5) bp, in a flow system. B-phycoerythrin (B-PE), commonly used in conventional cytometric applications that require high-sensitivity, was the first fluorophore detected in flow at the single-molecule level. METHODS: Dilute solutions of stained DNA fragments or B-PE were analyzed in a simplified, compact flow system, with enhanced performance and lower cost, utilizing a solid-state laser and a single-photon sensing avalanche photodiode detector (SSAPD). Extensive data processing and display software, developed specifically for the photon-counting data stream, extracts correlated height, width, and area features from bursts of photons due to discrete molecules passing through the sensing region in the flow channel. RESULTS: DNA fragment sizing in flow has now been demonstrated for SYTOX-orange-stained fragments ranging in size over 3.4 orders of magnitude, from 125 to 5 x 10(5) bp. For Lambda bacteriophage DNA (lambda DNA; 48.5 kbp) a CV of 1.2 % has been achieved. Analysis of a femtomolar B-PE solution demonstrates that the bursts of photons from individual molecules can be baseline-resolved with 0.5 mW of laser power at a signal to noise ratio (SNR) of approximately 30, with approximately 100 photons detected from each molecule. CONCLUSIONS: A compact, low-power, high-sensitivity system detects DNA fragments as small as 125 bp or individual B-PE molecules in a flowing liquid stream. Demonstrated linearity, sensitivity, and resolution indicate that <1.0 mW of laser power is optimal, permitting further miniaturization of the system and additional cost reduction. Comprehensive analytical software exploits the standard cytometric paradigm of multiple 2D graphs and gating to extract features from classes of individually analyzed biomolecules. This complete system is thus poised to engage high-sensitivity applications not amenable to conventional flow cytometric instrumentation.

DNA↗

PubMed1991

Polymerase chain reactions with alphoid-repeat primers in combination with Alu or LINEs primers, generate chromosome-specific DNA fragments.

Y alphoid primers in combination with Alu and LINEs primers generated new DNA fragments in polymerase chain reactions (PCR) on DNA from a Y-only somatic cell hybrid but not from X-only, 3-only, or 21-only hybrids. X alphoid primers used in a similar manner generated new DNA fragments from the X-only hybrid, and 1 of the primers (X2) also generated new DNA fragments on 3-only and 21-only hybrids when used in conjunction with Alu or LINEs primers. In all but one case, consensus alphoid primers generated new chromosome-specific fragments in PCR reactions with the Alu or LINEs primers. A search for cryptic Alu- or alphoid-alone PCR products as the source for one Alu-alphoid band (chosen at random) was negative. Partial sequencing of products demonstrated that alphoid and Alu sequences were indeed contiguous in some newly synthesized DNA fragments. While Alu or LINEs primers generate smears of DNA fragments on total human DNA, the alphoid-non-alphoid repeat combinations generated electrophoretically distinguishable bands of DNA when the template was total DNA. While these were distinguishable with different chromosome-specific alphoid primers, the DNA fragments were not of the same sizes as those generated with the chromosome-only hybrids.

Animals↗

PubMed1999

[Cloning of DNA fragment related to salt tolerance in Sinorhizobium meliloti 042B].

Total DNA partially digested by EcoR I was prepared for S. meliloti 042B, in which 15-25 kb DNA fragments were collected. Vector pLAFR I was purified and digested by EcoR I, and then the various DNA fragments of 042B were ligated with pLAFR I by T4DNA ligase. Gene library of S. meliloti 042B was constructed with pLAFR I using E. coli S17-1 as recipient. The number of bacterial recombinants obtained was about 8,000 and 95% of them contained foreign DNA fragments. Using NTG, 042B was mutated on FY plates and 12 sensitive strains were screened at 0.5 mol/L NaCl from 2,000 colonies. One of them was named GZ17 and selected as a recipient strain. By biparental mating the foreign DNA fragments were introduced from gene library of strain 042B into recipient strain GZ17 which is sensitive to 0.5 mol/L NaCl. Then the transconjugants were grown on FY plates containing tetracycline (20 micrograms/mL) and 0.5 mol/L NaCl. A 7 kb inserted DNA fragment related to salt tolerance was obtained. In subcloning experiment, a 4 kb DNA fragment related to salt tolerance was obtained.

Cloning, Molecular↗

PubMed2002

Internucleosomal DNA fragmentation during deprived and non-deprived olfactory development.

