Conservation of neutral substitution rate and substitutional asymmetries in mammalian genes.

Local variation in neutral substitution rate across mammalian genomes is governed by several factors, including sequence context variables and structural variables. In addition, the interplay of replication and transcription, known to induce a strand bias in mutation rate, gives rise to variation in substitutional strand asymmetries. Here, we address the conservation of variation in mutation rate and substitutional strand asymmetries using primate- and rodent-specific repeat elements located within the introns of protein-coding genes. We find significant but weak conservation of local mutation rates between human and mouse orthologs. Likewise, substitutional strand asymmetries are conserved between human and mouse, where substitution rate asymmetries show a higher degree of conservation than mutation rate. Moreover, we provide evidence that replication and transcription are correlated to the strength of substitutional asymmetries. The effect of transcription is particularly visible for genes with highly conserved gene expression. In comparison with replication and transcription, mutation rate influences the strength of substitutional asymmetries only marginally.

Phospholipid demixing and the birth of a lipid droplet.

The biogenesis of lipid droplets (LD) in the yeast Saccharomyces cerevisiae was theoretically investigated on basis of a biophysical model. In accordance with the prevailing model of LD formation, we assumed that neutral lipids oil-out between the membrane leaflets of the endoplasmic reticulum (ER), resulting in LD that bud-off when a critical size is reached. Mathematically, LD were modeled as spherical protuberances in an otherwise planar ER membrane. We estimated the local phospholipid composition, and calculated the change in elastic free energy of the membrane caused by nascent LD. Based on this model calculation, we found a gradual demixing of lipids in the membrane leaflet that goes along with an increase in surface curvature at the site of LD formation. During demixing, the phospholipid monolayer was able to gain energy during LD growth, which suggested that the formation of curved interfaces was supported by or even driven by lipid demixing. In addition, we show that demixing is thermodynamically necessary as LD cannot bud-off otherwise. In the case of Saccharomyces cerevisiae our model predicts a LD bud-off diameter of about 12 nm. This diameter is far below the experimentally determined size of typical yeast LD. Thus, we concluded that if the standard model of LD formation is valid, LD biogenesis is a two step process. Small LD are produced from the ER, which subsequently ripe within the cytosol through a series of fusions.

The reference limits and cut-off value for serum soluble transferrin receptors for diagnosing iron deficiency in infants.

Serum soluble transferrin receptors (sTfR) concentration is a useful test in the diagnosis of childhood iron deficiency (ID). The aims of this study were to establish reference limits and to evaluate the diagnostic characteristics of sTfR in the diagnosis of ID in infants aged 9-12 months. In addition to mean erythrocyte cell volume, haemoglobin and ferritin measurements, sTfR concentration was measured in 179 healthy children in Estonia using the IDeA and Tina-quant methods. Using the ID criteria of ferritin <10 microg/l, subjects were divided into healthy (n = 146) and ID (n = 33) groups. The reference limits (5th and 95th percentile) were calculated in the study group. We used receiver operating characteristic curves to find out the cut-off values for the best diagnostic characteristics. The reference limits for sTfR were 1.5-2.7 mg/l in the IDeA method and 4.1-7.8 mg/l in the Tina-quant) method. The methods had poor agreement, the mean ratio with 95% limits of agreement was 2.9 (2.4-3.6). The best cut-off value in order to identify ID by hypoferritinaemia in this population is an sTfR level > 2.4 mg/l in the IDeA (sensitivity 84%, specificity 94%) and an sTfR level > 7.4 mg/l in the Tina-quant (sensitivity 80%, specificity 92%). We conclude that sTfR concentration is an efficient tool in the diagnosis of ID, but that every method needs its own cut-off value.

Colloidal model system for island formation.

We present model calculations to explore the possibility of colloidal island formation over strained surfaces. Colloids, aggregating due to attractive depletion interactions, are deposited onto a colloidal surface whose lattice constant and geometry can be varied by optical forces. This allows precise control of the strain between the substrate and the colloidal adsorbate. Three different strain fields are considered: fields with either an unidirectional or a hexagonal variation of strain, and fields with a combination of both variations. We find that the unidirectional field induces the formation of infinitely extended ridges, while hexagonal strain fields lead to regular pyramidal island structures which can be distorted in a controlled way by adding the unidirectional strain component. We furthermore study the dependence of island size on strain strength for the hexagonal strain pattern and find that the area occupied by an island is a constant fraction of the strain field's repeat unit.

