TY - JOUR A1 - Xing, N. A1 - Höfler, T. A1 - Hearn, C. J. A1 - Nascimento, M. A1 - Camps Paradell, G. A1 - McMahon, Dino Peter A1 - Kunec, D. A1 - Osterrieder, N. A1 - Cheng, H. H. A1 - Trimpert, J. T1 - Fast-forwarding evolution - Accelerated adaptation in a proofreading-deficient hypermutator herpesvirus N2 - Evolution relies on the availability of genetic diversity for fitness-based selection. However, most deoxyribonucleic acid (DNA) viruses employ DNA polymerases (Pol) capable of exonucleolytic proofreading to limit mutation rates during DNA replication. The relative genetic stability produced by high-fidelity genome replication can make studying DNA virus adaptation and evolution an intensive endeavor, especially in slowly replicating viruses. Here, we present a proofreading-impaired Pol mutant (Y547S) of Marek’s disease virus that exhibits a hypermutator phenotype while maintaining unimpaired growth in vitro and wild-type (WT)-like pathogenicity in vivo. At the same time, mutation frequencies observed in Y547S virus populations are 2–5-fold higher compared to the parental WT virus. We find that Y547S adapts faster to growth in originally non-permissive cells, evades pressure conferred by antiviral inhibitors more efficiently, and is more easily attenuated by serial passage in cultured cells compared to WT. Our results suggest that hypermutator viruses can serve as a tool to accelerate evolutionary processes and help identify key genetic changes required for adaptation to novel host cells and resistance to antiviral therapy. Similarly, the rapid attenuation achieved through adaptation of hypermutators to growth in cell culture enables identification of genetic changes underlying attenuation and virulence, knowledge that could practically exploited, e.g. in the rational design of vaccines. KW - Polymerase mutant KW - Proofreading deficient KW - Hypermutation KW - Adaption KW - DNA polymerase KW - Marek's Disease Virus PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-565631 DO - https://doi.org/10.1093/ve/veac099 SN - 2057-1577 VL - 8 IS - 2 SP - 1 EP - 11 PB - Oxford University Press CY - Oxford, UK AN - OPUS4-56563 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Vogel, F. A1 - Cheng, J. A1 - Liang, S. B. A1 - Ke, C. B. A1 - Cao, S. S. A1 - Zhang, X. P. A1 - Zizak, I. A1 - Manzoni, Anna Maria A1 - Yu, J. M. A1 - Wanderka, N. A1 - Li, W. T1 - Formation and evolution of hierarchical microstructures in a Ni-based superalloy investigated by in situ high-temperature synchrotron X-ray diffraction N2 - Hierarchical microstructures are created when additional γ particles form in γ’ precipitates and they are linked to improved strength and creep properties in high-temperature alloys. Here, we follow the formation and evolution of a hierarchical microstructure in Ni86.1Al8.5Ti5.4 by in situ synchrotron X-ray diffraction at 1023 K up to 48 h to derive the lattice parameters of the γ matrix, γ’ precipitates and γ particles and misfits between phases. Finite element method-based computer simulations of hierarchical microstructures allow obtaining each phase's lattice parameter, thereby aiding peak identification in the in situ X-ray diffraction data. The simulations further give insight into the heterogeneous strain distribution between γ’ precipitates and γ particles, which gives rise to an anisotropic diffusion potential that drives the directional growth of γ particles. We rationalize a schematic model for the growth of γ particles, based on the Gibbs-Thomson effect of capillary and strain-induced anisotropic diffusion potentials. Our results highlight the importance of elastic properties, elastic anisotropy, lattice parameters, and diffusion potentials in controlling the behavior and stability of hierarchical microstructures. KW - XRD KW - Superalloy KW - Finite element method KW - Transmission electron microscopy PY - 2022 DO - https://doi.org/10.1016/j.jallcom.2022.165845 SN - 0925-8388 VL - 919 SP - 1 EP - 17 PB - Elsevier CY - Lausanne AN - OPUS4-55394 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Tan, K. H. A1 - Sattari, S. A1 - Donskyi, Ievgen A1 - Cuellar-Camacho, J. L. A1 - Cheng, C. A1 - Schwibbert, Karin A1 - Lippitz, Andreas A1 - Unger, Wolfgang A1 - Gorbushina, Anna A1 - Adeli, M. A1 - Haag, R. T1 - Functionalized 2D nanomaterials with switchable binding to investigate graphene–bacteria interactions N2 - Graphene and its derivatives have recently attracted much attention for sensing and deactivating pathogens. However, the mechanism of multivalent interactions at the graphene–pathogen interface is not fully understood. Since different physicochemical