Higher-order structure of mammalian chromatin deduced from viscoelastometry data

The results of viscoelastometry (VE) for mammalian DNA have been puzzling because they have two orders of magnitude smaller measured viscoelastic relaxation times for mammalian chromosomes than that expected for DNA linear coils of chromosomal size. In an attempt to resolve this discrepancy, we have applied a recent model of G1 chromosome structure (J.Y. Ostashevsky, Mol Biol. Cell 9, 3031-3040, 1998) in which the 30 nm chromatin fiber of each chromosome forms a string of loop clusters (micelles). This model has two parameters: the number of loops per micelle (f) and the average loop size (Mf), which can be estimated independently from VE data. Using our VE data for plateau phase V79 Chinese hamster cells (unirradiated and X-irradiated with doses up to 40 Gy) we show that f approximately 13 , which is close to other estimates made using the model (f ranges from 10-20), and Mf approximately 2 Mbp, which is similar to estimates made from our nucleoid data (1.3 Mbp) and to estimates made in the literature using a variety of techniques (1-3 Mbp).     

Convergence to Normality of the Asymptotic Quasi‐Score Function on a Linear Model

The asymptotic quasi‐likelihood method is considered for the model y_t = f_t(θ) + M_t, t = 0,1, …,T where f_tθ) is a linear predictable process of the parameter of interest θ, M_t is a martingale difference, and the nature of E(M_t² | ℱ_t–1) is unknown. This paper is concerned with the limiting distribution of the asymptotic quasi‐score function of such a model. Confidence intervals and hypothesis testing of θ is derived from the limiting distribution. Comparison is made between the estimates obtained through this method and those obtained through the least squares method.     

Consistency of the Asymptotic Quasi-Likelihood Estimate on Linear Models

Consider a model y_t = f_t(θ) + M_t, 0 ⩽ t ⩽ T where θ∈ Θ in an unknown parameter, f_t(θ) is a linear predictable process, M_t is a martingale difference, and the nature of E(M²_t/ℱ_t—1) is unknown. This paper presents an estimating procedure for θ based on the asymptotic quasi-likelihood methodology. Conditions under which the asymptotic quasi-likelihood estimate converges to the true parameter θ₀ are discussed. This method is applied to several simulated examples, and estimates of the unknown parameter are obtained by means of a two-stage technique. Comparison is made between the estimates obtained via this method and those obtained via the ordinary least squares method. Discussion is provided on the application of the model.     

DNA groove-binding and acid-base properties of a Ru(II) complex containing anthryl moieties

Abstract

DNA groove binders have been poorly studied as compared to the intercalators. A novel Ru(II) complex of [Ru(aeip)₂(Haip)](PF₆)₂ {Haip?=?2-(9-anthryl)-1H-imidazo[4,5-f][1,10]phenanthroline and aeip = 2-(anthracen-9-yl)-1-ethyl-imidazo[4,5-f][1, 10]phenanthroline} is synthesized and characterized by elemental analysis, ¹H NMR spectroscopy and mass spectrometry. The complex is evidenced to be a calf-thymus DNA groove binder with a large intrinsic binding constant of 10⁶ M^?1 order of magnitude as supported by UV–visible absorption spectral titrations, salt effects, DNA competitive binding with ethidium bromide, DNA melting experiment, DNA viscosity measurements and density functional theory calculations. The acid-base properties of the complex studied by UV–Vis spectrophotometric titrations are reported as well.     

The organization and repair of DNA in the mammalian chromosome. III. Determination of the molecular weight of a mammalian native DNA

The necessary conditions for a unique solution of the sedimentation vs DNA molecular weight equations are considered and applied to the native DNA of the L5178Y mouse leukemia cell. A brief review and critique of the literature of sedimentation anomalies is given to demonstrate that such anomalies are not present in the data reported here. It is shown that the chromosomal DNA of L5178Y cells comes in uniform packages of 1.0 (0.5–2.0) × 10¹⁰ daltons. All pieces are of an identical size which corresponds to the DNA content of about 1/13 the average chromatid. Both the size estimate and the number of such molecules/cell are confirmed by viscoelastometry. This DNA is shown to be free of radioactively demonstrable protein and/or lipid contaminants and of the same isopycnic density as T₄ DNA. Variance analysis is applied to determine the precision of all measurements and to pinpoint major sources of error. A relationship between [η] and M is derived for native DNA in 1.0M NaCl. A necessary conclusion from these data is that mammalian chromosome models requiring degrees of polynemy greater than 16-neme (in G₁) are incorrect (to the extent that the L5178Y cell is typical of mammalian cells).     

