Identification of a potential allosteric site of Golgi α-mannosidase II using computer-aided drug design

Golgi α-mannosidase II (GMII) is a glycoside hydrolase playing a crucial role in the N-glycosylation pathway. In various tumour cell lines, the distribution of N-linked sugars on the cell surface is modified and correlates with the progression of tumour metastasis. GMII therefore is a possible molecular target for anticancer agents. Here, we describe the identification of a non-competitive GMII inhibitor using computer-aided drug design methods including identification of a possible allosteric binding site, pharmacophore search and virtual screening.publishedVersio

Detecting species-site dependencies in large multiple sequence alignments

Multiple sequence alignments (MSAs) are one of the most important sources of information in sequence analysis. Many methods have been proposed to detect, extract and visualize their most significant properties. To the same extent that site-specific methods like sequence logos successfully visualize site conservations and sequence-based methods like clustering approaches detect relationships between sequences, both types of methods fail at revealing informational elements of MSAs at the level of sequence–site interactions, i.e. finding clusters of sequences and sites responsible for their clustering, which together account for a high fraction of the overall information of the MSA. To fill this gap, we present here a method that combines the Fisher score-based embedding of sequences from a profile hidden Markov model (pHMM) with correspondence analysis. This method is capable of detecting and visualizing group-specific or conflicting signals in an MSA and allows for a detailed explorative investigation of alignments of any size tractable by pHMMs. Applications of our methods are exemplified on an alignment of the Neisseria surface antigen LP2086, where it is used to detect sites of recombinatory horizontal gene transfer and on the vitamin K epoxide reductase family to distinguish between evolutionary and functional signals

Spin-texture inversion in the giant Rashba semiconductor BiTeI

Semiconductors with strong spin-orbit interaction as the underlying mechanism for the generation of spin-polarized electrons are showing potential for applications in spintronic devices. Unveiling the full spin texture in momentum space for such materials and its relation to the microscopic structure of the electronic wave functions is experimentally challenging and yet essential for exploiting spin-orbit effects for spin manipulation. Here we employ a state-of-the-art photoelectron momentum microscope with a multichannel spin filter to directly image the spin texture of the layered polar semiconductor BiTeI within the full two-dimensional momentum plane. Our experimental results, supported by relativistic ab initio calculations, demonstrate that the valence and conduction band electrons in BiTeI have spin textures of opposite chirality and of pronounced orbital dependence beyond the standard Rashba model, the latter giving rise to strong optical selection-rule effects on the photoelectron spin polarization. These observations open avenues for spin-texture manipulation by atomic-layer and charge carrier control in polar semiconductors.This work was supported by DFG (through SFB 1170 'ToCoTronics') and through FOR1162 (P3). We acknowledge the support by the Basque Departamento de Educacion, UPV/EHU (Grant Number IT-756-13), Spanish Ministerio de Economia y Competitividad (MINECO Grant Number FIS2013-48286-C2-2-P), Tomsk State University Academic D.I. Mendeleev Fund Program in 2015 (Research Grant Number 8.1.05.2015), the Russian Foundation for Basic Research (Grant Numbers 15-02-01797 and 15-02-589 02717). Partial support by the Saint Petersburg State University (Grant Number 15.61.202.2015) is also acknowledged

Identification of a potential allosteric site of Golgi α-mannosidase II using computer-aided drug design

Golgi α-mannosidase II (GMII) is a glycoside hydrolase playing a crucial role in the N-glycosylation pathway. In various tumour cell lines, the distribution of N-linked sugars on the cell surface is modified and correlates with the progression of tumour metastasis. GMII therefore is a possible molecular target for anticancer agents. Here, we describe the identification of a non-competitive GMII inhibitor using computer-aided drug design methods including identification of a possible allosteric binding site, pharmacophore search and virtual screening

Anamnestic risk factor questionnaire as reliable diagnostic instrument for osteoporosis (reduced bone morphogenic density)

<p>Abstract</p> <p>Background</p> <p>Osteoporosis is a major health problem worldwide, and is included in the WHO list of the top 10 major diseases. However, it is often undiagnosed until the first fracture occurs, due to inadequate patient education and lack of insurance coverage for screening tests. Anamnestic risk factors like positive family anamnesis or early menopause are assumed to correlate with reduced BMD.</p> <p>Methods</p> <p>In our study of 78 patients with metaphyseal long bone fractures, we searched for a correlation between anamnestic risk factors, bone specific laboratory values, and the bone morphogenic density (BMD). Each indicator was examined as a possible diagnostic instrument for osteoporosis. The secondary aim of this study was to demonstrate the high prevalence of osteoporosis in patients with metaphyseal fractures.</p> <p>Results</p> <p>76.9% of our fracture patients had decreased bone density and 43.6% showed manifest osteoporosis in DXA (densitometry) measurements. Our questionnaire, identifying anamnestic risk factors, correlated highly significantly (p = 0.01) with reduced BMD, whereas seven bone-specific laboratory values (p = 0.046) correlated significantly.</p> <p>Conclusions</p> <p>Anamnestic risk factors correlate with pathological BMD. The medical questionnaire used in this study would therefore function as a cost-effective primary diagnostic instrument for identification of osteoporosis patients.</p

