Changes In Deoxyribonucleic Acid Research Articles

Voltammetric Measurement of Antioxidant Activity by Prevention of Cu(II)-Induced Oxidative Damage on DNA Bases Using a Modified Electrode.

The protective effect of antioxidants using electrochemical techniques can be evaluated by examining the oxidative changes in deoxyribonucleic acid (DNA) nucleobases. In this study, a gold nanoparticle (AuNP)-decorated and multiwalled carbon nanotube (MWCNT)-Nafion-modified glassy carbon electrode (GCE/AuNP/MWCNT-Nafion) was developed to evaluate the preventive ability of antioxidants on oxidative DNA damage. A modified working electrode was prepared and characterized by cyclic voltammetry, electrochemical impedance spectroscopy, and scanning electron microscopy. The developed electrochemical method relies on two phenomena: (i) reactive species (RS) produced by dissolved oxygen in the presence of copper(II) partially damage the DNA immobilized on the electrode surface and (ii) antioxidant compounds prevent this damage by scavenging the formed RS. Changes in guanine, adenine, and cytosine oxidation signals resulting from DNA damage were measured using differential pulse stripping voltammetry before/after the interaction of dsDNA with Cu(II) while antioxidants were absent or present. The DNA protective ability of antioxidants was assessed for a number of antioxidant compounds (i.e., ascorbic acid, gallic acid, epicatechin, catechin, epicatechin gallate, glutathione, chlorogenic acid, N-acetyl cysteine, rosmarinic acid, quercetin, and rutin). Quercetin was found to show the highest antioxidant effect, and its limit of detection was determined as 1 μM. The manufactured biosensor was put in an application for the determination of antioxidant activity of herbal teas.

ROLE OF CIRCADIAN RHYTHM AND CLOCK IN MALIGNANCY

In dermatological condition there is a big role of disruption of circadian rhythm. Many research also says that we skin is continuously exposed to open environment then there may be effects of UV rays which can be seen by the change in deoxyribonucleic acid (DNA) and it can be also seen in the night mode. It is based on the certain principals of and literature of circadian rhythm in human life. It can be easily understand by the study of treatment and environment for effective skin treatment. Dermatologists should also be aware that adequate sleep is necessary for optimal DNA repair activity in the skin. All contemplation and essentially, a mind clock should be set with daily function for a healthy lifestyle.

Quantitative Analysis of DNA Methylation by Bisulfite Sequencing.

Changes in deoxyribonucleic acid (DNA) methylation are shown to occur with aging in mammals. Besides changes that seem to be essentially stochastic, methylation levels of certain CpG sites display a strong correlation with age. Collectively, methylation of such CpG sites could be used as "epigenetic clocks" to predict biological age. Numerous versions of the epigenetic clock have been proposed, all of them based on quantitative estimation of the methylation levels of individual CpG sites. Different methods were elaborated for quantitative measurements of DNA methylation, with the most reliable of these based on bisulfite treatment of DNA. We present here a protocol for assessment of the methylation levels of individual CpG sites in target DNA sequences by the direct sequencing of polymerase chain reaction (PCR) amplification products obtained from bisulfate-converted DNA.

Detecting differential peaks in ChIP-seq signals with ODIN.

Detection of changes in deoxyribonucleic acid (DNA)-protein interactions from ChIP-seq data is a crucial step in unraveling the regulatory networks behind biological processes. The simplest variation of this problem is the differential peak calling (DPC) problem. Here, one has to find genomic regions with ChIP-seq signal changes between two cellular conditions in the interaction of a protein with DNA. The great majority of peak calling methods can only analyze one ChIP-seq signal at a time and are unable to perform DPC. Recently, a few approaches based on the combination of these peak callers with statistical tests for detecting differential digital expression have been proposed. However, these methods fail to detect detailed changes of protein-DNA interactions. We propose an One-stage DIffereNtial peak caller (ODIN); an Hidden Markov Model-based approach to detect and analyze differential peaks (DPs) in pairs of ChIP-seq data. ODIN performs genomic signal processing, peak calling and p-value calculation in an integrated framework. We also propose an evaluation methodology to compare ODIN with competing methods. The evaluation method is based on the association of DPs with expression changes in the same cellular conditions. Our empirical study based on several ChIP-seq experiments from transcription factors, histone modifications and simulated data shows that ODIN outperforms considered competing methods in most scenarios.

