The architecture of chicken chromosome territories changes during differentiation

BACKGROUND: Between cell divisions the chromatin fiber of each chromosome is restricted to a subvolume of the interphase cell nucleus called chromosome territory. The internal organization of these chromosome territories is still largely unknown. RESULTS: We compared the large-scale chromatin structure of chromosome territories between several hematopoietic chicken cell types at various differentiation stages. Chromosome territories were labeled by fluorescence in situ hybridization in structurally preserved nuclei, recorded by confocal microscopy and evaluated visually and by quantitative image analysis. Chromosome territories in multipotent myeloid precursor cells appeared homogeneously stained and compact. The inactive lysozyme gene as well as the centromere of the lysozyme gene harboring chromosome located to the interior of the chromosome territory. In further differentiated cell types such as myeloblasts, macrophages and erythroblasts chromosome territories appeared increasingly diffuse, disaggregating to separable substructures. The lysozyme gene, which is gradually activated during the differentiation to activated macrophages, as well as the centromere were relocated increasingly to more external positions. CONCLUSIONS: Our results reveal a cell type specific constitution of chromosome territories. The data suggest that a repositioning of chromosomal loci during differentiation may be a consequence of general changes in chromosome territory morphology, not necessarily related to transcriptional changes

Axisymmetric Dynamic Response of Spherical and Cylindrical Shells

Axisymmetric dynamic response of spherical and cylindrical shell

Analyzing and reconstructing reticulation networks under timing constraints

Reticulation networks are now frequently used to model the history of life for various groups of organisms whose evolutionary past is likely to include reticulation events like horizontal gene transfer or hybridization. However, the reconstructed networks are rarely guaranteed to be temporal. If a reticulation network is temporal, then it satisfies the two biologically motivated timing constraints of instantaneously occurring reticulation events and successively occurring speciation events. On the other hand, if a reticulation network is not temporal, it is always possible to resolve this issue by adding a number of additional unsampled or extinct taxa. In the first half of the paper, we show that deciding whether a given number of additional taxa is sufficient to transform a non-temporal reticulation network into a temporal one is an NP-complete problem. As one is often given a set of gene trees instead of a network in the context of hybridization, this motivates the second half of the paper which provides an algorithm for reconstructing a temporal hybridization network that simultaneously explains the ancestral history of two trees or indicates that no such network exists. We highlight two practical applications of this algorithm and illustrate the second application on a grass data set

Understanding heterogeneities of flow paths for agricultural practice

Heterogeneous flow processes, especially preferential flow, facilitate the influx of contaminants (and nutrients) through the soil into the groundwater. With a combination of soil physical, soil chemical and soil geophysical methods we investigate the susceptibility of selected soils for such flow processes on agricultural fields in Lower Saxony. Investigations are performed within the EU Interreg project TOPSOIL which investigates opportunities to improve surface and groundwater quality as well as water management strategies under the consideration of climate adaptation challenges. The project addresses the transport behavior of percolation water in the unsaturated zone, the migration of nitrogen and veterinary pharmaceuticals in soils, and elaborates - together with different stakeholders (e.g. farmers, water supply companies) - common strategies to minimize the migration of these substances into the groundwater. We present results of a first soil scientific and soil geophysical census using radiometry and electrical conductivity which shows the heterogeneity of the site with regard to conductivity and radiation. We used the CMD explorer for electromagnetic mapping (horizontal and vertical dipoles, intercoil spacing of 1.48/2.82/4.49 m, investigation depths of appr. 0 - 6 m). The radiometry detector comprised five sodium-iodide crystals each with a volume of 4 litres. The spectral data are evaluated for potassium, uranium (Bi-214), thorium (T-208) and total counts. The geophysical measurements were used to generally differentiate areas of different soil properties. These areas were sampled for soil physics and soil chemistry (ram coring at 48 sites, 0 - 2 m) with the aim of determining the variability of the transport behavior on a field scale

A multideterminant assessment of mean field methods for the description of electron transfer in the weak coupling regime

