Effects of ethidium bromide on DNA loop organisation in human lymphocytes measured by anomalous viscosity time dependence and single cell gel electrophoresis.

The effects of ethidium bromide (EtBr) on human lymphocytes were studied by the method of anomalous viscosity time dependence (AVTD) and by the comet assay. EtBr at low concentrations increased the maximum viscosity and time of radial migration as measured with AVTD at neutral conditions of lysis. A pronounced relaxation of DNA loops was observed with the neutral comet assay. The maximal comet length corresponded to 2 Mb DNA loops. At high concentrations of EtBr, 2 mg/ml, significant reduction in AVTD below control level was seen that suggested hypercondensation of chromatin. The hypercondensation was directly observed with the neutral comet assay. EtBr did not induce DNA strand breaks as measured by the alkaline comet assay. The hypercondensed nuclei could be decondensed by irradiation with gamma-rays or exposure to light. The data provide evidence that EtBr at high concentrations resulted in hypercondensation of chromatin below control level. The comet assay confirmed that the increase in AVTD peaks deals with relaxation of loops and AVTD decrease is caused by chromatin condensation. The prediction of the AVTD theory for a correlation between time of radial migration and condensation of chromatin was verified. Further, the data show that the comet assay at neutral conditions of lysis is rather sensitive to DNA loop relaxation in the absence of DNA damage. Finally, donor specificity was found for the hypercondensation.     

Dynamic and static chromatin

It was found that the dependence of the viscosity of calf thymus chromatin dispersions and human leukocytes on ethidium bromide concentration had two peaks indicative of domains with circular supercoiled DNA and varying resistance to ultrasound in the cells and isolated chromatin. The hypothesis of V. D. Paponov and P. S. Gromov (Bull. Exp. Biol. Med., N5, 590, 1985) on the transformation of static relations of nucleosome DNA-containing nuclei into dynamic, after chromatin exposure to ultrasound due to DNA linearization in chromatin domains possessing circular supercoiled DNA, has been confirmed.     

Viscosity as an additional physico-chemical parameter for studying chromatin structure

The viscosity values of chromatin in higher order structures, which range from 0.1 to 0.4 dl/g, are considerably lower than those of isolated DNA. These low values are consistent with other physico-chemical parameters, such as sedimentation and diffusion coefficients. When deducing molecular mass and compact shape of chromatin molecules in solvents of nearly physiological ionic strength, all these parameters are in general agreement. A decrease in ionic strength increases viscosity and decreases s-value. Both effects are consistent with a chromatin model postulating a very compact quaternary structure which unravels in low ionic environment to an unfolded but not completely extended tertiary structure.     

Physicochemical characterization of konjac glucomannan

Four commercial konjac glucomannan (KGM) samples and a glucomannan derived from yeast were characterized by aqueous gel permeation chromatography coupled with multi angle laser light scattering (GPC-MALLS). Disaggregation of aqueous glucomannan solutions through controlled use of a microwave bomb facilitated reproducible molar mass distribution determination alleviating the need for derivatization of the polymer or the use of aggressive solvents. Further characterization was undertaken by use of capillary viscometry and photon correlation spectroscopy (PCS). The weight average molecular masses (M(w)) determined were in the region of 9.0 +/- 1.0 x 10(5) g mol(-1) for KGM samples and 1.3 +/- 0.4 x 10(5) g mol(-1) for the yeast glucomannan. The values determined for KGM in aqueous solution are in agreement with those reported for KGM in aqueous cadoxen. The degradation of samples observed upon autoclaving has been quantified by GPC-MALLS and intrinsic viscosity determination, allowing comparison with reported Mark-Houwink parameters. Shear flow experiments were undertaken for a range of KGM solutions of concentration 0.05 to 2.0% using a combination of controlled stress and controlled strain rheometers. The concentration dependence of the zero shear specific viscosity was determined by analysis of the data using the Ellis model. The dependence of the zero shear specific viscosity on the coil overlap parameter was defined and interpretation discussed in terms of the Martin and Tuinier equations.     

Method of the anomalous time dependence of viscosity for registration of changes in conformational state of Escherichia coli cell genome

The sensitivity of the anomalous time dependence of viscosity to the concentration of the DNA-protein complexes (DNA + histone-like proteins of bacteria or, in other words, the genome) such as chromatin and the conformations of these complexes in lysates of E. coli AB1157 cells were studied. A linear region of the anomalous viscosity time dependence on the concentration of E. coli cells was found in which the interactions between single DNA-protein complexes can be neglected. The response of the genome of E. coli to ethidium bromide at concentrations of 0.0003-3 mg/ml was studied. Significant differences in the effect of ethidium bromide on E. coli cells in the stationary and logarithmic growth phases were found. The effect of heating cell lysates, the molar concentration of NaCl in lysates, and the addition of proteins into lysates on the parameters of the anomalous viscosity time dependence was studied. It was shown that proteins do not contribute significantly to the effect of anomalous viscosity time dependence. The results obtained confirm that the method is sensitive to changes in the conformational state of the genome of E. coli cells.     