Special application of matrix-assisted laser desorption ionization time-of-flight mass spectrometry in clinical microbiological diagnostics

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry as a new possibility for rapid identification of bacteria and fungi revolutionized the clinical microbiological diagnostics. It has an extreme importance in the routine microbiological laboratories, as identification of the pathogenic species rapidly will influence antibiotic selection before the final determination of antibiotic resistance of the isolate. The classical methods for identification of bacteria or fungi, based on biochemical tests, are influenced by many environmental factors. The matrix-assisted laser desorption ionization time-of-flight mass spectrometry is a rapid method which is able to identify a great variety of the isolated bacteria and fungi based on the composition of conserved ribosomal proteins. Recently several other applications of the method have also been investigated such as direct identification of pathogens from the positive blood cultures. There are possibilities to identify bacteria from the urine samples in urinary tract infection or from other sterile body fluids. Using selective enrichment broth Salmonella sp from the stool samples can be identified more rapidly, too. The extended spectrum beta-lactamase or carbapenemase production of the isolated bacteria can be also detected by this method helping the antibiotic selection in some cases. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry based methods are suitable to investigate changes in deoxyribonucleic acid or ribonucleic acid, to carry out rapid antibiotic resistance determination or other proteomic analysis. The aim of this paper is to give an overview about present possibilities of using this technique in the clinical microbiological routine procedures.

Studies on paraquat toxicity on deoxyribonucleic acid of cultured mammalian cells using flow cytometry.

The beginning of the cell death process initiated by paraquat is caused by oxygen-free radicals produced through the redox cycle. We examined the next step driven by the radicals focusing on changes in deoxyribonucleic acid (DNA) utilizing flow cytometry. A significant decrease in the proportion of cells was observed in the G0/G1 phase, while a remarkable accumulation of cells was noted in the S phase. Forward light scattering (FSC) and side light scattering (SSC) histograms of the particles from cells treated with paraquat showed a change in the size, the refractive index and the granularity of the nucleoids. By contrast, leakage of lactate dehydrogenase (LDH) was not observed during the period in which changes in DNA occurred. These results suggest that paraquat-induced DNA damage constitutes one of the next steps driven by free radicals, leading to the process of cell death.

Heavy ion action on biological systems

Life is governed by molecular processes, particularly involving the expression and conservation of genetic information. Heavy ions deposit large amount of energy at very small scale comparable to the essential molecular structures of biological systems. This paper illustrates the special aspects of heavy ion radiobiology from a fundamental point of view. After a short summary of the structure and function of biological systems, concentrating on the cell and its constituents, the pattern of energy deposition by heavy ions is discussed. Experimental examples are the induction of molecular changes in deoxyribonucleic acid, cell killing and the formation of mutations. It is shown that a close link exists between the physical parameters and the inactivation of biological functions that is not restricted to direct particle traversals but may also be brought about by the action of far-reaching secondary electrons.

A histological and flow cytometric study of dog brain endothelial cell injuries in delayed radiation necrosis

