3D Analysis of chromosome architecture: advantages and limitations with SEM

Three-dimensional mitotic plant chromosome architecture can be investigated with the highest resolution with scanning electron microscopy compared to other microscopic techniques at present. Specific chromatin staining techniques making use of simultaneous detection of back-scattered electrons and secondary electrons have provided conclusive information on the distribution of DNA and protein in barley chromosomes through mitosis. Applied to investigate the structural effects of different preparative procedures, these techniques were the groundwork for the ``dynamic matrix model{''} for chromosome condensation, which postulates an energy-dependent process of looping and bunching of chromatin coupled with attachment to a dynamic matrix of associated protein fibers. Data from SEM analysis shows basic higher order chromatin structures: chromomeres and matrix fibers. Visualization of nanogold-labeled phosphorylated histone H3 (ser10) with high resolution on chromomeres shows that functional modifications of chromatin can be located on structural elements in a 3D context. Copyright (C) 2005 S. Karger AG, Basel

Extended Huckel theory for bandstructure, chemistry, and transport. II. Silicon

In this second paper, we develop transferable semi-empirical parameters for the technologically important material, silicon, using Extended Huckel Theory (EHT) to calculate its electronic structure. The EHT-parameters areoptimized to experimental target values of the band dispersion of bulk-silicon. We obtain a very good quantitative match to the bandstructure characteristics such as bandedges and effective masses, which are competitive with the values obtained within an $sp^3 d^5 s^*$ orthogonal-tight binding model for silicon. The transferability of the parameters is investigated applying them to different physical and chemical environments by calculating the bandstructure of two reconstructed surfaces with different orientations: Si(100) (2x1) and Si(111) (2x1). The reproduced $\pi$- and $\pi^*$-surface bands agree in part quantitatively with DFT-GW calculations and PES/IPES experiments demonstrating their robustness to environmental changes. We further apply the silicon parameters to describe the 1D band dispersion of a unrelaxed rectangular silicon nanowire (SiNW) and demonstrate the EHT-approach of surface passivation using hydrogen. Our EHT-parameters thus provide a quantitative model of bulk-silicon and silicon-based materials such as contacts and surfaces, which are essential ingredients towards a quantitative quantum transport simulation through silicon-based heterostructures.Comment: 9 pages, 9 figure

Quasiparticle spectra from a non-empirical optimally-tuned range-separated hybrid density functional

We present a method for obtaining outer valence quasiparticle excitation energies from a DFT-based calculation, with accuracy that is comparable to that of many-body perturbation theory within the GW approximation. The approach uses a range-separated hybrid density functional, with asymptotically exact and short-range fractional Fock exchange. The functional contains two parameters - the range separation and the short-range Fock fraction. Both are determined non-empirically, per system, based on satisfaction of exact physical constraints for the ionization potential and many-electron self-interaction, respectively. The accuracy of the method is demonstrated on four important benchmark organic molecules: perylene, pentacene, 3,4,9,10-perylene-tetracarboxylic-dianydride (PTCDA) and 1,4,5,8-naphthalene-tetracarboxylic dianhydride (NTCDA). We envision that for finite systems the approach could provide an inexpensive alternative to GW, opening the door to the study of presently out of reach large-scale systems

The quantitative soil pit method for measuring belowground carbon and nitrogen stocks

Many important questions in ecosystem science require estimates of stocks of soil C and nutrients. Quantitative soil pits provide direct measurements of total soil mass and elemental content in depth-based samples representative of large volumes, bypassing potential errors associated with independently measuring soil bulk density, rock volume, and elemental concentrations. The method also allows relatively unbiased sampling of other belowground C and nutrient stocks, including roots, coarse organic fragments, and rocks. We present a comprehensive methodology for sampling these pools with quantitative pits and assess their accuracy, precision, effort, and sampling intensity as compared to other methods. At 14 forested sites in New Hampshire, nonsoil belowground pools (which other methods may omit, double-count, or undercount) accounted for upward of 25% of total belowground C and N stocks: coarse material accounted for 4 and 1% of C and N in the O horizon; roots were 11 and 4% of C and N in the O horizon and 10 and 3% of C and N in the B horizon; and soil adhering to rocks represented 5% of total B-horizon C and N. The top 50 cm of the C horizon contained the equivalent of 17% of B-horizon carbon and N. Sampling procedures should be carefully designed to avoid treating these important pools inconsistently. Quantitative soil pits have fewer sources of systematic error than coring methods; the main disadvantage is that because they are time-consuming and create a larger zone of disturbance, fewer observations can be made than with cores

Renewable Hydrogen: Integration, Validation, and Demonstration

This paper is about producing hydrogen through the electrolysis of water and using the hydrogen in a fuel cell or internal combustion engine generator to produce electricity during times of peak demand, or as a transportation fuel

Reticulate evolution in Panicum (Poaceae): the origin of tetraploid broomcorn millet, P. miliaceum.