parameters of graphene play a role at this interface, control over graphene’s structure is necessary to study the mechanism of these interactions. In this work, different graphene derivatives and also zwitterionic graphene nanomaterials (ZGNMs) were synthesized with defined exposure, in terms of polymer coverage and functionality, and isoelectric points. Then, the switchable interactions of these nanomaterials with E. coli and Bacillus cereus were investigated to study the validity of the generally proposed “trapping” and “nano-knives” mechanisms for inactivating bacteria by graphene derivatives. It was found that the antibacterial activity of graphene derivatives strongly depends on the accessible area, i.e. edges and basal plane of sheets and tightness of their agglomerations. Our data clearly confirm the authenticity of “trapping” and “nano-knives” mechanisms for the antibacterial activity of graphene sheets. KW - XPS KW - Graphene KW - Graphene–bacteria interaction PY - 2018 DO - https://doi.org/10.1039/c8nr01347k SN - 2040-3364 SN - 2040-3372 VL - 10 IS - 20 SP - 9525 EP - 9537 PB - RSC CY - London AN - OPUS4-45084 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Reed, B. P. A1 - Cant, D.J.H. A1 - Spencer, S.J. A1 - Carmona-Carmona, A. J. A1 - Bushell, A. A1 - Herrara-Gómez, A. A1 - Kurokawa, A. A1 - Thissen, A. A1 - Thomas, A.G. A1 - Britton, A.J. A1 - Bernasik, A. A1 - Fuchs, A. A1 - Baddorf, A.P. A1 - Bock, B. A1 - Thellacker, B. A1 - Cheng, B. A1 - Castner, D.G. A1 - Morgan, D.J. A1 - Valley, D. A1 - Willneff, E.A. A1 - Smith, E.P. A1 - Nolot, E. A1 - Xie, F. A1 - Zorn, G. A1 - Smith, G.C. A1 - Yasukufu, H. A1 - Fenton, J.L. A1 - Chen, J. A1 - Counsell, J.D.P. A1 - Radnik, Jörg A1 - Gaskell, K.J. A1 - Artyushkova, K. A1 - Yang, L. A1 - Zhang, L. A1 - Eguchi, M. A1 - Walker, M. A1 - Hajdyla, M. A1 - Marzec, M.M. A1 - Linford, M.R. A1 - Kubota, N. A1 - Cortazar-Martinez, O. A1 - Dietrich, P. A1 - Satoh, R. A1 - Schroeder, S.L.M. A1 - Avval, T.G. A1 - Nagatomi, T. A1 - Fernandez, V. A1 - Lake, W. A1 - Azuma, Y. A1 - Yoshikawa, Y. A1 - Compean-Gonzalez, C.L. A1 - Ceccone, G. A1 - Shard, A.G. T1 - ERRATUM: “Versailles project on advanced materials and standards interlaboratory study on intensity calibration for x-ray photoelectron spectroscopy instruments using low-density polyethylene” [J. Vac. Sci. Technol. A 38, 063208 (2020)] N2 - The lead authors failed to name two collaborators as co-authors. The authors listed should include: Miss Claudia L. Compean-Gonzalez (ORCID: 0000-0002-2367-8450) and Dr. Giacomo Ceccone (ORCID: 0000-0003-4637-0771). These co-authors participated in VAMAS project A27, provided data that were analyzed and presented in this publication (and supporting information), and reviewed the manuscript before submission. KW - X-ray photoelectron spectroscopy KW - Transmission function KW - Low-density polyethylene PY - 2021 DO - https://doi.org/10.1116/6.0000907 VL - 39 IS - 2 SP - 027001 PB - American Vacuum Society AN - OPUS4-52380 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Liu, F. A1 - Lakey, P. S. J. A1 - Berkemeier, T. A1 - Tong, H. A1 - Kunert, A. T. A1 - Meusel, H. A1 - Cheng, Y. A1 - Su, H. A1 - Fröhlich-Nowoisky, J. A1 - Lai, S. A1 - Weller, Michael G. A1 - Shiraiwa, M. A1 - Pöschl, U. A1 - Kampf, C. J. T1 - Atmospheric protein chemistry influenced by anthropogenic air pollutants: nitration and oligomerization upon exposure to ozone and nitrogen dioxide N2 - The allergenic potential of airborne proteins may be enhanced via post-translational modification induced by air pollutants like ozone (O3) and nitrogen dioxide (NO2). The molecular mechanisms and kinetics of the chemical modifications that enhance the allergenicity of proteins, however, are still not fully understood. Here, protein tyrosine nitration and oligomerization upon simultaneous exposure of O3 and NO2 were studied in coated-wall flow-tube and bulk solution experiments under varying atmospherically relevant conditions (5–200 ppb O3, 5–200 ppb NO2, 45–96% RH), using bovine serum albumin as a model protein. Generally, more tyrosine residues were found to react via the nitration pathway than via the oligomerization pathway. Depending on reaction conditions, oligomer mass fractions and nitration degrees were in the ranges of 2.5–25% and 0.5–7%, respectively. The experimental results were well reproduced by the kinetic multilayer model of aerosol surface and bulk chemistry (KM-SUB). The extent of nitration and oligomerization strongly depends on relative humidity (RH) due to moisture-induced phase transition of proteins, highlighting the importance of cloud processing