The pathogenesis of delayed cerebral radiation necrosis was studied histologically and biochemically in 25 dogs with special attention to vascular endothelial cell injuries. The dogs were sacrificed 3 to 30 months after irradiation with a single dose of 15 Gy to the head. Brain specimens were appropriately fixed for light and electron microscopic studies, and capillary endothelial cells were isolated for flow cytometric study. The endothelial cells were stained with acridine orange, then the cell ratios in the reproductive phase (S + G2 + M) were investigated with flow cytometry. Thereafter, Feulgen hydrolysis and computer analysis of the hydrolysis curves were performed to examine the qualitative changes in deoxyribonucleic acid (DNA) of endothelial cells after irradiation. Under light microscopy, spongy degeneration with small cell infiltration was observed, especially in the frontal white matter, at 6 months after irradiation. At 9 months, necrotic foci appeared and developed until 15 months after irradiation. Blood vessels around the necrotic area showed luminal narrowing with endothelial hyperplasia and proliferation. At 30 months, no fresh necrotic lesions were observed. Under electron microscopy, endothelial cells of capillaries and small vessels around the necrotic area showed an increase of pinocytosis, and in the nuclei there was an increase of infoldings and euchromatin. The cell ratios in the reproductive phase were 14.5% to 23.3% (maximum at 9 months) in the irradiated group compared to 6.4% in the control group. The rate constant of apurinic acid production, a parameter correlating with DNA transcriptional activity, was minimum at 3 months and maximum at 9 months after irradiation. The data suggest that impairment of the microcirculation plays an important role in the pathogenesis of delayed radiation necrosis, and that the time of necrosis occurrence closely correlates with the cell cycle of vascular endothelial cells.

Genotyping of macerated stillborn fetuses

It is generally impossible to collect blood or to culture tissue from a macerated stillborn fetus. Accurate genotyping of such a fetus may, however, be critical for the diagnosis of genetic diseases and appropriate genetic counseling. In the East Flanders Prospective Twin Study, placental tissue of twin and triplet sets, in some of which one or both members were stillborn and macerated, has been stored at -20 degrees C. Of all these fetuses, sex and zygosity could be determined accurately on the placental deoxyribonucleic acid. We tested the possibility of nongenetic changes in deoxyribonucleic acid that result from maceration or tissue degradation over time in storage on placental samples from monochorionic twins in which only one member was stillborn and macerated. The deoxyribonucleic acid variants in these monozygotic twins were identical whether or not either cotwin was macerated. Thus deoxyribonucleic acid variants can be determined accurately on the placental tissue of macerated fetuses, even after prolonged freezing.

Changes in deoxyribonucleic acid linking number due to treatment of mammalian cells with the intercalating agent 4'-(9-acridinylamino)methanesulfon-m-anisidide.

Treatment of mammalian cells with DNA intercalating agents produces protein-associated DNA strand breaks. These breaks have been proposed to represent the action of a topoisomerase, which would alter the DNA linking number. Changes in DNA linking number in cells treated with the intercalating agent 4'-(9-acridinylamino)methanesulfon-m-anisidide (m-AMSA) were studied by ethidium titration of nucleoid sedimentation. m-AMSA treatment was found to produce an increase in DNA linking number. Previously, we had proposed that intercalator-induced protein-associated DNA breaks act to reduce DNA torsional strain that results from the intercalator-induced decrease in DNA twist. In such a model, linking number would be expected to decrease. The finding that the DNA linking number increased following m-AMSA treatment suggests that intercalators may block enzymes that normally decrease linking number. Such enzymes would have DNA gyrase like properties. Consistent with this possibility, a DNA gyrase inhibitor, novobiocin, inhibited the restoration of normal linking number and, to a lesser degree, the reversal of protein-associated strand breaks after removal of intercalator.

Conformational changes in deoxyribonucleic acid during transcription.

Circular dichroism (CD) was used to examine changes in secondary structure of calf thymus DNA during in vitro transcription. Formation of a binary complex between DNA and RNA polymerase (nucleoside triphosphate:nucleotidyltransferase, EC 2.7.7.6) did not alter the CD spectrum of the DNA. Alterations in ellipticity in the spectral region between 245 and 300 nm occurred during synthesis of RNA. This change was consistent with a B- to A-like form transition in polynucleotide conformation. The increment of ellipticity consisted of two separate compounds; component I was insensitive to treatment with pancreatic ribonuclease whereas component II was a ribonuclease labile fraction. Cleavage by restriction endonucleases did not produce or significantly alter the ellipticity of transcription. In contrast, between 50% and 60% of the component I ellipticity was sensitive to pancreatic DNase I. The data indicate that component I is a property of DNA and suggest that the alteration in secondary conformation which affects this component extends cooperatively beyond the DNase I insensitive DNA-RNA polymerase complexes.