Panicum miliaceum (broomcorn millet) is a tetraploid cereal, which was among the first domesticated crops, but is now a minor crop despite its high water use efficiency. The ancestors of this species have not been determined; we aimed to identify likely candidates within the genus, where phylogenies are poorly resolved. Nuclear and chloroplast DNA sequences from P. miliaceum and a range of diploid and tetraploid relatives were used to develop phylogenies of the diploid and tetraploid species. Chromosomal in situ hybridization with genomic DNA as a probe was used to characterize the genomes in the tetraploid P. miliaceum and a tetraploid accession of P. repens. In situ hybridization showed that half the chromosomes of P. miliaceum hybridized more strongly with labelled genomic DNA from P. capillare, and half with labelled DNA from P. repens. Genomic DNA probes differentiated two sets of 18 chromosomes in the tetraploid P. repens. Our phylogenetic data support the allotetraploid origin of P. miliaceum, with the maternal ancestor being P. capillare (or a close relative) and the other genome being shared with P. repens. Our P. repens accession was also an allotetraploid with two dissimilar but closely related genomes, the maternal genome being similar to P. sumatrense. Further collection of Panicum species, particularly from the Old World, is required. It is important to identify why the water-efficient P. miliaceum is now of minimal importance in agriculture, and it may be valuable to exploit the diversity in this species and its ancestors

Expression of nodal signalling components in cycling human endometrium and in endometrial cancer

<p>Abstract</p> <p>Background</p> <p>The human endometrium is unique in its capacity to remodel constantly throughout adult reproductive life. Although the processes of tissue damage and breakdown in the endometrium have been well studied, little is known of how endometrial regeneration is achieved after menstruation. Nodal, a member of the transforming growth factor-beta superfamily, regulates the processes of pattern formation and differentiation that occur during early embryo development.</p> <p>Methods</p> <p>In this study, the expression of Nodal, Cripto (co-receptor) and Lefty A (antagonist) was examined by RT-PCR and immunohistochemistry across the menstrual cycle and in endometrial carcinomas.</p> <p>Results</p> <p>Nodal and Cripto were found to be expressed at high levels in both stromal and epithelial cells during the proliferative phase of the menstrual cycle. Although immunoreactivity for both proteins in surface and glandular epithelium was maintained at relatively steady-state levels across the cycle, their expression was significantly decreased within the stromal compartment by the mid-secretory phase. Lefty expression, as has previously been reported, was primarily restricted to glandular epithelium and surrounding stroma during the late secretory and menstrual phases. In line with recent studies that have shown that Nodal pathway activity is upregulated in many human cancers, we found that Nodal and Cripto immunoreactivity increased dramatically in the transition from histologic Grade 1 to histologic Grades 2 and 3 endometrial carcinomas. Strikingly, Lefty expression was low or absent in all cancer tissues.</p> <p>Conclusion</p> <p>The expression of Nodal in normal and malignant endometrial cells that lack Lefty strongly supports an important role for this embryonic morphogen in the tissue remodelling events that occur across the menstrual cycle and in tumourogenesis.</p

Anisotropic interactions of a single spin and dark-spin spectroscopy in diamond

The nitrogen-vacancy (N-V) center in diamond is a promising atomic-scale system for solid-state quantum information processing. Its spin-dependent photoluminescence has enabled sensitive measurements on single N-V centers, such as: electron spin resonance, Rabi oscillations, single-shot spin readout and two-qubit operations with a nearby 13C nuclear spin. Furthermore, room temperature spin coherence times as long as 58 microseconds have been reported for N-V center ensembles. Here, we have developed an angle-resolved magneto-photoluminescence microscopy apparatus to investigate the anisotropic electron spin interactions of single N-V centers at room temperature. We observe negative peaks in the photoluminescence as a function of both magnetic field magnitude and angle that are explained by coherent spin precession and anisotropic relaxation at spin level anti-crossings. In addition, precise field alignment unmasks the resonant coupling to neighboring dark nitrogen spins that are not otherwise detected by photoluminescence. The latter results demonstrate a means of investigating small numbers of dark spins via a single bright spin under ambient conditions.Comment: 13 pages, 4 figure

Polarization and Strong Infra-Red Activity in Compressed Solid Hydrogen

Under a pressure of ~150 GPa solid molecular hydrogen undergoes a phase transition accompanied by a dramatic rise in infra-red absorption in the vibron frequency range. We use the Berry's phase approach to calculate the electric polarization in several candidate structures finding large, anisotropic dynamic charges and strongly IR-active vibron modes. The polarization is shown to be greatly affected by the overlap between the molecules in the crystal, so that the commonly used Clausius-Mossotti description in terms of polarizable, non-overlapping molecular charge densities is inadequate already at low pressures and even more so for the compressed solid.Comment: To appear in Phys. Rev. Let