Double strand break (DSB) repair in heterochromatin and heterochromatin proteins in DSB repair

Chromosomal translocations are a hallmark of cancer cells and they represent a major cause of tumorigenesis. To avoid chromosomal translocations, faithful repair of DNA double strand breaks (DSBs) has to be ensured in the context of high ordered chromatin structure. However, chromatin compaction is proposed to represent a barrier for DSB repair. Here we review the different mechanisms cells use to alleviate the heterochromatic barrier for DNA repair. At the same time, we discuss the activating role of heterochromatin-associated proteins in this process, therefore proposing that chromatin structure, more than being a simple barrier, is a key modulator of DNA repair.     

Shear creep of gelatin gels from mammalian and piscine collagens.

This paper describes new measurements on the creep rheological behaviour of gelatin gels from both traditional mammalian and piscine sources. Measurements on a series of concentrations of gels were obtained using a high-precision controlled stress rheometer. Results for the concentration dependence of compliance are close to those expected from dynamic oscillatory measurements of gel modulus, assuming ideal elasticity. The concentration dependence of viscosity approximates power law behaviour, with eta~C( approximately 2-3), lower than the exponent expected for semi-dilute solutions. The apparent contradiction implied by this is discussed and a novel gel viscosity versus concentration state diagram presented.     

Photoreceptors CRYTOCHROME2 and phytochrome B control chromatin compaction in Arabidopsis

Development and acclimation processes to the environment are associated with large-scale changes in chromatin compaction in Arabidopsis (Arabidopsis thaliana). Here, we studied the effects of light signals on chromatin organization. A decrease in light intensity induces a large-scale reduction in chromatin compaction. This low light response is reversible and shows strong natural genetic variation. Moreover, the degree of chromatin compaction is affected by light quality signals relevant for natural canopy shade. The photoreceptor CRYPTOCHROME2 appears a general positive regulator of low light-induced chromatin decompaction. Phytochrome B also controls light-induced chromatin organization, but its effect appears to be dependent on the genetic background. We present a model in which chromatin compaction is regulated by the light environment via CRYPTOCHROME2 protein abundance, which is controlled by phytochrome B action.     

Structure of micelles formed by monodisperse hexa-(γ-benzyl-L-glutamate) in solution

The angular dependence of light scattering and the concentration dependence of the relative viscosity have been measured in solutions of o-nitrophenylthio-hexa-(γ-benzyl-L -glutamate) ethylamide in ethylene dichloride. Both the reduced intensity of scattered light and the reduced viscosity of the solution suddenly increase above a certain critical concentration, below which both of them remain low and constant. The Debye plot of light scattering indicates that primary micelles having an aggregation number 48 are formed at the critical micelle concentration and that secondary micelles, each consisting of 294 molecules, then appear in increasing amounts with increasing concentration beyond the critical micelle concentration. The secondary micelle is rodlike and has a length of 1170 Å, if it is rigid. An analysis of the reduced viscosity leads to the intrinsic viscosity for the primary micelle, 0.360 dL g^?1, and to that of the secondary micelle, 1.28 dL g^?1. If the secondary micelle is represented by a prolate ellipsoid, it should have an axial ratio of 47. If the polypeptide chains are extended in the micelle, the observed aggregation number and axial ratio of the secondary micelle can well accommodate the intermolecularly hydrogen-bonded in-register β-structure of anti-parallel chains. In the primary micelle, some folded polypeptide chains are involved, and an intermolecularly hydrogen-bonded out-of-register structure would form a rather open network.     

