Ancient Horizontal Gene Transfer from Bacteria Enhances Biosynthetic Capabilities of Fungi

Polyketides are natural products with a wide range of biological functions and pharmaceutical applications. Discovery and utilization of polyketides can be facilitated by understanding the evolutionary processes that gave rise to the biosynthetic machinery and the natural product potential of extant organisms. Gene duplication and subfunctionalization, as well as horizontal gene transfer are proposed mechanisms in the evolution of biosynthetic gene clusters. To explain the amount of homology in some polyketide synthases in unrelated organisms such as bacteria and fungi, interkingdom horizontal gene transfer has been evoked as the most likely evolutionary scenario. However, the origin of the genes and the direction of the transfer remained elusive.We used comparative phylogenetics to infer the ancestor of a group of polyketide synthase genes involved in antibiotic and mycotoxin production. We aligned keto synthase domain sequences of all available fungal 6-methylsalicylic acid (6-MSA)-type PKSs and their closest bacterial relatives. To assess the role of symbiotic fungi in the evolution of this gene we generated 24 6-MSA synthase sequence tags from lichen-forming fungi. Our results support an ancient horizontal gene transfer event from an actinobacterial source into ascomycete fungi, followed by gene duplication.Given that actinobacteria are unrivaled producers of biologically active compounds, such as antibiotics, it appears particularly promising to study biosynthetic genes of actinobacterial origin in fungi. The large number of 6-MSA-type PKS sequences found in lichen-forming fungi leads us hypothesize that the evolution of typical lichen compounds, such as orsellinic acid derivatives, was facilitated by the gain of this bacterial polyketide synthase

Resonant soft X-ray emission spectroscopy of vanadium oxides andrelated compounds

In today's information world, bits of data are processed by semiconductor chips, and stored in the magnetic disk drives. But tomorrow's information technology may see magnetism (spin) and semiconductivity (charge) combined in one ''spintronic'' device that exploits both charge and ''spin'' to carry data (the best of two worlds). Spintronic devices such as spin valve transistors, spin light emitting diodes, non-volatile memory, logic devices, optical isolators and ultra-fast optical switches are some of the areas of interest for introducing the ferromagnetic properties at room temperature in a semiconductor to make it multifunctional. The potential advantages of such spintronic devices will be higher speed, greater efficiency, and better stability at a reduced power consumption. This Thesis contains two main topics: In-depth understanding of magnetism in Mn doped ZnO, and our search and identification of at least six new above room temperature ferromagnetic semiconductors. Both complex doped ZnO based new materials, as well as a number of nonoxides like phosphides, and sulfides suitably doped with Mn or Cu are shown to give rise to ferromagnetism above room temperature. Some of the highlights of this work are discovery of room temperature ferromagnetism in: (1) ZnO:Mn (paper in Nature Materials, Oct issue, 2003); (2) ZnO doped with Cu (containing no magnetic elements in it); (3) GaP doped with Cu (again containing no magnetic elements in it); (4) Enhancement of Magnetization by Cu co-doping in ZnO:Mn; and (5) CdS doped with Mn, and a few others not reported in this thesis. We discuss in detail the first observation of ferromagnetism above room temperature in the form of powder, bulk pellets, in 2-3 {micro}m thick transparent pulsed laser deposited films of the Mn (< 4 at.%) doped ZnO. High-resolution transmission electron microscopy (HRTEM) and electron energy loss spectroscopy (EELS) spectra recorded from 2 to 200nm areas showed homogeneous distribution of Mn substituting for Zn a 2{sup +} state in the ZnO lattice. Ferromagnetic Resonance (FMR) technique is used to confirm the existence of ferromagnetic ordering at temperatures as high as 425K. The ab initio calculations were found to be consistent with the observation of ferromagnetism arising from fully polarized Mn 2{sup +} state. The key to observed room temperature ferromagnetism in this system is the low temperature processing, which prevents formation of clusters, secondary phases and the host ZnO from becoming n-type. The electronic structure of the same Mn doped ZnO thin films studied using XAS, XES and RIXS. revealed a strong hybridization between Mn 3d and O 2p states, which is an important characteristic of a Dilute magnetic Semiconductor (DMS). It is shown that the various processing conditions like sintering temperature, dopant concentration and the properties of precursors used for making of DMS have a great influence on the final properties. Use of various experimental techniques to verify the physical properties, and to understand the mechanism involved to give rise to ferromagnetism is presented. Methods to improve the magnetic moment in Mn doped ZnO are also described. New promising DMS materials (such as Cu doped ZnO are explored). The demonstrated new capability to fabricate powder, pellets, and thin films of room temperature ferromagnetic semiconductors thus makes possible the realization of a wide range of complex elements for a variety of new multifunctional phenomena related to Spintronic devices as well as magneto-optic components

Self-doping processes between planes and chains in the metal-to-superconductor transition of YBa2Cu3O6.9

The interplay between the quasi 1-dimensional CuO-chains and the 2-dimensional CuO2 planes of YBa2Cu3O6+x (YBCO) has been in focus for a long time. Although the CuO-chains are known to be important as charge reservoirs that enable superconductivity for a range of oxygen doping levels in YBCO, the understanding of the dynamics of its temperature-driven metal-superconductor transition (MST) remains a challenge. We present a combined study using x-ray absorption spectroscopy and resonant inelastic x-ray scattering (RIXS) revealing how a reconstruction of the apical O(4)-derived interplanar orbitals during the MST of optimally doped YBCO leads to substantial hole-transfer from the chains into the planes, i.e. self-doping. Our ionic model calculations show that localized divalent charge-transfer configurations are expected to be abundant in the chains of YBCO. While these indeed appear in the RIXS spectra from YBCO in the normal, metallic, state, they are largely suppressed in the superconducting state and, instead, signatures of Cu trivalent charge-transfer configurations in the planes become enhanced. In the quest for understanding the fundamental mechanism for high-Tc-superconductivity (HTSC) in perovskite cuprate materials, the observation of such an interplanar self-doping process in YBCO opens a unique novel channel for studying the dynamics of HTSC.Comment: 9 pages, 4 Figure

Digging up bulk band dispersion buried under a passivation layer

Atomically controlled crystal growth of thin films has established foundations of nanotechnology aimed at the development of advanced functional devices. Crystallization under non-equilibrium conditions allows engineering of new materials with their atomically-flat interfaces in the heterostructures exhibiting novel physical properties. From a fundamental point of view, knowledge of the electronic structures of thin films and their interfaces is indispensable to understand the origins of their functionality which further evolves into realistic device application. In view of extreme surface sensitivity of the conventional vacuum-ultraviolet (VUV) angle-resolved photoemission spectroscopy (ARPES), with a probing depth of several angstroms, experiments on thin films have to use sophisticated in-situ sample transfer systems to avoid surface contamination. In this Letter, we put forward a method to circumvent these difficulties using soft X-ray (SX) ARPES. A GaAs:Be thin film in our samples was protected by an amorphous As layer with an thickness of $\sim 1$ nm exceeding the probing depth of the VUV photoemission with photon energy $h\nu$ around 100 eV. The increase of the probing depth with increasing $h\nu$ towards the SX region has clearly exposed the bulk band dispersion without any surface treatment. Any contributions from potential interface states between the thin film and the amorphous capping layer has been below the detection limit. Our results demonstrate that SX-ARPES enables the observation of coherent three-dimensional band dispersion of buried heterostructure layers through an amorphous capping layer, breaking through the necessity of surface cleaning of thin film samples. Thereby, this opens new frontiers in diagnostics of authentic momentum-resolved electronic structure of protected thin-film heterostructures.Comment: 5 pages, 3 figure

Microservice-based Architecture for the Integration of Data Backends and Dashboard Applications in the Energy and Environment Domains

This article presents a software architecture based on the onion architecture that uses the concept of application microservices in order to integrate data backends with dashboard applications. Its main goal is to reduce the complexity in the architecture\u27s frontend and therefore to increase the performance of the application for the user. The concept of the added application layer as well as its interaction with the other parts of the architecture is described in detail. Then an evaluation of its advantages is presented which shows the benefits of the concept regarding performance and simplicity using a real-world use case in the energy and environmental domains

Guessing probability distributions from small samples

We propose a new method for the calculation of the statistical properties, as e.g. the entropy, of unknown generators of symbolic sequences. The probability distribution $p(k)$ of the elements $k$ of a population can be approximated by the frequencies $f(k)$ of a sample provided the sample is long enough so that each element $k$ occurs many times. Our method yields an approximation if this precondition does not hold. For a given $f(k)$ we recalculate the Zipf--ordered probability distribution by optimization of the parameters of a guessed distribution. We demonstrate that our method yields reliable results.Comment: 10 pages, uuencoded compressed PostScrip

Finite-sample frequency distributions originating from an equiprobability distribution

Given an equidistribution for probabilities p(i)=1/N, i=1..N. What is the expected corresponding rank ordered frequency distribution f(i), i=1..N, if an ensemble of M events is drawn?Comment: 4 pages, 4 figure

High-resolution soft x-ray spectrometry using the electron-multiplying charge-coupled device (EM-CCD)

The Electron-Multiplying Charge-Coupled Device (EM-CCD) shares a similar structure to the CCD except for the inclusion of a gain register that multiplies signal before the addition of read-noise, offering sub-electron effective readnoise at high frame-rates. EM-CCDs were proposed for the dispersive spectrometer on the International X-ray Observatory (IXO) to bring sub-300 eV X-rays above the noise, increasing the science yield. The high-speed, low-noise performance of the EMCCD brought added advantages of reduced dark current and stray-light per frame, reducing cooling and filtering requirements. To increase grating efficiency, several diffracted spectral orders were co-located so the inherent energy resolution of the detector was required for order separation. Although the spectral resolution of the EM-CCD is degraded by the gain process, it was shown that the EM-CCD could achieve the required separation. The RIXS spectrometer at the Advanced Resonant Spectroscopy beamline (ADRESS) of the Swiss Light Source (SLS) at the Paul Scherrer Institute currently uses a CCD, with charge spreading between pixels limiting the spatial resolution to 24 μm (FWHM). Through improving the spatial resolution below 5 μm alongside upgrading the grating, a factor of two energy resolution improvement could theoretically be made. With the high-speed, low-noise performance of the EM-CCD, photon-counting modes could allow the use of centroiding techniques to improve the resolution. Using various centroiding techniques, a spatial resolution of 2 μm (FWHM) has been achieved experimentally, demonstrating the benefits of this detector technology for soft X-ray spectrometry. This paper summarises the use of EM-CCDs from our first investigations for IXO through to our latest developments in ground-based testing for synchrotron-research and looks beyond to future possibilities