The organization and repair of DNA in the mammalian chromosome. I. Calibration procedures and errors in the determination of the molecular weight of a native DNA

The semiautomated sucrose gradient system of Lange and Liberman (1974) (Anal. Biochem. 59 , 129–145) has been used to determine an accurate value of the exponent k of the Burgi and Hershey equation (1963) (Biophys. J. 3 , 309–321) under conditions of 1M salt. A complete analysis of the variance of k was done for data from both systems. The results lead to the conclusion that the value k = 0.401 (±0.012 for reproducibility; ±0.019 for total error) obtained here is considerably more accurate than that of Burgi and Hershey (even when corrected for DNA concentration effects and the improved size estimates of T₄ DNA size). The use of the Burgi and Hershey relationship and a T₄ DNA metric to determine molecular weights of mammalian DNA requires the utmost precision in the exponent if useful estimates are to be obtained. This also has implications for double-strand breakage and repair estimates.     

DNA binding,prominent photonuclease activity and antibacterial PDT of cobalt(II) complexes of phenanthroline based photosensitizers

Abstract

The chemistry of Co(II) complexes showing efficient light induced DNA cleavage activity, binding propensity to calf thymus DNA and antibacterial PDT is summarized in this article. Complexes of formulation [Co(mqt)(B)₂]ClO₄ 1–3 where mqt is 4-methylquinoline-2-thiol and B is N,N-donor heterocyclic base, viz. 1,10-phenanthroline (phen 1), dipyrido[3,2-d:2′,3′-f]quinoxaline (dpq 2) and dipyrido[3,2-a:2′,3′-c]phenazine (dppz 3) have been prepared and characterized. The DNA-binding behaviors of these three complexes were explored by absorption spectra, viscosity measurements and thermal denaturation studies. The DNA binding constants for complexes 1, 2 and 3 were determined to be 1.6?×?10³?M^?1, 1.1?×?10⁴?M^?1 and 6.4?×?10⁴?M^?1 respectively. The experimental results suggest that these complexes interact with DNA through groove binding mode. The complexes show significant photocleavage of supercoiled (SC) DNA proceeds via a type-II process forming singlet oxygen as the reactive species. Antimicrobial photodynamic therapy was studied using photodynamic antimicrobial chemotherapy (PACT) assay against E. coli and all complexes exhibited significant reduction in bacterial growth on photoirradiation.     

The Affinity of DNA-Microtubule Protein Complexes and their Disruption by Tubulin Binding Drugs

Abstract

Using the gel shift assay system, we have measured the apparent affinity constant for the interaction of two different DNAs with MAP proteins found in both total calf brain microtubules and heat stable brain preparations. Both DNAs studied contained centromere/kinetochore sequences- one was enriched in the calf satellite DNA; the other was a large restriction fragment containing the yeast CEN11 DNA sequence. Complexes formed using both DNAs had similar K_app values in the range of 2.1×10⁷ M^?1 to 2.0×10⁸ M^?1. CEN11 DNA-MTP complexes had by far the highest K_app value of 2.0×10⁸ M^?1. The CEN11 DNA sequence is where the yeast kinetochore of chromosome 11 is formed and where the single yeast microtubule is bound in vivo. The CEN11 conserved region II known binding sites -(dA/dT)n runs- for mammalian MAP2 protein, are in good agreement with this higher K_app value. The effects of the classical tubulin binding drugs colchicine, podophyllotoxin and vinblastine on the DNA-MAP protein complex stability were investigated by determining the drug concentrations where the complexes were destabilized. Only the complexes formed from total microtubule protein (tubulin containing) were destabilized over a wide drug concentration range. Heat stable brain protein complexes (no tubulin) were largely unaffected. Furthermore, it took 10–100 fold higher drug concentrations to disrupt the CEN 11 DNA complexes compared to the calf thymus satellite DNA enriched complexes. These data support our previous results suggesting that there is a DNA sequence dependent interaction with MAP proteins that appears to be conserved in evolution (Marx et. al., Biochim. Biophys. Acta. 783, 383–392,1984; Marx and Denial, Molecular Basis of Cancer 172B,65-15 1985). In addition, these results imply that the classical tubulin binding drugs may exert their biological effects in cells at least in part by disrupting DNA-Protein complexes of the type we have studied here.     