Exposure of rat brain to 915 MHz GSM microwaves induces changes in gene expression but not double stranded DNA breaks or effects on chromatin conformation

We investigated whether exposure of rat brain to microwaves (MWs) of global system for mobile communication (GSM) induces DNA breaks, changes in chromatin conformation and in gene expression. An exposure installation was used based on a test mobile phone employing a GSM signal at 915 MHz, all standard modulations included, output power level in pulses 2 W, specific absorption rate (SAR) 0.4 mW/g. Rats were exposed or sham exposed to MWs during 2 h. After exposure, cell suspensions were prepared from brain samples, as well as from spleen and thymus. For analysis of gene expression patterns, total RNA was extracted from cerebellum. Changes in chromatin conformation, which are indicative of stress response and genotoxic effects, were measured by the method of anomalous viscosity time dependencies (AVTD). DNA double strand breaks (DSBs) were analyzed by pulsed-field gel electrophoresis (PFGE). Effects of MW exposure were observed on neither conformation of chromatin nor DNA DSBs. Gene expression profiles were obtained by Affymetrix U34 GeneChips representing 8800 rat genes and analyzed with the Affymetrix Microarray Suite (MAS) 5.0 software. In cerebellum from all exposed animals, 11 genes were upregulated in a range of 1.34-2.74 fold and one gene was downregulated 0.48-fold (P < .0025). The induced genes encode proteins with diverse functions including neurotransmitter regulation, blood-brain barrier (BBB), and melatonin production. The data shows that GSM MWs at 915 MHz did not induce PFGE-detectable DNA double stranded breaks or changes in chromatin conformation, but affected expression of genes in rat brain cells.     

The use of ultraviolet light in the fractionation of chromatin containing unsubstituted and bromodeoxyuridine-substituted DNA.

Two procedures are described for the fractionation of chromatin containing unsubstituted (LL) DNA and DNA unifilarly substituted with bromodeoxyuridine (HL). The two procedures rely upon the sensitivity of bromodeoxyuridine-containing DNA to UV light to induce either strand breakage or protein crosslinking. When a mixture of LL and HL chromatin is irradiated with UV light, the HL DNA fragments into molecules of smaller molecular weight than the LL DNA and crosslinks more chromosomal protein than the LL DNA. LL and HL chromatin can be fractionated on the basis of size by centrifuging through a neutral sucrose gradient. The HL DNA-protein adducts that are generated by the UV light have a unique buoyant density and may be isolated by isopycnic centrifugation in CS2SO4. The ability to fractionate LL and HL chromatin permits certain studies on the structure of replicating chromatin.     

The arrangement of proteins on the deoxyribonucleic acid in chromatin

The arrangement of the protein component on the DNA of the chromatin complex was studied by comparing the rate of release of oligonucleotides and of protein after addition of deoxyribonuclease I and deoxyribonuclease II to rat thymus chromatin. Also the action of deoxyribonuclease I on normal chromatin and on chromatin depleted of non-histone protein was compared, to elucidate the role of the latter protein in chromatin structure. As a preliminary to the above, the rate of action of deoxyribonuclease I on DNA and on chromatin at the same DNA concentration, and the dependence of the action of this enzyme on the Mg(2+) concentration, were studied. It was found that: (1) little if any DNA in chromatin is present in extensive, truly ;free' zones, i.e. completely uncovered by protein; (2) at relatively low concentrations of added Mg(2+), deoxyribonuclease I degrades chromatin more rapidly than DNA; (3) the non-histone protein is not attached directly to the DNA in chromatin.     

Diffusive motions control the folding and unfolding kinetics of the apomyoglobin pH 4 molten globule intermediate

The sperm whale apomyoglobin pH 4 folding intermediate exists in two forms, Ia and Ib, that mimic transient kinetic intermediates in the folding of the native protein at pH 6. To characterize the nature of the kinetic barrier that controls the formation of the earliest intermediate Ia, we have investigated the effects of small viscogenic cosolvents on its folding and unfolding kinetics. The kinetics are measurable by stopped-flow fluorescence and follow a cooperative two-state model in the absence and presence of cosolvents. Small cosolvents stabilize Ia, but, by applying the isostability test to separate the viscogenic effect of the cosolvent from its stabilizing effect, we found that, in both folding and unfolding conditions, the apparent rate constant decreases when solvent viscosity increases. The unitary inverse dependence of the apparent rate constant on solvent viscosity indicates a diffusion-controlled reaction. This result is consistent with the hypothesis that folding of the apomyoglobin pH 4 intermediate obeys a diffusion-collision model. Additionally, the temperature dependence of the reaction rate at constant viscosity indicates that the formation of Ia is also controlled by an energy barrier. Linear free energy relationships show that the transition state of the U <==> Ia reaction is compact and buries 45% of the surface area that is buried in native apomyoglobin. We conclude that the transition state of the U <==> Ia reaction resembles that for the formation of native proteins; namely, it is dry and its compactness is closer to that of the folded (Ia) form than of the unfolded form.     

Changes in chromatin conformation during radiation-induced apoptosis in human lymphocytes

Human peripheral lymphocytes in G(0) phase were irradiated with 1-5 Gy of gamma rays. The biochemical and morphological changes characteristic of apoptosis were examined for 72 h after irradiation. In parallel, changes in chromatin conformation were studied by the method of anomalous viscosity time dependence (AVTD) and by measurements of nuclear halo size. An immediate and dose-dependent relaxation of chromatin, which became saturated at doses above 2-3 Gy, was revealed by the AVTD method. The state of relaxed chromatin lasted up to 12-24 h after irradiation, a response considerably longer than the time attributable to repair of radiation-induced DNA breaks. Measurements of nuclear halo size also indicated the initial relaxation of chromatin in the irradiated cells and its subsequent condensation. This condensation of chromatin as revealed with AVTD correlated well with nuclear condensation, as measured with dual fluorescence staining, and with DNA fragmentation, as measured by conventional and pulsed-field gel electrophoresis (PFGE). Late apoptotic cells did not contribute significantly to the AVTD signal, showing that the chromatin of these cells was completely condensed and fragmented.     

Ionic strength dependence of the binding of methylene blue to chromatin and calf thymus DNA.

The binding of the intercalating dye methylene blue (MB) to chromatin and to free DNA has been studied as a function of ionic strength at very low binding ratios (1 MB/400 DNA bases) using absorption spectroscopy. With increasing salt concentration MB is displaced from chromatin to a higher extent than from DNA. The free energy change for MB binding to chromatin is found to be approximately 5 kJ/mole lower than for binding to DNA. This difference can be explained by the reduced number of high affinity binding sites in chromatin due to the presence of histone proteins. The difference in binding energy is virtually independent of the degree of chromatin condensation and also of the valence of counter ions, suggesting that neither the affinity for, nor the number of intercalation sites in the linker DNA is markedly changed upon the salt-induced condensation. The unaffected thermodynamics of the linker binding suggests that factors such as DNA superhelicity and the electrostatic influence from the chromatosomes remain unchanged during chromatin condensation.     

Fractionation of rat fibroblasts in a zonal rotor by means of a viscosity barrier.

Cell fractionation procedures involving differential sedimentation followed by resuspension of pellets and isopycnic centrifugation are very difficult to apply to the small amounts of material available from tissue culture cells. We have explored the possibility of successive differential and isopycnic sedimentation in a zonal rotor using a short viscosity barrier for the differential sedimentation. The marker enzymes used were cytochrome oxidase, acid phosphatase, catalase, and 5′-nucleotidase. The results of these procedures are compared to the results of one-step isopycnic separations in gradients of sucrose and Stractan. The Stractan gradient was much more effective than the sucrose gradient in separating the marker enzymes from the proteins of a postnuclear supernatant, but neither type of gradient could significantly purify the marker enzymes one from another. A two-step procedure using a viscosity barrier was effective in separating particles carrying catalase from the other marker enzymes assayed and from most of the protein. A three-step procedure resulted in similar purification of mitochondria. Modification of barrier composition and centrifugation times would probably result in further improvement of separations according to individual requirements for yield, purification, and freedom from specific contamination by other subcellular particles.     

ELF magnetic field affects proliferation of SPD8/V79 Chinese hamster cells but does not interact with intrachromosomal recombination

Extremely low-frequency (ELF) magnetic fields have previously been shown to affect conformation of chromatin, cell proliferation, and calcium metabolism. Possible mutagenic and carcinogenic effects of ELF have also been discussed and tested. In this study, intrachromosomal recombination in the hprt gene after exposure to ELF magnetic field was investigated using the SPD8 recombination assay. SPD8 cells, derived from V79 Chinese hamster cells were exposed to ELF at a specific combination of static and ELF magnetic fields, that has been proven to have effects on chromatin conformation in several cell types. The genotoxic agent camptothecin (CPT) was used either as a positive control or simultaneously with ELF. We also analysed the effect of ELF and CPT on chromatin conformation with the anomalous viscosity time dependence (AVTD) technique, cell growth kinetics, and cell survival with clonogenic assay. DNA fragmentation was analysed by pulsed field gel electrophoresis (PFGE). ELF did not induce recombination alone, neither did ELF modify the recombinogenic effect of CPT. Although, there was no effect on cell survival in response to ELF exposure, inhibition of cell growth was observed. On the other hand, ELF exposure partly counteracted the growth inhibition seen with CPT. The data suggest that ELF exposure may stimulate or inhibit cell growth depending on the state of the cells. Although, ELF did not induce recombination, a weak but statistically significant DNA fragmentation comparable with CPT-induced fragmentation was observed with PFGE 48h after exposure to ELF.