DNA fragmentation is a key marker of neuronal death during development, yet little is known about the size, pattern or quantities of fragments generated during normal and sensory-deprived development. Since there are few neurons dying at any particular time, it has not been possible to obtain sufficient quantities of material to make such a determination. By using a highly sensitive Taq polymerase-based technique, we revealed DNA fragments of 180 base pairs and multiples thereof both in bulbs and cortex of young rats (P4-P31). The bulbs subjected to olfactory deprivation at P1 had higher levels of internucleosomal DNA fragmentation at P16 than the contra-lateral, non-deprived bulbs. Interestingly, the DNA fragmentation induced by olfactory deprivation displayed a characteristic internucleosomal fragmentation pattern, suggesting that the cells induced to die may do so by apoptosis. A significant inverse correlation between DNA fragmentation and the natural variation in normal bulb size was found, suggesting that bulb size may be related to cell death.

Animals↗

PubMed2003

Chromosomal DNA fragmentation in apoptosis and necrosis induced by oxidative stress.

Chromosomal DNA dysfunction plays a role in mammalian cell death. Oxidative stress producing reactive oxygen species (ROS) induces chromatin dysfunction such as single- and double-strand DNA fragmentation leading to cell death through apoptosis or necrosis. More than 1 Mbp giant DNA, 200-800 or 50-300 kbp high molecular weight (HMW) DNA and internucleosomal DNA fragments are produced by oxidative stress and by some agents producing ROS during apoptosis or necrosis in several types of mammalian cells. Some nucleases involved in the chromosomal DNA fragmentation in apoptosis or necrosis are classified. ROS-mediated DNA fragmentation is caused and enhanced by polyunsaturated fatty acids (PUFAs) or their hydroperoxides through lipid peroxidation. A reduction of intracellular GSH levels induced by the inhibition of cystein transport or GSH biosynthesis leads to cell death through over production and accumulation of ROS in some types of mammalian cells. The ROS accumulation system has been used as a model of oxidative stress to discuss whether ROS-mediated DNA fragmentation associated with cell death is based on apoptosis or necrosis.

Animals↗

PubMedDate not supplied

Human mast cells induce caspase-independent DNA fragmentation in leukemic T cells.

Mast cells are known to play an important role in inflammation and host defense. Recent evidence suggests that mast cells may also participate in immune surveillance against cancer cells. In this study, we demonstrate that human mast cells are able to trigger apoptosis in Jurkat T leukemia cells. Fragmentation of Jurkat cell DNA was detectable by JAM assay within 4 h of exposure to HMC-1 mast cells or cultured human cord blood-derived mast cells. HMC-1 mast cells that were fixed with paraformaldehyde retained the ability to induce apoptosis in Jurkat cells while cell-free conditioned supernatants from HMC-1 cell cultures failed to elicit DNA fragmentation, suggesting that mast cells mediate anti-tumor activity via a cell-surface molecule. Surprisingly, the apoptosis-inducing activity of HMC-1 mast cells was not mediated by known tumor necrosis factor (TNF) superfamily members (TNF-alpha, Fas ligand, TRAIL, TWEAK), nor did the fragmentation of Jurkat cell DNA by mast cells require the activity of caspase-3, -8, or -9. Collectively, these data indicate that mast cells trigger caspase-independent apoptosis in leukemic cells via a novel cell-surface molecule, and are consistent with a role for mast cells as anti-tumor effector cells.

Apoptosis Regulatory Proteins↗

PubMed1993

DNA polymerase-catalyzed addition of nontemplated extra nucleotides to the 3' end of a DNA fragment.

Some prokaryotic and eukaryotic DNA polymerases are capable of adding an additional nontemplated nucleotide residue at the 3' end of a DNA fragment (Clark et al., 1987; Clark, 1988). The extra nucleotide at the 3' end of the PCR product has been shown to be a critical factor determining the efficiency of cloning PCR products into plasmids and can affect mutation analyses with a PCR-denaturing gradient gel electrophoresis (DGGE) approach (Pfeiffer and Hu, 1993). In the present work, the ability of various DNA polymerases to add an extra nontemplated nucleotide at the 3' end of DNA was studied. The results show that out of the eight studied enzymes, five can add, with varying efficiencies, an extra nucleotide residue at the 3' end of DNA. Which extra nucleotide is added depends on the terminal residue and the DNA polymerase. Among the enzymes, thermostable Pfu DNA polymerase is found to be the best choice for PCR due to its relatively high fidelity (Scott et al., 1991; Coller, unpublished), and ability to produce blunt-ended DNA fragments. The relationship between the DNA polymerases' ability to add an extra nucleotide and their 3'-->5' exonuclease activity is also discussed.

