Torsion dynamics and depolarization of fluorescence of linear macromolecules: II. Fluorescence polarization anisotropy measurements on a clean viral φ29 DNA

The decay of the fluorescence polarization anisotropy (FPA) of ethidium bromide bound to DNA has been studied over a range of time-spans from 18 ns to 120 ns with the aid of a picosecond dye laser. These FPA data have been fitted to three different functional forms: (1) the single-exponential-decay-plus-baseline employed by Wahl et al.; (2) the Initial Exponential Decay Zone formula of a recently developed rigid-rod and torsion spring model for the torsion dynamics of DNA; (3) the Intermediate Zone formula of that same model. At any fixed experimental time-span the formulas (2) and (3) provide slightly better fits than formula (1), but cannot be distinguished from each other by reduced chi-squaied values alone. However, only the Intermediate Zone formula fits the data from all different time-spans with the same set of physical parameters. The parameters determined for formulas (1) and (2) vary with the time-span of the experiment in a characteristic manner that can be rationalized in the event that the FPA actually follows the Intermediate Zone curve. The fact that the torsion dynamics for this DNA is well described by the Intermediate Zone formula discounts the possibility of distinct widely spaced torsion joints in such Clean DNAs. We are able to provide the first reliable value for the torsional rigidity of DNA, C= 1.29 ± 0.10 × 10^?19 dyne cm² in 0.01 M NaCl at 25° C.     

Dynamic light scattering from weakly bending rods: estimation of the dynamic bending rigidity of the M13 virus

A theory is presented for the dynamic structure factor [S(K,t]) of weakly bending rods. This treatment is based on a discrete bead model for the Brownian dynamics in which all bead motions associated with bending are constrained to occur in a plane perpendicular to the end-to-end vector, thus prohibiting extension or contraction along that axis. Preset hydrodynamic interactions are incorporated in a numerically exact manner. The predicted normalized dynamic structure factor S(K,t)/S(K,0) should be valid for short times t such that the rms rotation of the end-to-end vector around any transverse axis is much less than 1.0 radian. With geometrical parameters appropriate for the M13 virus, the intensity autocorrelation function G(2) (K,t) = 1 + magnitude of S(K,t)/S(K,0)2 is calculated over a range of times and scattering vectors K for selected values of the persistence length P. The calculated G(2) (K,t) are fitted to a single exponential with unit baseline over the same range of times as the experimental photon correlation functions, and the apparent diffusion coefficients Dapp (K) are obtained from the best-fit relaxation times. For the sake of completeness, an exact expression is derived for the apparent diffusion coefficient obtained from the initial slope of the dynamic structure factor. However, this does not reduce to the known correct result in the rigid rod limit. To obtain the correct result, the limit of infinite bending rigidity must be taken before the limit of zero time. For this and other reasons, the initial slope value of Dapp (K) is not useful for weakly bending rods. Photon correlation functions are measured for the M13 virus, which is virtually identical to the often-studied fd virus. The experimental photon correlation functions are fitted over 8 relaxation times to a single-exponential plus baseline, and the Dapp (K) are calculated from the best-fit relaxation times. Theoretical curves of Dapp (K) vs K2 for selected values of P are compared with the experimental data, which are satisfactorily reproduced when P = 22000 +/- 2000 A. This dynamic value is close to the static value, P = 20000 +/- 2000 A, reported for the very similar fd virus. The most recent theories of Maeda and Fujime and their dynamic light scattering studies of fd virus are compared with the present results in some detail. Their optimum value of P is in surprisingly good agreement with the present value.     

Study of cerebral energy metabolism using the rat hippocampal slice preparation.

This article describes methods and experimental paradigms used in combination with the rat hippocampal slice preparation in an attempt to better understand cerebral energy metabolism under the following conditions: normal resting conditions, conditions of oxygen and/or glucose deprivation, and conditions of activation (excitation). The outcome of this attempt, as described herewith, demonstrates the unmatched usefulness of the brain slice preparation as an in vitro tool in the field of neuroscience.     

Phylogeographic history of mitochondrial haplogroup J in Scandinavia

Background

Mitochondrial DNA haplogroup J is the third most frequent haplogroup in modern-day Scandinavia, although it did not originate there. To infer the genetic history of haplogroup J in Scandinavia, we examined worldwide mitogenome sequences using a maximum-likelihood phylogenetic approach.

Methods

Haplogroup J mitogenome sequences were gathered from GenBank (n = 2245) and aligned against the ancestral Reconstructed Sapiens Reference Sequence. We also analyzed haplogroup J Viking Age sequences from the European Nucleotide Archive (n = 54). Genetic distances were estimated from these data and projected onto a maximum likelihood rooted phylogenetic tree to analyze clustering and branching dates.

Results

Haplogroup J originated approximately 42.6 kya (95% CI: 30.0–64.7), with several of its earliest branches being found within the Arabian Peninsula and Northern Africa. J1b was found most frequently in the Near East and Arabian Peninsula, while J1c occurred most frequently in Europe. Based on phylogenetic dating, subhaplogroup J1c has its early roots in the Mediterranean and Western Balkans. Otherwise, the majority of the branches found in Scandinavia are younger than those seen elsewhere, indicating that haplogroup J dispersed relatively recently into Northern Europe, most plausibly with Neolithic farmers.

Conclusions

Haplogroup J appeared when Scandinavia was transitioning to agriculture over 6 kya, with J1c being the most common lineage there today. Changes in the distribution of haplogroup J mtDNAs were likely driven by the expansion of farming from West Asia into Southern Europe, followed by a later expansion into Scandinavia, with other J subhaplogroups appearing among Scandinavian groups as early as the Viking Age.

     

Polyelectrolyte contribution to the persistence length of DNA

The difference between the theories of Manning, on the one hand, and of Odijk and Skolnick and Fixman, on the other, for the polyelectrolyte contribution to the persistence length of DNA is shown to arise entirely from a subtle geometrical error in the theory of Manning. The corrected theory of Manning predicts a negligible polyelectrolyte contribution in 1.0M NaCl and only 33 Å in 0.01M NaCl, thus giving a change in total persistence length by a factor of only 1.07 over that range, in agreement with Odijk. Pertinent data in the literature indicate that the persistence length must change by a factor of ≤ 1.6 between 1.0 and 0.01M NaCl, and very likely by less than a factor of 1.4. Evidently, the intrinsic rigidity of the uncharged double-strand filament dominates the bending rigidity at NaCl concentrations above 0.01M.     

Electrophysiological support in favor of multiple opiate receptors in the caudate and the central gray of the rat

1. The present study compares the direct actions of morphine on two brain sites known to be rich in opiate receptors, namely, the caudate nucleus and the central gray. Recordings and morphine injections were made through a multibarrel glass micropipette using microiontophoresis. 2. Four different patterns of neuronal response to increasing currents of morphine were recorded in both brain regions. 3. Differences in the response to morphine between the two sites were detected in morphine-dependent rats. While the caudate neurons exhibited super-sensitivity to morphine, the neurons in the central gray displayed tolerance, and in some instances, dependence was evident when naloxone was administered. 4. The distribution of spontaneously active neurons within these two brain areas was found to be different in morphine-naive and morphine-dependent rats. 5. The electrophysiological findings of this study support the hypothesis of multiple opiate receptors.