Multideterminant calculations have been performed on model systems to emphasize the role of many-body effects in the general description of charge quantization experiments. We show numerically and derive analytically that a closed-shell ansatz, the usual ingredient of mean-field methods, does not properly describe the step-like electron transfer characteristic in weakly coupled systems. With the multideterminant results as a benchmark, we have evaluated the performance of common ab initio mean field techniques, such as Hartree Fock (HF) and Density Functional Theory (DFT) with local and hybrid exchange correlation functionals, with a special focus on spin-polarization effects. For HF and hybrid DFT, a qualitatively correct open-shell solution with distinct steps in the electron transfer behaviour can be obtained with a spin-unrestricted (i.e., spin-polarized) ansatz though this solution differs quantitatively from the multideterminant reference. We also discuss the relationship between the electronic eigenvalue gap and the onset of charge transfer for both HF and DFT and relate our findings to recently proposed practical schemes for calculating the addition energies in the Coulomb blockade regime for single molecule junctions from closed-shell DFT within the local density approximation

Triton calculations with π\pi and ρ\rho exchange three-nucleon forces

The Faddeev equations are solved in momentum space for the trinucleon bound state with the new Tucson-Melbourne $\pi$ and $\rho$ exchange three-nucleon potentials. The three-nucleon potentials are combined with a variety of realistic two-nucleon potentials. The dependence of the triton binding energy on the $\pi NN$ cut-off parameter in the three-nucleon potentials is studied and found to be reduced compared to the case with pure $\pi$ exchange. The $\rho$ exchange parts of the three-nucleon potential yield an overall repulsive effect. When the recommended parameters are employed, the calculated triton binding energy turns out to be very close to its experimental value. Expectation values of various components of the three-nucleon potential are given to illustrate their significance for binding.Comment: 17 pages Revtex 3.0, 4 figures. Accepted for publication in Phys. Rev.

Relativistic calculation of the triton binding energy and its implications

First results for the triton binding energy obtained from the relativistic spectator or Gross equation are reported. The Dirac structure of the nucleons is taken into account. Numerical results are presented for a family of realistic OBE models with off-shell scalar couplings. It is shown that these off-shell couplings improve both the fits to the two-body data and the predictions for the binding energy.Comment: 5 pages, RevTeX 3.0, 1 figure (uses epsfig.sty

Shaking a Box of Sand

We present a simple model of a vibrated box of sand, and discuss its dynamics in terms of two parameters reflecting static and dynamic disorder respectively. The fluidised, intermediate and frozen (`glassy') dynamical regimes are extensively probed by analysing the response of the packing fraction to steady, as well as cyclic, shaking, and indicators of the onset of a `glass transition' are analysed. In the `glassy' regime, our model is exactly solvable, and allows for the qualitative description of ageing phenomena in terms of two characteristic lengths; predictions are also made about the influence of grain shape anisotropy on ageing behaviour.Comment: Revised version. To appear in Europhysics Letter

Fractal geometry of spin-glass models

Stability and diversity are two key properties that living entities share with spin glasses, where they are manifested through the breaking of the phase space into many valleys or local minima connected by saddle points. The topology of the phase space can be conveniently condensed into a tree structure, akin to the biological phylogenetic trees, whose tips are the local minima and internal nodes are the lowest-energy saddles connecting those minima. For the infinite-range Ising spin glass with p-spin interactions, we show that the average size-frequency distribution of saddles obeys a power law $\sim w^{-D}$, where w=w(s) is the number of minima that can be connected through saddle s, and D is the fractal dimension of the phase space

Covariant equations for the three-body bound state

The covariant spectator (or Gross) equations for the bound state of three identical spin 1/2 particles, in which two of the three interacting particles are always on shell, are developed and reduced to a form suitable for numerical solution. The equations are first written in operator form and compared to the Bethe-Salpeter equation, then expanded into plane wave momentum states, and finally expanded into partial waves using the three-body helicity formalism first introduced by Wick. In order to solve the equations, the two-body scattering amplitudes must be boosted from the overall three-body rest frame to their individual two-body rest frames, and all effects which arise from these boosts, including the Wigner rotations and rho-spin decomposition of the off-shell particle, are treated exactly. In their final form, the equations reduce to a coupled set of Faddeev-like double integral equations with additional channels arising from the negative rho-spin states of the off-shell particle.Comment: 57 pages, RevTeX, 6 figures, uses epsf.st