Titanium dioxide nanoparticles preferentially bind in subdomains IB,IIA of HSA and minor groove of DNA

Titanium dioxide nanoparticles (TiO₂-NPs) interaction with human serum albumin (HSA) and DNA was studied by UV–visible spectroscopy, spectrofluorescence, circular dichroism (CD), and transmission electron microscopy (TEM) to analyze the binding parameters and protein corona formation. TEM revealed protein corona formation on TiO₂-NPs surface due to adsorption of HSA. Intrinsic fluorescence quenching data suggested significant binding of TiO₂-NPs (avg. size 14.0 nm) with HSA. The Stern–Volmer constant (K_sv) was determined to be 7.6 × 10² M^?1 (r² = 0.98), whereas the binding constant (K_a) and number of binding sites (n) were assessed to be 5.82 × 10² M^?1 and 0.97, respectively. Synchronous fluorescence revealed an apparent decrease in fluorescence intensity with a red shift of 2 nm at Δλ = 15 nm and Δλ = 60 nm. UV–visible analysis also provided the binding constant values for TiO₂-NPs–HSA and TiO₂-NPs-DNA complexes as 2.8 × 10² M^?1 and 5.4 × 10³ M^?1. The CD data demonstrated loss in α-helicity of HSA and transformation into β-sheet, suggesting structural alterations by TiO₂-NPs. The docking analysis of TiO₂-NPs with HSA revealed its preferential binding with aromatic and non-aromatic amino acids in subdomain IIA and IB hydrophobic cavity of HSA. Also, the TiO₂-NPs docking revealed the selective binding with A-T bases in minor groove of DNA.     

The effects of structural variations of thiophene-containing Ru(II) complexes on the acid–base and DNA binding properties

A phenylthiophenyl-bearing Ru(II) complex of [Ru(bpy)₂(Hbptip)](PF₆)₂ {bpy?=?2,2′-bipyridine, Hbptip?=?2-(4-phenylthiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline} was synthesized and characterized by elemental analysis, ¹H NMR spectroscopy, and electrospray ionization mass spectrometry. The ground- and excited-state acid–base properties of the complex were studied by UV–visible absorption and photoluminescence spectrophotometric pH titrations and the negative logarithm values of the ground-state acid ionization constants were derived to be pK _a1?=?1.31?±?0.09 and pK _a2?=?5.71?±?0.11 with the pK _a2 associated deprotonation/protonation process occurring over 3 pK _a units more acidic than thiophenyl-free parent complex of [Ru(bpy)₂(Hpip)]²⁺ {Hpip?=?2-phenyl-1H-imidazo[4,5-f][1,10]phenanthroline}. The calf thymus DNA-binding properties of [Ru(bpy)₂(Hbptip)]²⁺ in Tris–HCl buffer (pH 7.1 and 50?mM NaCl) were investigated by DNA viscosities and density functional theoretical calculations as well as UV–visible and emission spectroscopy techniques of UV–visible and luminescence titrations, steady-state emission quenching by [Fe(CN)₆]^4?, DNA competitive binding with ethidium bromide, DNA melting experiments, and reverse salt effects. The complex was evidenced to bind to the DNA intercalatively with binding affinity being greater than those for previously reported analogs of [Ru(bpy)₂(Hip)]²⁺, [Ru(bpy)₂(Htip)]²⁺, and [Ru(bpy)₂(Haptip)]²⁺ {Hip?=?1H-imidazo[4,5-f][1,10]phenanthroline, Htip?=?2-thiophenimidazo[4,5-f][1,10]phenanthroline, Haptip?=?2-(5-phenylthiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline}.     