Is there an acceleration of the CpG transition rate during the mammalian radiation?

MOTIVATION: In this article we build a model of the CpG dinucleotide substitution rate and use it to challenge the claim that, that rate underwent a sudden mammalian-specific increase approximately 90 million years ago. The evidence supporting this hypothesis comes from the application of a model of neutral substitution rates able to account for elevated CpG dinucleotide substitution rates. With the initial goal of improving that model's accuracy, we introduced a modification enabling us to account for boundary effects arising by the truncation of the Markov field, as well as improving the optimization procedure required for estimating the substitution rates. RESULTS: When using this modified method to reproduce the supporting analysis, the evidence of the rate shift vanished. Our analysis suggests that the CpG-specific rate has been constant over the relevant time period and that the asserted acceleration of the CpG rate is likely an artifact of the original model.

Exponential decay of GC content detected by strand-symmetric substitution rates influences the evolution of isochore structure.

The distribution of guanine and cytosine nucleotides throughout a genome, or the GC content, is associated with numerous features in mammals; understanding the pattern and evolutionary history of GC content is crucial to our efforts to annotate the genome. The local GC content is decaying toward an equilibrium point, but the causes and rates of this decay, as well as the value of the equilibrium point, remain topics of debate. By comparing the results of 2 methods for estimating local substitution rates, we identify 620 Mb of the human genome in which the rates of the various types of nucleotide substitutions are the same on both strands. These strand-symmetric regions show an exponential decay of local GC content at a pace determined by local substitution rates. DNA segments subjected to higher rates experience disproportionately accelerated decay and are AT rich, whereas segments subjected to lower rates decay more slowly and are GC rich. Although we are unable to draw any conclusions about causal factors, the results support the hypothesis proposed by Khelifi A, Meunier J, Duret L, and Mouchiroud D (2006. GC content evolution of the human and mouse genomes: insights from the study of processed pseudogenes in regions of different recombination rates. J Mol Evol. 62:745-752.) that the isochore structure has been reshaped over time. If rate variation were a determining factor, then the current isochore structure of mammalian genomes could result from the local differences in substitution rates. We predict that under current conditions strand-symmetric portions of the human genome will stabilize at an average GC content of 30% (considerably less than the current 42%), thus confirming that the human genome has not yet reached equilibrium.

Lattice dynamics of two-dimensional colloidal crystals subject to external light potentials.

By exposing two-dimensional crystals to tunable substrate potentials one can selectively manipulate the crystal's phonon band structure. We explore this idea and study the overdamped lattice dynamics of colloidal crystals subject to commensurate substrate potentials with sinusoidal modulations in up to two spatial directions. We furthermore show that the mean-square displacement of colloids in the crystal can be understood as the Laplace transform of the phonon spectrum and discuss how our results can best be verified experimentally.

Frank's constant in the hexatic phase.

Using videomicroscopy data of a two-dimensional colloidal system the bond-order correlation function G{6} is calculated and used to determine both the orientational correlation length xi{6} in the liquid phase and the modulus of orientational stiffness, Frank's constant F{A}, in the hexatic phase. The latter is an anisotropic fluid phase between the crystalline and the isotropic liquid phase. F{A} is found to be finite within the hexatic phase, takes the value 72/pi at the hexatic<-->isotropic liquid phase transition, and diverges at the hexatic<-->crystal transition as predicted by the Kosterlitz-Thouless-Halperin-Nelson-Young theory. This is a quantitative test of the mechanism of breaking the orientational symmetry by disclination unbinding.

Macroion virial contribution to the osmotic pressure in charge-stabilized colloidal suspensions.

Our interest goes to the different virial contributions to the equation of state of charged colloidal suspensions. Neglect of surface effects in the computation of the colloidal virial term leads to spurious and paradoxical results. This pitfall is one of the several facets of the danger of a naive implementation of the so called one component model, where the microionic degrees of freedom are integrated out to only keep in the description the mesoscopic (colloidal) degrees of freedom. On the other hand, due incorporation of wall induced forces dissolves the paradox brought forth in the naive approach, provides a consistent description, and confirms that for salt-free systems, the colloidal contribution to the pressure is dominated by the microionic one. Much emphasis is put on the no salt case but the situation with added electrolyte is also discussed.