Bacterial Proteins↗

PubMed2001

Effect of graded hypoxia on cerebral cortical genomic DNA fragmentation in newborn piglets.

Previous studies have shown that hypoxia is associated with modification of the cerebral cortical nuclear membrane, leading to increased intranuclear calcium. The increased intranuclear calcium activates calcium-dependent endonucleases, resulting in DNA fragmentation. The present study tests the hypothesis that the fragmentation of neuronal genomic DNA increases with an increase in the degree of cerebral tissue hypoxia. Sixteen newborn piglets were anesthetized, ventilated and divided into normoxic and hypoxic groups with varying degrees of hypoxia. Cerebral hypoxia was documented biochemically by measuring tissue levels of ATP and phosphocreatine. Isolation of cerebral cortical neuronal nuclei and DNA and their purity was confirmed by standard techniques. DNA samples were separated by electrophoresis on 1% agarose gel and stained with ethidium bromide. In the hypoxic samples, multiple low-molecular-weight DNA fragments were present as a smear pattern from 200 to 2,000 base pairs. Levels of high-energy phosphates were compared to the area of each smear for each animal to correlate the degree of hypoxia with the degree of DNA fragmentation. DNA fragmentation increased when high-energy phosphate levels decreased. We conclude that there is a critical threshold value of oxidative metabolism beyond which there are progressive changes in the cortical neuronal cells, leading to DNA fragmentation.

Adenosine Triphosphate↗

PubMed1984

Specific amino acid substitutions in bacterioopsin: Replacement of a restriction fragment in the structural gene by synthetic DNA fragments containing altered codons.

To study the mechanism of light-dependent proton translocation by bacteriorhodopsin, we have introduced single-codon changes in the gene so as to produce the following specific amino acid substitutions in the protein: Tyr-185 to Phe, Pro-186 to Leu, Trp-189 to Phe, Ser-193 to Ala, and Glu-194 to Gln. The strategy involved replacement of a 62-base-pair restriction fragment by synthetic DNA duplexes containing the modified nucleotide sequences. This required a unique restriction site (Xho I) at Ile-203 which was created by oligonucleotide-directed point mutagenesis. The six DNA duplexes corresponding to the modified native and mutant restriction fragments were all prepared by DNA ligase-catalyzed joining of chemically synthesized deoxyribooligonucleotides. The bacterioopsin expression plasmids reconstructed by using the synthetic DNA fragments were characterized by restriction analysis and DNA sequence determination. An extremely rapid, efficient, and general method for purification of the synthetic oligonucleotides and of DNA fragments was developed.

Journal Article↗

PubMed1999

Pasteurella haemolytica leukotoxin induced apoptosis of bovine lymphocytes involves DNA fragmentation.

It has been reported that Pasteurella haemolytica leukotoxin (LKT) induces morphologic changes in bovine leukocytes consistent with apoptosis in vitro, but DNA fragmentation was not observed. We investigated whether bovine lymphocytes undergo DNA fragmentation during LKT-induced apoptosis. Bovine peripheral blood lymphocytes were isolated by density gradient centrifugation and exposed to LKT or inactive pro-LKT protein from a lktC- mutant strain. After exposure, DNA fragmentation in lymphocytes was quantified colorimetrically by diphenylamine assay and visualized by agarose gel electrophoresis. At high LKT concentrations, bovine lymphocytes were lysed, but at low concentrations, LKT caused DNA fragmentation characteristic of apoptosis. Maximal DNA fragmentation in bovine lymphocytes was induced by 0.1 TU ml(-1) LKT following 3 h exposure, but only background level of DNA fragmentation was observed with the inactive pro-LKT. Equine lymphocytes that are resistant to LKT intoxication did not show DNA fragmentation following exposure to LKT. Preincubation of LKT with a neutralizing anti-LKT monoclonal antibody inhibited LKT-induced DNA fragmentation. Electrophoresis of DNA from bovine lymphocytes treated with 0.1 TU ml(-1) LKT demonstrated the typical 'ladder' pattern of internucleosomal DNA cleavage, the hallmark of apoptosis associated with activation of endonucleases. LKT-induced DNA fragmentation was inhibited by 0.5 mM ZnCl2, an endonuclease inhibitor. The results indicated that LKT at low concentrations induced apoptotic cell death of bovine lymphocytes, which may play a role in initiation and persistence of P. haemolytica infection.