The German National Pandemic Cohort Network (NAPKON): rationale, study design and baseline characteristics

Schons M, Pilgram L, Reese J-P, et al. The German National Pandemic Cohort Network (NAPKON): rationale, study design and baseline characteristics. European Journal of Epidemiology . 2022.The German government initiated the Network University Medicine (NUM) in early 2020 to improve national research activities on the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic. To this end, 36 German Academic Medical Centers started to collaborate on 13 projects, with the largest being the National Pandemic Cohort Network (NAPKON). The NAPKON's goal is creating the most comprehensive Coronavirus Disease 2019 (COVID-19) cohort in Germany. Within NAPKON, adult and pediatric patients are observed in three complementary cohort platforms (Cross-Sectoral, High-Resolution and Population-Based) from the initial infection until up to three years of follow-up. Study procedures comprise comprehensive clinical and imaging diagnostics, quality-of-life assessment, patient-reported outcomes and biosampling. The three cohort platforms build on four infrastructure core units (Interaction, Biosampling, Epidemiology, and Integration) and collaborations with NUM projects. Key components of the data capture, regulatory, and data privacy are based on the German Centre for Cardiovascular Research. By April 01, 2022, 34 university and 40 non-university hospitals have enrolled 5298 patients with local data quality reviews performed on 4727 (89%). 47% were female, the median age was 52 (IQR 36-62-) and 50 pediatric cases were included. 44% of patients were hospitalized, 15% admitted to an intensive care unit, and 12% of patients deceased while enrolled. 8845 visits with biosampling in 4349 patients were conducted by April 03, 2022. In this overview article, we summarize NAPKON's design, relevant milestones including first study population characteristics, and outline the potential of NAPKON for German and international research activities.Trial registration https://clinicaltrials.gov/ct2/show/NCT04768998 . https://clinicaltrials.gov/ct2/show/NCT04747366 . https://clinicaltrials.gov/ct2/show/NCT04679584. © 2022. The Author(s)

Titanium Dioxide Nanoparticles: Synthesis, X-Ray Line Analysis and Chemical Composition Study

TiO2 nanoparticleshave been synthesized by the sol-gel method using titanium alkoxide and isopropanolas a precursor. The structural properties and chemical composition of the TiO2 nanoparticles were studied usingX-ray diffraction, scanning electron microscopy, and X-ray photoelectron spectroscopy.The X-ray powder diffraction pattern confirms that the particles are mainly composed of the anatase phase with the preferential orientation along [101] direction.The physical parameters such as strain, stress and energy density were investigated from the Williamson- Hall (W-H) plot assuming a uniform deformation model (UDM), and uniform deformation energy density model (UDEDM). The W-H analysis shows an anisotropic nature of the strain in nanopowders. The scanning electron microscopy image shows clear TiO2 nanoparticles with particle sizes varying from 60 to 80nm. The results of mean particle size of TiO2 nanoparticles show an inter correlation with the W-H analysis and SEM results. Our X-ray photoelectron spectroscopy spectra show that nearly a complete amount of titanium has reacted to TiO2

Electronic structure of semiconductor surfaces with strong spin-orbit interactions: topology, spin polarisation and robustness

