Supramolecular ordering of DNA in the cholesteric liquid crystalline phase: an ultrastructural study.

Aqueous solutions of 146-base pair DNA fragments form a cholesteric liquid crystalline phase in the range of about 160-290 mg/ml. We present a structural analysis of this phase by comparing the data obtained from polarizing and electron microscopy. This phase shows multiple aspects or "textures" which are presented and interpreted. They mainly depend on the orientation of the structure relative to the observation plane and on the nature, distribution, and amount of defects present in the phase. These defects are then analyzed with the two methods, and the molecular orientations can be defined precisely in their core. The biological interest of such structural analyses is discussed in relation with the understanding of chromatin structure and function.     

Linear demasking techniques are unreliable for estimating the circadian phase of ambulatory temperature data.

Clinical investigators often use ambulatory temperature monitoring to assess the endogenous phase and amplitude of an individual's circadian pacemaker for diagnostic and research purposes. However, an individual's daily schedule includes changes in levels of activity, in posture, and in sleep-wake state, all of which are known to have masking or evoked effects on core body temperature (CBT) data. To compensate for or to correct these masking effects, many investigators have developed "demasking" techniques to extract the underlying circadian phase and amplitude data. However, the validity of these methods is uncertain. Therefore, the authors tested a variety of analytic methods on two different ambulatory data sets from two different studies in which the endogenous circadian pacemaker was not synchronized to the sleep-wake schedule. In both studies, circadian phase estimates calculated from CBT collected when each subject was ambulatory (i.e., free to perform usual daily activities) were compared to those calculated during the same study when the same subject's activities were controlled. In the first study, 24 sighted young and older subjects living on a 28-h scheduled "day" protocol were studied for approximately 21 to 25 cycles of 28-h each. In the second study, a blind man whose endogenous circadian rhythms were not synchronized to the 24-h day despite his maintenance of a regular 24-h sleep-wake schedule was studied for more than 80 consecutive 24-h days. During both studies, the relative phase of the endogenous (circadian) and evoked (scheduled activity-rest) components of the ambulatory temperature data changed progressively and relatively slowly, enabling analysis of the CBT rhythm at nearly all phase relationships between the two components. The analyses of the ambulatory temperature data demonstrate that the masking of the CBT rhythm evoked by changes in activity levels, posture, or sleep-wake state associated with the evoked schedule of activity and rest can significantly obscure the endogenous circadian component of the signal, the object of study. In addition, the masking effect of these evoked responses on temperature depends on the circadian phase at which they occur. These nonlinear interactions between circadian phase and sleep-wake schedule render ambulatory temperature data unreliable for the assessment of endogenous circadian phase. Even when proposed algebraic demasking techniques are used in an attempt to reveal the endogenous temperature rhythm, the phase estimates remain severely compromised.     

On the evolution of dominance modifiers II: a non-equilibrium approach to the evolution of genetic systems

The evolution of dominance is both the simplest and best investigated example of the evolution of genetic systems. Nevertheless, there exists striking empirical material, e.g. industrial melanism, for which no satisfactory explanation could so far be provided. In this paper we take an approach to this classical problem based on a global analysis together with computer simulations. It reveals that during the evolution of dominance one has to distinguish a "nonequilibrium phase" and a "Fisherian phase". The non-equilibrium phase appears to be characterized by the fact that in general the selection intensity at the primary locus does not affect the degree of modifier selection but only the time necessary for passing through this phase. A further essential conclusion is that modifier evolution only obtains a reasonable amount of efficiency if the population reaches the Fisherian phase already with a high modifier frequency. Using these results, predictions on the population genetic prerequisites for the evolution of dominance are derived. From these we conclude that even in populations in which dominance evolution has occurred it cannot be expected that back-crosses into relics of the ancestral population lead to a breakdown of dominance within a few generations. These predictions are in accordance with empirical data on Biston betularia and Odontopera bidentata.     

Estimates of the Daily Phase and Amplitude of the Endogenous Component of the Circadian Rhythm of Core Temperature in Sedentary Humans Living Nychthemerally

Fifteen healthy female subjects were studied for eight days while living conventionally. Subjects were free to choose the ways they spent their time within a framework of regular times of retiring and rising; in practice, much of the waking time was spent in sedentary activities. Nine of the subjects were aware of the natural light-dark cycle, this approximating to a 12:12 L:D schedule at the time of year when the study took place. Before the study, subjects were assessed for their degree of "morningness" by questionnaire; throughout the study, they wore a rectal probe, and an activity meter on their non-dominant wrist. The timing (phase) and amplitude of the circadian rectal temperature rhythm were assessed on each day by cosinor analysis as well as by a me thod based on visual inspection of the data. These two parameters were also assessed after the temperature data for each day had been "purified" by a number of methods. From these results it was possible to investigate the effect of purification upon the amplitude of the circadian rhythm of temperature. Also, the day-by-day variability of phase, and the relationship between morningness and phase, were compared using these methods of phase estimation, and using cross-correlation between data sets from adjacent days; in all cases, raw and purified temperature data were used. There was a significantly greater amount of daily variation in phase using purified rather than raw data sets, and this difference was present with all methods of purification as well as with all methods for estimating phase. Purifi cation decreased the amplitude of the circadian temperature rhythm by about 30%. Finally, there was a significant correlation between the morningness score of the subjects and the phase of the circadian temperature rhythm, the phase becoming earlier with increasing morningness; when this relationship was re-examined using purified data, it became more marked. These results reflect the masking effects exerted upon raw temperature data by lifestyle. The extent to which the purification methods enable the endogenous component of a circadian rhythm – and, by implication, the output of the endogenous circadian oscillator – to be estimated in subjects living normally is addressed.     

Estimates of the Daily Phase and Amplitude of the Endogenous Component of the Circadian Rhythm of Core Temperature in Sedentary Humans Living Nychthemerally

Fifteen healthy female subjects were studied for eight days while living conventionally. Subjects were free to choose the ways they spent their time within a framework of regular times of retiring and rising; in practice, much of the waking time was spent in sedentary activities. Nine of the subjects were aware of the natural light-dark cycle, this approximating to a 12:12 L:D schedule at the time of year when the study took place. Before the study, subjects were assessed for their degree of "morningness" by questionnaire; throughout the study, they wore a rectal probe, and an activity meter on their non-dominant wrist. The timing (phase) and amplitude of the circadian rectal temperature rhythm were assessed on each day by cosinor analysis as well as by a me thod based on visual inspection of the data. These two parameters were also assessed after the temperature data for each day had been "purified" by a number of methods. From these results it was possible to investigate the effect of purification upon the amplitude of the circadian rhythm of temperature. Also, the day-by-day variability of phase, and the relationship between morningness and phase, were compared using these methods of phase estimation, and using cross-correlation between data sets from adjacent days; in all cases, raw and purified temperature data were used. There was a significantly greater amount of daily variation in phase using purified rather than raw data sets, and this difference was present with all methods of purification as well as with all methods for estimating phase. Purifi cation decreased the amplitude of the circadian temperature rhythm by about 30%. Finally, there was a significant correlation between the morningness score of the subjects and the phase of the circadian temperature rhythm, the phase becoming earlier with increasing morningness; when this relationship was re-examined using purified data, it became more marked. These results reflect the masking effects exerted upon raw temperature data by lifestyle. The extent to which the purification methods enable the endogenous component of a circadian rhythm - and, by implication, the output of the endogenous circadian oscillator - to be estimated in subjects living normally is addressed.     