conditions for accelerated protein chemistry. Dimeric and nitrated species were major products in the liquid phase, while protein oligomerization was observed to a greater extent for the solid and semi-solid phase states of proteins. Our results show that the rate of both processes was sensitive towards ambient ozone concentration but rather insensitive towards different NO2 levels. An increase of tropospheric ozone concentrations in the Anthropocene may thus promote pro-allergic protein modifications and contribute to the observed increase of allergies over the past decades. KW - Oxidation KW - Nitration KW - Cross-linking KW - Ozone KW - Nitrogen dioxide KW - Dimer KW - Air pollution KW - Diesel KW - Aeroallergens KW - Pollen KW - Tyrosine KW - Nitrotyrosine KW - BSA KW - Albumin PY - 2017 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-418482 DO - https://doi.org/10.1039/c7fd00005g SN - 1359-6640 VL - 200 SP - 413 EP - 427 PB - Royal Society of Chemistry CY - London AN - OPUS4-41848 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Reed, B. P. A1 - Cant, D.J.H. A1 - Spencer, J. A1 - Carmona-Carmona, A. J. A1 - Bushell, A. A1 - Herrara-Gómez, A. A1 - Kurokawa, A. A1 - Thissen, A. A1 - Thomas, A.G. A1 - Britton, A.J. A1 - Bernasik, A. A1 - Fuchs, A. A1 - Baddorf, A. P. A1 - Bock, B. A1 - Thellacker, B. A1 - Cheng, B. A1 - Castner, D.G. A1 - Morgan, D.J. A1 - Valley, D. A1 - Willneff, E.A. A1 - Smith, E.F. A1 - Nolot, E. A1 - Xie, F. A1 - Zorn, G. A1 - Smith, G.C. A1 - Yasukufu, H. A1 - Fenton, J. L. A1 - Chen, J. A1 - Counsell, J..D.P. A1 - Radnik, Jörg A1 - Gaskell, K.J. A1 - Artyushkova, K. A1 - Yang, L. A1 - Zhang, L. A1 - Eguchi, M. A1 - Walker, M. A1 - Hajdyla, M. A1 - Marzec, M.M. A1 - Linford, M.R. A1 - Kubota, N. A1 - Cartazar-Martínez, O. A1 - Dietrich, P. A1 - Satoh, R. A1 - Schroeder, S.L.M. A1 - Avval, T.G. A1 - Nagatomi, T. A1 - Fernandez, V. A1 - Lake, W. A1 - Azuma, Y. A1 - Yoshikawa, Y. A1 - Shard, A.G. T1 - Versailles Project on Advanced Materials and Standards interlaboratory study on intensity calibration for x-ray photoelectron spectroscopy instruments using low-density polyethylene N2 - We report the results of a Versailles Project on Advanced Materials and Standards interlaboratory study on the intensity scale calibration of x-ray photoelectron spectrometers using low-density polyethylene (LDPE) as an alternative material to gold, silver, and copper. An improved set of LDPE reference spectra, corrected for different instrument geometries using a quartz-monochromated Al Kα x-ray source, was developed using data provided by participants in this study. Using these new reference spectra, a transmission function was calculated for each dataset that participants provided. When compared to a similar calibration procedure using the NPL reference spectra for gold, the LDPE intensity calibration method achieves an absolute offset of ∼3.0% and a systematic deviation of ±6.5% on average across all participants. For spectra recorded at high pass energies (≥90 eV), values of absolute offset and systematic deviation are ∼5.8% and ±5.7%, respectively, whereas for spectra collected at lower pass energies (<90 eV), values of absolute offset and systematic deviation are ∼4.9% and ±8.8%, respectively; low pass energy spectra perform worse than the global average, in terms of systematic deviations, due to diminished count rates and signal-to-noise ratio. Differences in absolute offset are attributed to the surface roughness of the LDPE induced by sample preparation. We further assess the usability of LDPE as a secondary reference material and comment on its performance in the presence of issues such as variable dark noise, x-ray warm up times, inaccuracy at low count rates, and underlying spectrometer problems. In response to participant feedback and the results of the study, we provide an updated LDPE intensity calibration protocol to address the issues highlighted in the interlaboratory study. We also comment on the lack of implementation of a consistent and traceable intensity calibration method across the community of x-ray photoelectron spectroscopy (XPS) users and, therefore, propose a route to achieving this with the assistance of instrument manufacturers, metrology laboratories, and experts leading to an international standard for XPS intensity scale calibration. KW - X-ray photoelectron spectroscopy KW - Transmission function KW - Intensity scale calibration KW - Reference spectra KW - Low-density polyethylene (LDPE) PY - 2020 DO - https://doi.org/10.1116/6.0000577 VL - 38 IS - 6 SP - 063208 AN - OPUS4-51655 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -