Multi-collector Inductively Coupled Plasma Mass Spectrometry: New Developments and Basic Concepts for High-precision Measurements of Mass-dependent Isotope Signatures

Due to the development of multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS) around 25 years ago, the isotopes of a large range of elements (masses from Li to U) are now analyzed with high enough precision and accuracy to resolve subtle natural variations. These so-called 'non-traditional stable isotope systems' opened many new research avenues and are applied at an increasing rate in research and industry projects and in a broad range of different disciplines, including archeology, biology, physics, cosmochemistry and geology. Here, we briefly summarize the most basic concepts of MC-ICP-MS, introduce new technical developments and address important points on how to acquire accurate high-precision isotope measurements of non-traditional stable isotopes

Analysis of Oct4-dependent transcriptional networks regulating self-renewal and pluripotency in human embryonic stem cells

The POU domain transcription factor OCT4 is a key regulator of pluripotency in the early mammalian embryo and is highly expressed in the inner cell mass of the blastocyst. Consistent with its essential role in maintaining pluripotency, Oct4 expression is rapidly downregulated during formation of the trophoblast lineage. To enhance our understanding of the molecular basis of this differentiation event in humans, we used a functional genomics approach involving RNA interference-mediated suppression of OCT4 function in a human ESC line and analysis of the resulting transcriptional profiles to identify OCT4-dependent genes in human cells. We detected altered expression of >1,000 genes, including targets regulated directly by OCT4 either positively (NANOG, SOX2, REX1, LEFTB, LEFTA/EBAF DPPA4, THY1, and TDGF1) or negatively (CDX2, EOMES, BMP4, TBX18, Brachyury [T], DKK1, HLX1, GATA6, ID2, and DLX5), as well as targets for the OCT4-associated stem cell regulators SOX2 and NANOG. Our data set includes regulators of ACTIVIN, BMP, fibroblast growth factor, and WNT signaling. These pathways are implicated in regulating human ESC differentiation and therefore further validate the results of our analysis. In addition, we identified a number of differentially expressed genes that are involved in epigenetics, chromatin remodeling, apoptosis, and metabolism that may point to underlying molecular mechanisms that regulate pluripotency and trophoblast differentiation in humans. Significant concordance between this data set and previous comparisons between inner cell mass and trophectoderm in human embryos indicates that the study of human ESC differentiation in vitro represents a useful model of early embryonic differentiation in humans

Unit cell of graphene on Ru(0001): a 25 x 25 supercell with 1250 carbon atoms

The structure of a single layer of graphene on Ru(0001) has been studied using surface x-ray diffraction. A surprising superstructure has been determined, whereby 25 x 25 graphene unit cells lie on 23 x 23 unit cells of Ru. Each supercell contains 2 x 2 crystallographically inequivalent subcells caused by corrugation. Strong intensity oscillations in the superstructure rods demonstrate that the Ru substrate is also significantly corrugated down to several monolayers, and that the bonding between graphene and Ru is strong and cannot be caused by van der Waals bonds. Charge transfer from the Ru substrate to the graphene expands and weakens the C-C bonds, which helps accommodate the in-plane tensile stress. The elucidation of this superstructure provides important information in the potential application of graphene as a template for nanocluster arrays.Comment: 9 pages, 3 figures, paper submitted to peer reviewed journa

An engineered mammalian band-pass network

Gene expression circuitries, which enable cells to detect precise levels within a morphogen concentration gradient, have a pivotal impact on biological processes such as embryonic pattern formation, paracrine and autocrine signalling, and cellular migration. We present the rational synthesis of a synthetic genetic circuit exhibiting band-pass detection characteristics. The components, involving multiply linked mammalian trans-activator and -repressor control systems, were selected and fine-tuned to enable the detection of ‘low-threshold’ morphogen (tetracycline) concentrations, in which target gene expression was triggered, and a ‘high-threshold’ concentration, in which expression was muted. In silico predictions and supporting experimental findings indicated that the key criterion for functional band-pass detection was the matching of componentry that enabled sufficient separation of the low and high threshold points. Using the circuitry together with a fluorescence-encoded target gene, mammalian cells were genetically engineered to be capable of forming a band-like pattern of differentiation in response to a tetracycline chemical gradient. Synthetic gene networks designed to emulate naturally occurring gene behaviours provide not only insight into biological processes, but may also foster progress in future tissue engineering, gene therapy and biosensing applications

Differential Photoelectron Holography: A New Approach for Three-Dimensional Atomic Imaging

We propose differential holography as a method to overcome the long-standing forward-scattering problem in photoelectron holography and related techniques for the three-dimensional imaging of atoms. Atomic images reconstructed from experimental and theoretical Cu 3p holograms from Cu(001) demonstrate that this method suppresses strong forward-scattering effects so as to yield more accurate three-dimensional images of side- and back-scattering atoms.Comment: revtex, 4 pages, 2 figure

Temperature dependence of the Kondo resonance and its satellites in CeCu_2Si_2

We present high-resolution photoemission spectroscopy studies on the Kondo resonance of the strongly-correlated Ce system CeCu$_2$Si$_2$. Exploiting the thermal broadening of the Fermi edge we analyze position, spectral weight, and temperature dependence of the low-energy 4f spectral features, whose major weight lies above the Fermi level $E_F$. We also present theoretical predictions based on the single-impurity Anderson model using an extended non-crossing approximation (NCA), including all spin-orbit and crystal field splittings of the 4f states. The excellent agreement between theory and experiment provides strong evidence that the spectral properties of CeCu$_2$Si$_2$ can be described by single-impurity Kondo physics down to $T \approx 5$ K.Comment: 4 pages, 3 figure

Intronically encoded siRNAs improve dynamic range of mammalian gene regulation systems and toggle switch

Applications of conditional gene expression, whether for therapeutic or basic research purposes, are increasingly requiring mammalian gene control systems that exhibit far tighter control properties. While numerous approaches have been used to improve the widely used Tet-regulatory system, many applications, particularly with respect to the engineering of synthetic gene networks, will require a broader range of tightly performing gene control systems. Here, a generically applicable approach is described that utilizes intronically encoded siRNA on the relevant transregulator construct, and siRNA sequence-specific tags on the reporter construct, to minimize basal gene activity in the off-state of a range of common gene control systems. To demonstrate tight control of residual expression the approach was successfully used to conditionally express the toxic proteins RipDD and Linamarase. The intronic siRNA concept was also extended to create a new generation of compact, single-vector, autoinducible siRNA vectors. Finally, using improved regulation systems a mammalian epigenetic toggle switch was engineered that exhibited superior in vitro and in vivo induction characteristics in mice compared to the equivalent non-intronic system