Computational Methods for Estimation of Cell Cycle Phase Distributions of Yeast Cells

Two computational methods for estimating the cell cycle phase distribution of a budding yeast (Saccharomyces cerevisiae) cell population are presented. The first one is a nonparametric method that is based on the analysis of DNA content in the individual cells of the population. The DNA content is measured with a fluorescence-activated cell sorter (FACS). The second method is based on budding index analysis. An automated image analysis method is presented for the task of detecting the cells and buds. The proposed methods can be used to obtain quantitative information on the cell cycle phase distribution of a budding yeast S. cerevisiae population. They therefore provide a solid basis for obtaining the complementary information needed in deconvolution of gene expression data. As a case study, both methods are tested with data that were obtained in a time series experiment with S. cerevisiae. The details of the time series experiment as well as the image and FACS data obtained in the experiment can be found in the online additional material at http://www.cs.tut.fi/sgn/csb/yeastdistrib/.     

Dual effect of osmotic cell swelling on prolactin secretion by acutely dispersed adenohypophyseal cells

Cell swelling induced by acute exposure to the permeant molecule urea or by medium hyposmolarity evoked a prompt PRL secretory burst from dispersed rat anterior pituitary cells. However, during continuous exposure greater than or equal to 10 min to these conditions inhibition of basal and TRH-induced PRL secretion occurred and there was an "off" burst of PRL secretion following return to basal conditions. Compared with continuous TRH stimulation which causes biphasic PRL secretion with a rapid high amplitude first phase secretory burst followed by a sustained low level second phase of secretion, cell swelling induced only "first phase" secretion. Removing Ca2+ from the medium or adding 50 microM verapamil markedly depressed the "off" secretory burst following return to basal conditions but had no effect on the initial high amplitude burst. Our data suggest that the effect of cell swelling on PRL secretion is complex and that there are at least two mechanisms for PRL secretion in normal anterior pituitary cells; these are differently affected by cell swelling and Ca2+ influx.     

Fluorescence methods to detect phase boundaries in lipid bilayer mixtures

Phase diagrams of lipid mixtures can show several different regions of phase coexistence, which include liquid-disordered, liquid-ordered, and gel phases. Some phase regions are small, and some have sharp boundaries. The identity of the phases, their location in composition space, and the nature of the transitions between the phases are important for understanding the behavior of lipid mixtures. High fidelity phase boundary detection requires high compositional resolution, on the order of 2% compositional increments. Sample artifacts, especially the precipitation of crystals of anhydrous cholesterol, can occur at higher cholesterol concentrations unless precautions are taken. Fluorescence resonance energy transfer (FRET) can be used quantitatively to find the phase boundaries and even partition coefficients of the dyes between coexisting phases, but only if data are properly corrected for non-FRET contributions. Self-quenching of the dye fluorescence can be significant, distorting the data at dye concentrations that intuitively might be considered acceptable. Even more simple than FRET experiments, measurements of single-dye fluorescence can be used to find phase boundaries. Both FRET and single-dye fluorescence readily detect the formation of phase domains that are much smaller than the wavelength of light, i.e. "nanoscopic" domains.     

Phase equilibria and structure of dry and hydrated egg lecithin

The behavior of purified egg lecithin in water has been investigated in relation to the quantity of water present and the temperature. The complete binary phase diagram of egg lecithin-water is presented as well as X-ray diffraction data on selected mixtures. Dry egg lecithin is present in at least partially crystalline form until about 40 degrees C. Above this temperature it forms a "wax-like" phase up to about 88 degrees C. From 88 to 109 degrees C it forms a viscous isotropic phase which gives face-centered cubic spacings by X-ray analysis. Above 110 degrees C its texture is "neat" and the structure is assumed to be lamellar until its final melting point at 231 degrees C. Hydrated lecithin forms (except for a small zone of cubic phase at low water concentrations and high temperature) a lamellar liquid crystalline phase. This phase contains up to 45% water at 20 degrees C. Mixtures containing more water separate into two phases, the lamellar liquid crystalline phase and water. In the melting curve of hydrated lecithin a eutectic is noted at about 16% water and the cubic phase seen when less water is present disappears at this composition of the mixture. These facts, along with previous vapor pressure measurements, suggest that there is a structural change at about 16% water. X-ray diffraction studies of lecithin at 24 degrees C and calculations from these data suggest that the reason for this may be the presence of a "free water layer" when more than 16% water is present.     