Neue Erkenntnisse über elektronische Eigenschaften von Festkörpern legen den Grundstein für innovative Anwendungen der Zukunft. Von zentraler Bedeutung sind insbesondere die Eigenschaften der Elektronenspins. Um diese besser zu verstehen, befasst sich die vorliegende Arbeit mit der experimentellen Analyse der elektronischen Struktur von topologischen Isolatoren (Sb$_2$Te$_3$ , Bi$_2$Se$_x$Te$_{3−x}$, Bi$_{1.5}$Sb$_{0.5}$Te$_{1.8}$Se$_{1.2} und Bi$_{1.4}$Sb$_{1.1}$Te$_{2.2}$S$_{0.3}$) und Kristallen mit starker Spin-Bahn-Wechselwirkung (BiTeI) mittels Photoelektronenspektroskopie. Zu Beginn werden die zum Verständnis dieser Arbeit benötigten Grundlagen erklärt sowie die unterschiedlichen zum Einsatz kommenden Techniken eingeführt. Der Hauptteil der Arbeit teilt sich in drei Forschungsschwerpunkte. Der erste Teil befasst sich mit den elektronischen Eigenschaften der Valenzbandstruktur von Sb2Te3 und den auftretenden Oberflächenzuständen. Durch gezielte Variation der Energie der anregenden Strahlung wird der Charakter der Wellenfunktion des topologischen Oberflächenzustands und dessen Wechselwirkung mit Valenzzuständen erforscht. Dabei spielt die Topologie der Volumenbandstruktur eine grundlegende Rolle. Der zusätzliche Vergleich zu Photoemissionsrechnungen ermöglicht detaillierte Einblicke in die Wechselwirkung zwischen Oberflächen- und Volumenzuständen und gibt Aufschluss darüber, wie diese vermittelt werden. Im zweiten Abschnitt wird durch die Analyse des gemessenen Photoelektronenspins das Zusammenspiel der Spintextur des Grundzustands und Endzuständen in Bi2Te3 untersucht. Dabei treten, im Gegensatz zu Grundzustandsrechnungen, Radialkomponenten des Polarisationsvektors in nichtsymmetrischer Messgeometrie auf. Sowohl deren Energieabhängigkeit als auch deren Auftreten in Photoemissionsrechnungen (1-Schritt-Modell) deutet darauf hin, dass diese ihren Ursprung in Übergangsmatrixelementen des Photoemissionsprozesses haben. Dieses Ergebnis wird mit Spinpolarisationsmessungen am Oberflächenzustand des nicht-topologischen Schichtsystems BiTeI verglichen. Im dritten Teil werden Auswirkungen unterschiedlicher Manipulationen der untersuchten Materialien auf deren elektronische Eigenschaften beschrieben. Die Adsorption von Bruchteilen einer monoatomaren Lage des Alkalimetalls Caesium auf die Oberfläche des topologischen Isolators Sb2Te3 wird systematisch untersucht. Dadurch kann dessen intrinsische p-Dotierung teilweise abgebaut werden, wobei die Valenzbandstruktur trotz der Reaktivität des Adsorbats intakt bleibt. Des Weiteren werden Auswirkungen von Änderungen der Kristallstöchiometrie durch Volumendotierung vergleichend diskutiert. Ausblickend befasst sich das Kapitel mit dem Verhalten geringer Mengen ferromagnetischer Materialen (Fe, Ni) auf den Oberflächen der topologischen Isolatoren. Für die verschiedenen Adsorbate werden Trends aufgezeigt, die von Temperatur und Zusammensetzung des Substratkristalls abhängen.New findings about electronic properties lay the foundation for future applications. The spin properties of systems with large spin-orbit coupling are particularly important. The content of this thesis therefore treats the experimental study of the surface electronic structure of topological insulators (Sb$_2$Te$_3$, Bi$_2$Se$_x$Te$_{3−x}$, Bi$_{1.5}$Sb$_{0.5}$Te$_{1.8}$Se$_{1.2} and Bi$_{1.4}$Sb$_{1.1}$Te$_{2.2}$S$_{0.3}$) and topologically trivial BiTeI crystals using photoelectron spectroscopy. At the beginning basic knowledge to understand this thesis, as well as exploited techniques are addressed. The main part of this thesis separates into three research topics. The first part focuses on the electronic properties of the valence band structure and the wave functions of the occuring surface states. Via variation of the energy of the exciting radiation the character of the wavefunction of the respective topologically non trivial surface state as well as its interaction with valence states is explored. The bulk boundary correspondence and the topology of the bulk electronic structure is of special importance for this interaction. Additionally, it is concluded from photoemission calculations, that the interaction between surface and bulk valence states is mediated by a surface resonance state. The second section presents an analysis of photoelectron spins to investigate the respective contributions of the spin texture of the initial state and final states. This thesis reports on non-vanishing radial components of the polarization vector which do not appear in groundstate calculations. The energy dependance in combination with one-step photoemission calculations indicates that these radial components find their origin in transition matrix elements of the photoemission process. The result is compared to spin resolved measurements of the surface state of the layered material BiTeI which is not a topological insulator. In the third part the consequences of various manipulations of the analyzed materials on their respective electronic structure are described. The systematic adsorption of submonolayer amounts of the alkalimetal Caesium on the surface of the topological insulator Sb2Te3(0001) reduces its intrinsic p-doping without altering its valence band structure despite the reactivity of the adsorbate. Furthermore the effects of stoichiometric changes of elemental composition and bulk doping are being discussed. Finally the behavior of small amounts of ferromagnetic materials (Fe, Ni) on the surface of the respective topological insulators are being addressed. For the different adsorbates trends are shown, which depend on temperature and chemical composition of the substrate