Marker-based estimates of identity by descent and alikeness in state among maize inbreds

Molecular markers are useful for determining relationships and similarity among inbreds, especially if the proportion of marker loci with alleles common to inbreds i and j is partitioned into: (1) the probability that marker alleles are identical by descent (_Mf_ij); and (2) the conditional probability that marker alleles are alike in state, given that they are not identical by descent ( _ij). Our objectives were to: develop a method, based on tabular analysis of restriction fragment length polymorphism marker data, for estimating _Mf_ij, _ij, and the parental contribution to inbred progeny; validate the accuracy of the method with a simulated data set; and compare the pedigree-based coefficient of coancestry (f_ij) and _Mf_ij among a set of maize (Zea mays L.) inbreds. Banding patterns for 73 probeenzyme combinations were determined among 13 inbreds. Iterative estimation of _Mf_ij, _ij, and the parental contribution to progeny was performed with procedures similar to a tabular analysis of pedigree data. Deviations of _Mf_ij from pedigree-based f_ij ranged from 0.002 to 0.288, indicating large effects of selection and/or drift during inbreeding for some inbreds. Differences between marker-based estimates and expected values of parental contribution to inbred progeny were as large as 0.205. Results for a simulated set of inbreds indicated that tabular analysis of marker data provides more accurate estimates of _Mf_ij and _ij than other methods described in the literature. Tabular analysis requires the availability of marker data for all the progenitors of each inbred. When marker data are not available for the parents of a given inbred, _Mf_ij and _ij may still be calculated if parental contributions to the inbred are assumed equal to their expectations.     

Inversion of net ecosystem CO2 flux measurements for estimation of canopy PAR absorption

The fractional absorption of photosynthetically active radiation (f_PAR) is frequently a key variable in models describing terrestrial ecosystem–atmosphere interactions, carbon uptake, growth and biogeochemistry. We present a novel approach to the estimation of the fraction of incident photosynthetically active radiation absorbed by the photosynthetic components of a plant canopy (f_Chl). The method uses micrometeorological measurements of CO₂ flux and incident radiation to estimate light response parameters from which canopy structure is deduced. Data from two Ameriflux sites in Oklahoma, a tallgrass prairie site and a wheat site, are used to derive 7‐day moving average estimates of f_Chl during three years (1997–1999). The inverse estimates are compared to long‐term field measurements of PAR absorption. Good correlations are obtained when the field‐measured f_PAR is scaled by an estimate of the green fraction of total leaf area, although the inverse technique tends to be lower in value than the field measurements. The inverse estimates of f_Chl using CO₂ flux measurements are different from measurements of f_PAR that might be made by other, more direct, techniques. However, because the inverse estimates are based on observed canopy CO₂ uptake, they might be considered more biologically relevant than direct measurements that are affected by non‐physiologically active components of the canopy. With the increasing number of eddy covariance sites around the world the technique provides the opportunity to examine seasonal and inter‐annual variation in canopy structure and light harvesting capacity at individual sites. Furthermore, the inverse f_Chl provide a new source of data for development and testing of f_PAR retrieval using remote sensing. New remote sensing algorithms, or adjustments to existing algorithms, might thus become better conditioned to ‘biologically significant’ light absorption than currently possible.     

On the origin of telocentric chromosomes in mammals

The origin of mammalian telocentric chromosomes is considered under the classical (fusion) and fission hypotheses using both theoretical analyses of the mechanisms proposed under the two hypotheses, and the published chromosomal data for 723 mammal species. Telocentrics are defined on the basis of short arm size (S_w) as chromosomes with S_w < 0·1(Imai, 1976). The fusion hypothesis lacks adequate models for producing these telocentrics, but their origin is readily understood under the fission hypothesis. Based on these analyses, I propose a cyclical model of chromosome change, symbolized:

in which T, A, and $\text{M}$ are, respectively, telocentric, acrocentric, and meta-, submeta- and subtelocentric chromosomes. The chief elements of this model are centric fission $\text{(}\text{M}\text{→ T + T)}$, tandem growth of constitutive heterochromatin (T → A), and pericentric inversion $\text{(A →}\text{M}\text{)}$. Under this model, therefore, mammalian karyotypes have an overall tendency, with occasional reversals, to evolve higher numbers of both chromosomes and chromosome arms.     