Animals↗

PubMed2001

[Stress-induced DNA fragmentation in cardiomyocytes of MDX and C57Bl mice].

The study deals with apoptosis of cardiomyocytes of adult mdx mice. Our previous investigation of the total DNA from mdx mice myocardium in 0.5% agarose and 5% PAAG revealed middle sized DNA fragments about 64 kb only. The DNA electrophoresis in 5% PAAG after alpha-32P-dATP incorporation into DNA, fragments mediated by terminal transferase, showed no presence of smaller DNA fragments. The low size DNA fragments (0.2, 0.4 and 11.0 kb) were observed only following stress (a 5 min swimming in water bath) by means of alpha-32P-dATP incorporation mediated by TdT reaction. DNA fragmentation lasted for 48 h after the stress. A study of the total DNA extracts of C57B1 mice also demonstrated middle and low molecular sized DNA fragmentation 2 h after the stress under the same condition of the experiment. But during the next 48 h the signs of DNA fragmentation of the total DNA disappeared. The authors conclude that the first stage of apoptosis is a permanent property of cardiomyocytes of mdx mice.

Animals↗

PubMed1995

Cloning and nucleotide sequence of a specific DNA fragment from Paracoccidioides brasiliensis.

We cloned and sequenced a species-specific 110-bp DNA fragment from Paracoccidioides brasiliensis. The DNA fragment was generated by PCR with primers complementary to the rat beta-actin gene under a low annealing temperature. Comparison of the nucleotide sequence, after excluding the primers, with those in the GenBank database identified approximately 60% homology with an exon of a major surface glycoprotein gene from Pneumocystis carinii and a fragment of unknown function in Saccharomyces cerevisiae chromosome VIII. By Southern hybridization analysis, the 32P-labelled fragment detected 1.0- and 1.9-kb restriction fragments within whole-cell genomic DNA of P. brasiliensis digested with HindIII and PstI, respectively, but failed to hybridize to genomic DNAs from Candida albicans, Blastomyces dermatitidis, Cryptococcus neoformans, Aspergillus fumigatus, Saccharomyces cerevisiae, Pneumocystis carinii, rat tissue, or humans under low-stringency hybridization conditions. Additionally, the specific DNA fragment from three different P. brasiliensis isolates (Pb18, RP18, RP17) was amplified by PCR with primers mostly complementary to nonactin sequences of the 110-bp DNA fragment. In contrast, there were no amplified products from other fungus genomic DNAs previously tested, including Histoplasma capsulatum. To date, this is the first species-specific DNA fragment cloned from P. brasiliensis which might be useful as a diagnostic marker for the identification and classification of different P. brasiliensis isolates.

Animals↗

PubMed2004

Effects of short and long incubations on DNA fragmentation of testicular sperm.

DNA fragmentation in testicular sperm from men with obstructive azoospermia is increased by 4-hour and 24-hour incubations and after cryopreservation with the effect is intensified by post-thaw incubation. Testicular sperm for use in intracytoplasmic sperm injection (ICSI) should be injected without delay.

Cell Culture Techniques↗

PubMed1989

Discriminatory 32P 3'-end labeling of restriction endonuclease co-digested DNA fragments.

We present an improved method for selectively labeling specific DNA fragments in a mixture of restriction fragments. lambda DNA, used to develop the procedure, was digested with a combination of restriction enzymes and treated, at various incubation temperatures, with reverse transcriptase and one or more [alpha-32P]dNTP molecules. The labeled fragments were subjected to agarose gel electrophoresis and detected by autoradiography. We were able to direct the 3'-end labeling to precise subpopulations of DNA fragments, generated by multiple restriction enzyme digestions. We also show that labeling selectivity of DNA restriction fragments, by reverse transcriptase, is affected by the incubation temperature used during the labeling reaction. This paper describes an approach to 3'-end label select DNA fragments with reverse transcriptase and [alpha-32P]dNTPs. The procedure permits the bypassing of time-consuming isolation and purification steps required, by conventional radiolabeling techniques, to radiolabel specific DNA fragments.

Autoradiography↗