Inhibitory effect of novobiocin on ribonucleic acid synthesis during germination of Bacillus subtilis spores.

Novobiocin inhibited ribonculeic acid synthesis during germination of Bacillus subtilis spores. Transcription of certain kinds of genes probably required a preceding conformational change in deoxyribonucleic acid.

Effect of microwaves (2450-MHz) on the immune system in mice: studies of nucleic acid and protein synthesis.

CBA/J adult male mice were given single or triple exposures to 2450-mHz microwaves in an environmentally controlled wave guide facility. The average absorbed dose rate for a single exposure varied from 12 to 15 mW/g. Sham-exposed mice served as controls. Lymphoid cells were collected and tested for metabolic activity on days 3, 6, and 9 following a single exposure, and on days 9, 12, and 16 following triple exposures on days 0, 3, and 6. Cells were cultured in vitro for four hours to seven days before their metabolic rates were assayed. Under these conditions, microwaves failed to produce any detectable change in deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein synthesis, as measured by the incorporation of methyl(3H)-thymidine (3H-TDR) (DNA substrate), 3H-uridine (3H-UR) (RNA substrate), and 3H-leucine (protein substrate) by spleen, bone marrow, and peripheral blood lymphocytes (PBL) in vitro. These data suggest that microwave-induced increases in the frequency of complement-receptor (CR)- or surface-immunoglobulin (sIg)-bearing cells were not associated with a concomitant increase in cell proliferation and/or protein synthesis, and favor the concept that microwaves under these conditions stimulate already existing B-cell precursors for maturation.

Alterations of rabbit articular cartilage by intra-articular injections of glucocorticoids

The destruction of rabbit articular cartilage after intra-articular injections of hydrocortisone acetate was investigated using histological, biochemical, and tracer methods. Fissures and cysts increased in number as increasing amounts of hydrocortisone were given. A linear decrease of hexosamine to less than 50 per cent after twelve injections was accompanied by insigificant changes in deoxyribonucleic acid and hydroxyproline content. The synthesis of proteoglycans and proteins was reduced to one-third, while the production of collagen dropped to less than one-fifth. The changes in thymidine incorporation were not significant. Based on these data, a model indicating the sequence of events which leads to joint destruction after intra-articular injections of glucocorticoid is proposed.

Structural Changes in Deoxyribonucleic Acid during Early Stages of Lens Regeneration in Triturus

Abstract When the lens is removed from the newt Triturus, a new lens will form from epithelial cells of the dorsal iris. DNA was isolated from dorsal irises of animals which had been engaged in lens regeneration for 0, 3, 5, and 7 days. The nitrocellulose affinities of the DNA preparations were: 0-day, 12%; 3-day, 15%; 5-day, 86%; and 7-day, 60%. This suggests that structural alterations occur during the early stages of lens regeneration (and initiation of DNA synthesis). These structural changes can be correlated with the cell cycle. The DNA preparations were characterized by hydroxyapatite chromatography, buoyant density in CsCl and CsSO4(Hg), thermal denaturation, and sedimentation in neutral and alkaline sucrose gradients. The DNA isolated from 0-day regenerates (G0 phase of the cell cycle) behaved as native duplex structures containing few nicks. The DNA from 3-day regenerates (early G1 phase) contained a significant number of nicks. The DNA from 5-day regenerates (late G1 phase) contained gaps or missing runs of nucleotides. The DNA from 7-day regenerates (S phase) existed in two configurations. One possessed a great deal of single-stranded character, and the other was similar, but not identical, to the DNA from 5-day regenerates. These results lead us to suggest that prior to entry into the cell cycle, DNA exists in vivo as chromosomal duplexes which are isolated as structures possessing a maximum charge density. During G1, DNA is activated for replication by a process which at first leads to nicks, then gaps. During replication much of the DNA exists in vivo as an extended structure which is isolated as molecules which possess a great deal of single-stranded character.

