Search

Zygotic genome activation (ZGA), the onset of transcription after initial quiescence, is a major developmental step in many species, which occurs after ten cell divisions in Zebrafish embryos. How transcription factor-chromatin interactions evolve during early development to support ZGA is largely unknown. We established single molecule tracking in live developing Zebrafish embryos using reflected light-sheet microscopy to visualize the general transcription factor TATA-binding protein (TBP), and developed a novel data acquisition and analysis scheme to extract kinetic information during fast cell cycles. The chromatin-bound fraction of TBP increases during early development, compatible with increasing transcriptional activity. By quantifying TBP and DNA concentrations and their binding kinetics, we device a physical model of how the nuclear volume, which decreases during early development, enhances TBP-chromatin associations. Our single molecule data suggest that the shrinking nucleus is a major driving force and timer of ZGA in Zebrafish embryos.

Response time and transcription level are vital parameters of gene regulation. They depend on how fast transcription factors (TFs) find and how efficient they occupy their specific target sites. It is well known that target site search is accelerated by TF binding to and sliding along unspecific DNA and that unspecific associations alter the occupation frequency of a gene. However, whether target site search time and occupation frequency can be optimized simultaneously is mostly unclear. We developed a transparent and intuitively accessible state-based formalism to calculate search times to target sites on and occupation frequencies of promoters of arbitrary state structure. Our formalism is based on dissociation rate constants experimentally accessible in live cell experiments. To demonstrate our approach, we consider promoters activated by a single TF, by two coactivators or in the presence of a competitive inhibitor. We find that target site search time and promoter occupancy differentially vary with the unspecific dissociation rate constant. Both parameters can be harmonized by adjusting the specific dissociation rate constant of the TF. However, while measured DNA residence times of various eukaryotic TFs correspond to a fast search time, the occupation frequencies of target sites are generally low. Cells might tolerate low target site occupancies as they enable timely gene regulation in response to a changing environment.

In single molecule laser optical tweezer (LOT) pulling experiments a protein or RNA is juxtaposed between DNA handles that are attached to beads in optical traps. The LOT generates folding trajectories under force in terms of time-dependent changes in the distance between the beads. How to construct the full intrinsic folding landscape (without the handles and the beads) from the measured time series is a major unsolved problem. By using rigorous theoretical methods---which account for fluctuations of the DNA handles, rotation of the optical beads, variations in applied tension due to finite trap stiffness, as well as environmental noise and the limited bandwidth of the apparatus---we provide a tractable method to derive intrinsic free energy profiles. We validate the method by showing that the exactly calculable intrinsic free energy profile for a Generalized Rouse Model, which mimics the two-state behavior in nucleic acid hairpins, can be accurately extracted from simulated time series in a LOT setup regardless of the stiffness of the handles. We next apply the approach to trajectories from coarse grained LOT molecular simulations of a coiled-coil protein based on the GCN4 leucine zipper, and obtain a free energy landscape that is in quantitative agreement with simulations performed without the beads and handles. Finally, we extract the intrinsic free energy landscape from experimental LOT measurements for the leucine zipper, which is independent of the trap parameters., Comment: Main text: 10 pages, 5 figures; SI: 23 pages, 7 figures

The doping of graphene to tune its electronic structure is essential for its further use in carbon based electronics. Adapting strategies from classical silicon based semiconductor technology, we use the incorporation of heteroatoms in the 2D graphene network as a straightforward way to achieve this goal. Here, we report on the synthesis of boron-doped graphene on Ni(111) in a chemical vapor deposition process of triethylborane on the one hand and by segregation of boron from the bulk on the other hand. The chemical environment of boron was determined by x-ray photoelectron spectroscopy and angle resolved photoelectron spectroscopy was used to analyze the impact on the band structure. Doping with boron leads to a shift of the graphene bands to lower binding energies. The shift depends on the doping concentration and for a doping level of 0.3 ML a shift of up to 1.2 eV is observed. The experimental results are in agreement with density-functional calculations. Furthermore, our calculations suggest that doping with boron leads to graphene preferentially adsorbed in the top-fcc geometry, since the boron atoms in the graphene lattice are then adsorbed at substrate fcc-hollow sites. The smaller adsorption distance of boron compared to carbon leads to a bending of the graphene sheet in the vicinity of the boron atoms. By comparing calculations of doped and undoped graphene on Ni(111), as well as the respective free-standing cases, we are able to distinguish between the effects that doping and adsorption have on the band structure of graphene. Both, doping and bonding to the surface, result in opposing shifts on the graphene bands.

Synthesis in 1% oxygen at 930C leads to non-superconducting RuSr2GdCu2O8 in which superconductivity subsequently can be induced with oxygen annealings without observable stoichiometric changes. Detailed ac susceptibility and zero-field muon spin rotation experiments reveal that the superconducting compounds always exhibit a lower temperature of the magnetic transition and larger values of the internal magnetic field in the ordered state of the Ru sublattice. The same annealings in oxygen, however, lead to non-superconducting RuSr2EuCu2O8. The magnetic properties of a newly discovered series of Ru1-xSr2GdCu2+xO8-y superconductors (maximum Tc=72 K for x=0.4) are reported. Low temperature behavior of the magnetization shows a significant contribution of the paramagnetic system of Gd ions to the magnetic response below the superconducting transition. Muon-spin rotation experiments reveal the presence of bulk magnetic transitions at low temperature for compounds with x<=0.4. XANES Cu-K absorption edge data show an increase in Cu valence with x., Comment: to be published in Physica C, Proceedings of New 3SC-3 Int.Conf., January 15-19, 2001, Honolulu, HI