Proportion of mated females, female mating experience, and sex ratio of the osmund sawfly, Strongylogaster osmundae (Hymenoptera, Tenthredinidae)

The proportion of mated females (M _f) of the osmund sawfly, Strongylogaster osmundae, and the sex ratio of the eggs they deposited (r, proportion of males) were estimated in the wild by collecting egg masses. The proportion of mated females at oviposition varied from 0 to 1.0. M _f was high (often 1.0) among the females that emerged after hibernation, and lower in the subsequent generations. Mated females of the hibernated generation deposited equal numbers of eggs of both sexes. Mated females of the first and subsequent generations produced more female than male eggs. These results qualitatively agreed with the prediction provided by an evolutionarily stable strategy (ESS) model (if M _f < 1 then r < 0.5). However, the quantitative prediction provided by the model [M _f (1 − r) = 0.5] was not always observed in the wild, especially where the population density and M _f were high. The value of r was often lower than the predicted one. The following simple hypothesis was tested by experimentation: “Females that encounter males frequently estimate the proportion of mated females to be high and deposit eggs with a 1:1 sex ratio.” However, results did not support this hypothesis. Females that copulated soon after emergence and were courted by males two or more times did not show a higher offspring sex ratio than those which mated 1 or 2 days after emergence and experienced no other sexual encounter. Another mechanism for determination of r is suggested, and the reason why the population sex ratio of sawflies is often female-biased (r < 0.5) is discussed.     

A note on imitative behavior

In a preceding paper (Bull. Math. Biophysics,27, 175–185) the distribution function ofφ=ɛ ₁-ɛ ₂,—the difference of excitations in the two mutually inhibiting centers, has been derived in terms of the distribution functionsf ₁(ɛ ₁) andf ₂(ɛ ₂) of the two excitations. In the present note some properties of the distribution functionf(ϕ) in terms of the propertiesf ₁(ɛ ₁) andf ₂(ɛ ₂) are derived.     

Osmotic Pressure of DNA Solutions and Effective Diameter of the Double Helix

Abstract

A simple osmometer with nuclear filters (polymer films with pores of a preset diameter) were used to measure the osmotic pressure of Col El plasmid DNA solutions in the concentration range of 1–4 mg/ml DNA. Linear and open circular DNA forms proved to have the same osmotic pressure within the experimental accuracy. The results of the measurements were used for calculating the second virial coefficient A ₂ of the solution of DNA segments and the effective chain diameter d _eff in the ionic strength range of 10^?2-0.1 M, As the ionic strength is lowered from 0.1 to 10^?2 M the effective diameter of DNA increases from 80 to 220 A. The results are in rather good agreement with theory and with other experimental data.     

STUDIES ON THE POPULATION KINETICS OF THE WALKER CARCINOMA BY AUTORADIOGRAPHY AND PULSE CYTOPHOTOMETRY

The proliferation parameters of the Walker carcinoma were estimated from both in vivo and in vitro measurements. The transplantable Walker carcinoma 256 was grown in male inbred BD1 rats. During exponential growth, 5-6 days after transplantation, a PLM curve was performed, yielding estimates of Tc ? 18.0 hr, Ts ? 6.4 hr, T_G2+M? 4.1 hr. With the double labelling technique in vitro under 2.2 atm oxygen we obtained: Tc ? 18.2hr, Ts ? 8.2 hr, T_G2+M? 2.0hr. From pulse cyto-photometry DNA content histograms the fractions of cells in the cell cycle phases were calculated using a computer program: f_G1? (47.6 ± 1.1)%, f_s? (34.1 ± 1.0)%, f_G2+M? (18.3 ± 1.5)%. These fractions remained constant between the fifth and the twelfth day after transplantation. At that time the tumour growth had already slowed down appreciably. The growth fraction determined by repetitive labelling was 0.96 on the fifth and 0.93 on the seventh and eleventh day. The cell loss factor was φ? 17% during exponential tumor growth and increased to about 100% between the tenth and twelfth day. The agreement of the cell kinetic data determined by autoradiography from solid tumours in vivo (PLM, continuous labelling) and autoradiography as well as pulse cytophotometry from in vitro experiments (excised material) was satisfactory.     