Noncentral forces in crystals of charged colloids.

The elastic properties of fcc crystals consisting of charge stabilized colloidal particles are determined from real space imaging experiments using confocal microscopy. The normal modes and the force constants of the crystal are obtained from the fluctuations of the particles around their lattice sites using the equipartition theorem. We show that the Cauchy relation is not fulfilled and that only noncentral many-body forces can account for the elastic properties.

Growth during the first 6 months of life in infants using formula enriched with Lactobacillus rhamnosus GG: double-blind, randomized trial.

BACKGROUND: Probiotic bacteria have beneficial effects on the immune system and gastrointestinal tract, but the impacts of their long-term consumption on health and growth in early infancy are not well documented. The aim of this study was to evaluate the influence of Lactobacillus rhamnosus GG (LGG)-enriched formula on growth and faecal microflora during the first 6 months of life in normal healthy infants. MATERIALS AND METHODS: One hundred and twenty healthy infants (up to 2 months) received LGG-supplemented formula or regular formula in a double-blind, randomized manner until the age of 6 months. Weight, length and head circumference were measured monthly and transformed into standard deviation scores (SDS). Faecal samples were obtained from a random sample of infants (n=25) at entry and at the end of the study. RESULTS: One hundred and five infants (51 in the LGG group) completed the study. Children receiving LGG-supplemented formula grew better: their changes in their length and weight SDS (DeltaSDS) at the end of the study were significantly higher than those receiving regular formula (0.44+/- 0.37 versus 0.07+/- 0.06, P< 0.01 and 0.44+/- 0.19 versus 0.07+/- 0.06, P< 0.005, respectively). The LGG group had a significant, higher defecation frequency 9.1+/-2.06 versus 8.0+/- 2.8 (P<0.05). More frequent colonization with lactobacilli was found in the LGG group, 91% versus 76% (P<0.05) at the end of the study. CONCLUSIONS Infants fed with LGG-enriched formula grew better than those fed with regular formula. Further studies are necessary to clarify the mechanism of LGG in infant growth.

Pair interaction of dislocations in two-dimensional crystals.

The pair interaction between crystal dislocations is systematically explored by analyzing particle trajectories of two-dimensional colloidal crystals measured by video microscopy. The resulting pair energies are compared to Monte Carlo data and to predictions derived from the standard Hamiltonian of the elastic theory of dislocations. Good agreement is found with respect to the distance and temperature dependence of the interaction potential, but not regarding the angle dependence where discrete lattice effects become important. Our results on the whole confirm that the dislocation Hamiltonian allows a quantitative understanding of the formation and interaction energies of dislocations in two-dimensional crystals.

Variations in substitution rate in human and mouse genomes.

We present a method to quantify spatial fluctuations of the substitution rate on different length scales throughout genomes of eukaryotes. The fluctuations on large length scales are found to be predominantly a consequence of a coarse-graining effect of fluctuations on shorter length scales. This is verified for both the mouse and the human genome. We also found that the relative standard deviation of fluctuations in substitution rate is about a factor three smaller in mouse than in human. The method allows furthermore to determine time-resolved substitution rate maps of the genomes, where the corresponding autocorrelation functions quantify the velocity of spatial chromosomal reorganization.

Harmonic lattice behavior of two-dimensional colloidal crystals.

Using positional data from videomicroscopy and applying the equipartition theorem for harmonic Hamiltonians, we determine the wave-vector-dependent normal mode spring constants of a two-dimensional colloidal model crystal and compare the measured band structure to predictions of the harmonic lattice theory. We find good agreement for both the transversal and the longitudinal modes. For q-->0, the measured spring constants are consistent with the elastic moduli of the crystal.

Elastic behavior of a two-dimensional crystal near melting.

Using positional data from video microscopy, we determine the elastic moduli of two-dimensional colloidal crystals as a function of temperature. The moduli are extracted from the wave-vector-dependent normal-mode spring constants in the limit q-->0 and are compared to the renormalized Young's modulus of the Kosterlitz-Thouless-Halperin-Nelson-Young theory. An essential element of this theory is the universal prediction that Young's modulus must approach 16 pi at the melting temperature. This is indeed observed in our experiment.

Three-particle correlations in simple liquids.