The action of insulin, growth hormone, and epinephrine on cell growth in liver, muscle, and brain of the hypophysectomized rat.

Extract: This study explores changes in deoxyribonucleic acid (DNA), ribonucleic acid (RNA), protein, and water content of muscle, liver, and cerebrum in hypophysectomized rats and the effects of injecting growth hormone, insulin, or growth hormone with epinephrine conjointly over an eleven-day period. Male hypophysectomized rats, 26 to 49 days of age, fed an ad libitum diet were studied. At 38 days of age they were injected with insulin, 0.4 to 1.8 units per day, with bovine growth hormone (250 μUg/day) or with the same amount of growth hormone and epinephrine, 5 to 20 μUg/day, concomitantly, or were untreated until the 49th day of age. Control rats of the same age were either pair-fed to untreated hypophysectomized rats or given an ad libitum diet. Untreated hypophysectomized rats showed poor body weight gain per unit food intake and reduced skeletal growth. The nucleic acid and protein content of liver, muscle, and cerebrum was reduced when compared with controls of the same age. The ratio of protein: DNA (cell size) was increased for body size but reduced for age. Administration of insulin caused hypertrophy of liver cells and increased the protein content of liver, but did not affect muscle and cerebrum. DNA content of liver or cerebrum did not increase, and the gain in DNA content of muscle was not remarkable. There was a definite increase in RNA content of muscle, liver, and cerebrum and in the ratios of RNA: DNA and protein: DNA of liver. Injections of growth hormone caused an increase in DNA (cell number), RNA, and protein content in liver, muscle, and cerebrum. There was a reduction in the ratio of cytoplasm to nucleus. The protein increment was nullified by the injection of epinephrine in conjunction with growth hormone. DNA content of muscle and liver was increased, but not to the level produced by growth hormone alone. The increase in RNA content of liver, muscle, and cerebrum was again significant; the ratio of RNA: DNA increased only in liver. Caloric intake of untreated hypophysectomized rats and those treated with growth hormone or insulin was comparable. Rats injected with epinephrine showed a significant increase in caloric intake. The results indicate that insulin is involved with growth in cell size, while growth hormone is active with respect to the increase in cell number. Both hormones are required for optimal growth. Speculation: The present study indicates that both growth hormone and insulin are required for optimum cell growth. Epinephrine administration retards the increase in cell number that normally occurs in hypophysectomized rats receiving growth hormone. This suggests that overactivity of the sympathetic pathways may retard growth and produce effects that simulate hypopituitarism.

Changes in deoxyribonucleic acid, collagen and ascorbic acid during the development of carrageenan granuloma

Changes in deoxyribonucleic acid, collagen and ascorbic acid during the development of carrageenan granuloma

Molecular Changes in Deoxyribonucleic Acid Induced by X-rays

A chromatographic study of molecular changes in DNA after in vitro exposure to x-rays revealed little effect on the DNA macromolecule when either intact red cells of frog or DNA isolated from these cells was exposed to 1000 r. Increasing the dose to 10,000 r resulted in a significant shift from gradients of lower molecular weight to the higher gradients. These data suggest that cross-linking of DNA occurred at the higher radiation level.

Visual observation of deoxyribonucleic acid changes in bacteria during growth of bacteriophage.

Fluorescence Microscopy in the Study of Nucleic Acids: Visual Observation of Deoxyribonucleic Acid Changes in Bacteria during Growth of Bacteriophage

Changes in Deoxyribonucleic Acid and Total Nitrogen in Planarian Worms during Starvation

ABSTRACT The changes in total nitrogen and in deoxyribosides (DNA) have been followed during starvation of the planarian worm, Polycelis nigra. It was found that total nitrogen content after 60 days had been reduced to about 14 per cent, of its initial value. It is not possible to exclude with certainty the occurrence of any DNA loss, but it is clear that the loss, if any, is much smaller than the loss in nitrogen. The implications of these results for previous morphological investigations of the effects of starvation on planarian worms are discussed.