Analysis of the electrophoretic properties of double-stranded DNA and RNA in agarose gels at a finite voltage gradient

The electrophoretic mobilities of double-stranded (ds) DNAs and ds RNAs of various lenths, L, were measured in gels of 0.4–1.8% (w/v) agarose at a voltage gradient of 1.0 V/cm. Differences in the electrophoresis of ds DNA and ds RNA are presented and discussed. A general expression is derived that describes the electrophoretic mobility, M, of either type of ds nucleic acid as a function of the gel concentration and the nucleic acid length: M = M′₁(L/L₀)^?x ? M₂, where M′₁ and L₀ are constants, and x and M₂ depend on the agarose gel concentration. The results obtained by fitting our data with this equation are consistent with the mobilities of nucleic acids in a wide range of gel concentrations, including free electrophoresis in solution and electrophoresis in gles of high agarose concentration in which nuleic acids are expected to reptate through the gel matrix. Finally, various methods of plotting agarose gel electrophoresis data are discussed.     

Genetical assessment of induced quantitative variation following hierarchical selfing

The method of Virk, Jinks and Pooni⁽⁷⁾ has been further elaborated and illustrated with a simple example from the plant height data of Borojević and Borojević⁽³⁾ experiment on 15 kR gamma-ray-irradiated Bankut-1205 wheat variety in the M₅, M₆ and M₇ generations. A substantial amount of the induced variation for plant height has been found to be of additive and fixable nature. The practical utility of the method for testing the adequacy of a simple model and estimating the genetical components of variation has been amply demonstrated.The simplicity and distinctiveness of the new approach arises from the omission of rank 0 statistics corresponding to the M₁ plants and arriving at the genetical equivalance of rank 1 statistics in the hierarchical analysis of variance performed on the simple pedigreed data generated in a selfing series initiated in the M₁ generation following mutagenic treatment of a pure-breeding line. The new analysis avoids any assumptions about the independence or kind of dependence of mutational events and provides estimates of the additive and dominance genetical components of variation, from a single generation from M₃ onwards.     

Accounting for residual heterogeneity in double-observer sightability models decreases bias in burro abundance estimates

Feral burros (Equus asinus) and horses (E. ferus caballus) inhabiting public land in the western United States are intended to be managed at population levels established to promote a thriving, natural ecological balance. Double-observer sightability (M_DS) models, which use detection records from multiple observers and sighting covariates, perform well for estimating feral horse abundances, but their effectiveness for use in burro populations is less understood. These M_DS models help minimize detection bias, yet bias can be further reduced with models that account for unmodeled variation, or residual heterogeneity, in detection probability. In populations containing radio-marked individuals, residual heterogeneity can be estimated with M_DS models by including a covariate that corresponds to the marked status of a group (M_H models). Another approach is to use information from detections missed by both observers to account for the characteristics that make groups more or less likely to be detected, or recaptured, by the second observer (M_R models). We used aerial survey data from 3 burro populations (Sinbad Herd Management Area, UT [2016–2018], Lake Pleasant Herd Management Area, AZ [2017], and Fort Irwin National Training Center, CA [2016–2017]) to develop M_DS models applicable for feral burros in the southwestern United States. Our objectives were to quantify precision and bias of standard M_DS surveys for feral burros and to examine which model type for incorporating residual heterogeneity (M_H or M_R) would result in the least-biased estimates of burro populations relative to the minimum number known alive (MNKA) within the Sinbad Herd Management Area. Standard M_DS model estimates achieved a mean coefficient of variation of 0.08, while underestimating MNKA by an average of 27.1%. Accounting for residual heterogeneity through recapture probability in M_R models resulted in estimates closer to MNKA than M_H models (9.5% vs. 16.5% less than MNKA). Our results indicate that M_DS models can achieve precise enough estimates to monitor feral burro populations, but they routinely produce negatively biased estimates. We encourage the use of radio-collars to reduce bias in future burro surveys by accounting for residual heterogeneity through M_R models.