We use videomicroscopy to follow the phase-space trajectory of a two-dimensional colloidal model liquid and calculate three-point correlation functions from the measured particle configurations. Approaching the fluid-solid transition by increasing the strength of the pair-interaction potential, one observes the gradual formation of a crystal-like local order due to triplet correlations, while being still deep inside the fluid phase. Furthermore, we show that in a strongly interacting system the Born-Green equation can be satisfied only with the full triplet correlation function but not with three-body distribution functions obtained from superposing pair correlations (Kirkwood superposition approximation).

The effect of lipid demixing on the electrostatic interaction of planar membranes across a salt solution.

We study the effect of lipid demixing on the electrostatic interaction of two oppositely-charged membranes in solution, modeled here as an incompressible two-dimensional fluid mixture of neutral and charged mobile lipids. We calculate, within linear and nonlinear Poisson-Boltzmann theory, the membrane separation at which the net electrostatic force between the membranes vanishes, for a variety of different system parameters. According to Parsegian and Gingell, contact between oppositely-charged surfaces in an electrolyte is possible only if the two surfaces have exactly the same charge density (sigma(1) = -sigma(2)). If this condition is not fulfilled, the surfaces can repel each other, even though they are oppositely charged. In our model of a membrane, the lipidic charge distribution on the membrane surface is not homogeneous and frozen, but the lipids are allowed to freely move within the plane of the membrane. We show that lipid demixing allows contact between membranes even if there is a certain charge mismatch, /sigma(1)/ not equal /sigma(2)/, and that in certain limiting cases, contact is always possible, regardless of the value of sigma(1)/sigma(2) (if sigma(1)/sigma(2) < 0). We furthermore find that of the two interacting membranes, only one membrane shows a major rearrangement of lipids, whereas the other remains in exactly the same state it has in isolation and that, at zero-disjoining pressure, the electrostatic mean-field potential between the membranes follows a Gouy-Chapman potential from the more strongly charged membrane up to the point of the other, more weakly charged membrane.

Charged colloids and proteins at an air-water interface: the effect of dielectric substrates on interaction and phase behavior.

We study a two-dimensional (2D) system of macroions, trapped at the interface between air and an aqueous electrolyte solution, in the presence of a dielectric substrate approaching the air-water interface from the water side. Working within the linear Debye-Hückel theory, we investigate how the microion-averaged interaction potential between the macroions is affected by the presence of the dielectric substrate. Using these potentials in a Monte Carlo simulation, we further study the changes in the structural and phase behavior of the 2D colloidal system in response to the approaching substrate. Our scope of investigation covers two classes of colloidal particles, namely, highly charged latex particles of tens of nanometers radius, and protein particles of few nanometers radius carrying relatively small numbers of total charge. Probing the bond-orientational order parameter Phi(6) as a function of the 2D particle surface fraction phi(surf) and the air-water-substrate-water separation distance L, our simulations show that structural formations at the air-water interface are strongly influenced by the presence and the dielectric nature of the supporting substrate. Specifically, our [phi(surf): L] phase diagrams reveal that the transition from the fluid to the crystalline phase is shifted to higher surface fractions, if the approaching substrate is metallic, and to lower surface fractions, if it has a very low dielectric constant. These phase diagrams may be useful for finding materials and substrate interfaces for growing, e.g., 2D crystals of protein particles.

Three-body forces between charged colloidal particles.

Within nonlinear Poisson-Boltzmann theory we calculate the pair and triplet interactions between charged colloidal spheres, specifically in the nonlinear regime of low salt concentrations and high charges. We find repulsive pair interactions and attractive triplet interactions. Within a van der Waals-like mean-field theory we estimate in which parameter regime a gas-liquid coexistence is to be expected.

Counterion evaporation.

We study the adsorption behavior of a highly charged rodlike polyelectrolyte approaching an oppositely charged planar wall in an unbounded electrolyte solution. The grand potential, the entropy, and the total number of screening particles are calculated as functions of the rod-wall distance, using input parameters that are typical of a DNA-molecule and charged lipid bilayers. It is found that counterions which are bound to the polyelectrolyte at infinite rod-wall distances will be released, or "evaporated," as the DNA molecule moves closer to the charged wall. This effect can be regarded as the opposite of the ion-condensation process. The transition of ions from the system of screening ions into the reservoir of bulk ions can lead to an increase of the enthalpy. This gain of enthalpy for the whole system manifests itself as an attractive contribution to the effective interaction between the wall and the polyelectrolyte.