Direct determination of crystallographic phases for diffraction data from phospholipid multilamellar arrays.

Direct determination of crystallographic phases based on probabilistic of sigma 1 and sigma 2 "triplet" structure invariants has been found to be an effective technique for structure analysis with lamellar x-ray or electron diffraction intensity data from phospholipids. In many cases, nearly all phase values are determined, permitting a structure density (electron density for x-ray diffraction; electrostatic potential for electron diffraction) map to be calculated, which is directly interpretable in terms of known bilayer lipid structure. The major source of error is found to be due to the distortion of observed electron diffraction intensity data by incoherent multiple scattering, which can significantly affect the appearance of the electrostatic potential map, but not the success of the phase determination, as long as the observed Patterson function can be interpreted.     

Cross-correlation and merging of crystallographic reflections derived from cryoelectron micrographs of 3D crystals: application to the Limulus acrosomal bundle

A method is described for merging in reciprocal space of electron microscopic data from three-dimensional crystals of the acrosomal bundle. Permutation of indices was required to find the proper alignment of data from different bundles. The method utilizes a statistical evaluation of the significance of the cross-correlation results to indicate the proper order for merging. The three-dimensional (3D) merging is a reference-free operation that does not depend on choosing a "zero-tilt" user-defined starting point. Results from the merging are given and the merged 3D data to 9.5A resolution is evaluated for coherence. General issues such as statistical significance of cross-correlation function peaks, symmetry evaluation, and phase coherence as a function of amplitude are discussed.     

K+ conduction phenomena applicable to the low frequency impedance of squid axon

Summary The incorporation of four amphiphilic flavins (amphiflavins) as fluorescence markers bearing C₁₈-hydrocarbon chains at various positions of the chromophore into artificial membrane vesicles has been investigated. The vesicles utilized were made from three different saturated phospholipids. The stability of the flavin-charged vesicles was found to be good over several days, depending somewhat on the temperature, the pH, and their concentration. A marked increase of the fluorescence quantum yield near the vesicle phase transition (crystalline liquid crystalline) was found which was taken to indicate that the flavin nuclei are imbedded more deeply into the hydrophobic portion of the membranes. This is further supported by a hypsochromic shift of the near flavin UV-peak and the increase of absorbance at 450 nm upon melting. Rotational relaxation times of the various amphiflavins bound to the different vesicles are obtained from measurements of the fluorescence polarizations as a function of temperature. From these data, the microviscosities in the region of the chromophors are calculated. Measurements of the fluorescence polarization as a function of the solvent viscosity and vesicle phase (crystalline-liquid crystalline) indicate that below the phase transition the flavin nucleus is protected from the suspension medium by a lipid-water interphase, which softens above phase transition. The dependence of the flavin orientation and microenvironment on the position of the substitution of the aliphatic chain is reflected in the differences of the fluorescence yields and the shape of the emission spectra.     

Neural networks with constrained inputs as models for pattern formation in primate visual cortex

We present a neural network model for the formation of ocular dominance stripes on primate visual cortex and examine the generic phase behavior and dynamics of the model. The dynamical equation of ocular dominance development can be identified with a class of Langevin equations with a nonconserved order parameter. We first set up and examine an Ising model with long-range interactions in an external field, which is equivalent to the model described by the Langevin equation. We use both mean-field theory and Monte-Carlo simulations to study the equilibrium phase diagram of this equivalent Ising model. The phase diagram comprises three phases: a striped phase, a hexagonal bubble phase, and a uniform paramagnetic phase. We then examine the dynamics of the striped phase by solving the Langevin equation both numerically and by singular perturbation theory. Finally, we compare the results of the model with physiological data. The typical striped structure of the ocular dominance columns corresponds to the zero-field configurations of the model. Monocular deprivation can be simulated by allowing the system to evolve in the absence of an external field at early times and then continuing the simulation in the presence of an external field. The physical and physiological applications of our model are discussed in the conclusion.     

Physiology of polyol formation by free and immobilized cells of the osmotolerant yeast Pichia farinosa

Summary Some physiological data of cells of Pichia farinosa immobilized on sintered glass Raschig rings were compared with data from free cells. Glucose consumption and productivity of total polyols (arabitol, glycerol and erythritol) showed a simultaneous inter-lag phase. Enzymes that catalyse steps of the pentosephosphate pathway (glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, transaldolase and polyol dehydrogenase) showed a distinct increase after transfer of the cells into production medium. The activity of glycerol-3-phosphate dehydrogenase was generally low. Only alcohol dehydrogenase presented the inter-lag phase mentioned above.Offprint requests to: H.-J. Rehm     

A method for determining the dielectric constant and the conductivity of membrane-bounded particles of biological relevance.

Numerical assessment is made regarding Pauly and Schwan's theory which describes the dielectric behavior of a suspension of "shell spheres" as a model of biological membrane-bounded particles. The results indicate that approximate expressions of the theory may give rise to serious errors when applied to particles smaller than about 1 mum in diameter. With a view to performing analysis according to a general expression of the theory, some of the characteristic responses of dielectric parameters upon changes in phase parameters are examined with particular reference to some numerical ranges of biological interest. On this basis a simplified and systematic procedure is proposed for estimating the phase parameters of particles whose shell phase can be regarded as non-conductive. As the application of the procedure proposed, a set of dielectric data of a synaptosome suspension is analyzed, so that the following three phase parameters are successfully determined: membrane capacitance (or shell phase dielectric constant), interval phase conductivity and internal phase dielectric constant. Some limitations of the procedure are discussed for the cases of conducting shells and small particles.     

Impacts on type I error rate with inappropriate use of learn and confirm in confirmatory adaptive design trials

A two-stage adaptive design trial is a single trial that combines the learning data from stage 1 (or phase II) and the confirming data in stage 2 (or phase III) for formal statistical testing. We call it a "Learn and Confirm" trial. The studywise type I error rate remains to be at issue in a "Learn and Confirm" trial. For studying multiple doses or multiple enpdoints, a "Learn and Confirm" adaptive design can be more attractive than a fixed design approach. This is because intuitively the learning data in stage 1 should not be subjected to type I error scrutiny if there is no formal interim analysis performed and only an adaptive selection of design parameters is made at stage 1. In this work, we conclude from extensive simulation studies that the intuition is most often misleading. That is, regardless of whether or not there is a formal interim analysis for making an adaptive selection, the type I error rates are always at risk of inflation. Inappropriate use of any "Learn and Confirm" strategy should not be overlooked.     

Comparison of synonymous codon distribution patterns of bacteriophage and host genomes.

Synonymous codon usage patterns of bacteriophage and host genomes were compared. Two indexes, G + C base composition of a gene (fgc) and fraction of translationally optimal codons of the gene (fop), were used in the comparison. Synonymous codon usage data of all the coding sequences on a genome are represented as a cloud of points in the plane of fop vs. fgc. The Escherichia coli coding sequences appear to exhibit two phases, "rising" and "flat" phases. Genes that are essential for survival and are thought to be native are located in the flat phase, while foreign-type genes from prophages and transposons are found in the rising phase with a slope of nearly unity in the fgc vs. fop plot. Synonymous codon distribution patterns of genes from temperate phages P4, P2, N15 and lambda are similar to the pattern of E. coli rising phase genes. In contrast, genes from the virulent phage T7 or T4, for which a phage-encoded DNA polymerase is identified, fall in a linear curve with a slope of nearly zero in the fop vs. fgc plane. These results may suggest that the G + C contents for T7, T4 and E. coli flat phase genes are subject to the directional mutation pressure and are determined by the DNA polymerase used in the replication. There is significant variation in the fop values of the phage genes, suggesting an adjustment to gene expression level. Similar analyses of codon distribution patterns were carried out for Haemophilus influenzae, Bacillus subtilis, Mycobacterium tuberculosis and their phages with complete genomic sequences available.