Article
Astronomy & Astrophysics
Xiongbang Yang, Gang Cao
Summary: The paper investigates the high-energy emission properties of pulsars using numerical simulations and computing magnetospheres, finding that the FIDO model can reproduce the observed characteristics successfully.
ASTROPHYSICAL JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Vinardas Kelpsas, Claes von Wachenfeldt
Summary: Deuterium, a low abundance stable hydrogen isotope, negatively affects cell growth in high concentrations. Through laboratory evolution, strains with increased fitness in deuterium-based media were isolated, showing multiple genetic adaptations pathways. Deuteration of proteins is crucial for structural biology applications, and evolved strains adapted for efficient production of perdeuterated soluble and membrane proteins.
Article
Biochemistry & Molecular Biology
Nhu-Ngoc Dang, Hoang-Nam Pham, Isabelle Kleiner, Martin Schwell, Jens-Uwe Grabow, Ha Vinh Lam Nguyen
Summary: The gas-phase structures of the fruit ester methyl hexanoate have been determined using molecular jet Fourier-transform microwave spectroscopy and quantum chemistry. Two conformers were assigned, with internal rotation observed in the methoxy methyl group CH3-O. Comparison of barriers to methyl internal rotation in different molecules revealed a relatively constant barrier height at about 420 cm(-1) that decreases in molecules with longer R groups.
Article
Astronomy & Astrophysics
Samarth G. Kashyap, Shravan M. Hanasoge
Summary: The study utilizes data from the Solar Dynamics Observatory to obtain multiscale convective spectra, infer poloidal and toroidal flow spectra through a designed pipeline, and finds a preference for latitudinal convective flows based on peak power in the poloidal flow spectrum. Vertical motion power increases with wavenumber, reaching 8% at l = 1500, and the flows show nearly no temporal-frequency dependence.
ASTROPHYSICAL JOURNAL
(2021)
Article
Biochemical Research Methods
Sarah Schleicher, Gavin O'Connor, Petra Mischnick
Summary: The methyl distribution of methyl cellulose (MC) is commonly studied by analyzing cello-oligosaccharides (COS) with ESI-MS after perdeuteromethylation. Isotope labeling with (CH3)-C-13 instead of CD3-etherified COS can provide more precise and accurate results. (CH3)-C-13 is more robust in determining the methyl distribution of MCs.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Environmental Sciences
Jiaqi Chen, Zhe Jiang, Rui Li, Chenggong Liao, Kazuyuki Miyazaki, Dylan B. A. Jones
Summary: Recent studies have shown the challenges in explaining wintertime tropospheric NO2 changes in China, and emphasized the importance of integrating surface NO2 observations for better analysis.
ENVIRONMENTAL RESEARCH LETTERS
(2022)
Article
Geochemistry & Geophysics
T. Lokajicek, R. Vasin, T. Svitek, M. Petruzalek, M. Kotrly, I Turkova, R. Onysko, H. R. Wenk
Summary: The study found significant elastic anisotropy in Westerly granite, mainly due to the formation of microcracks and the crystal orientation of major minerals in the rock. Applying hydrostatic pressure can reduce the anisotropy, but at high pressure, the direction of anisotropy is reversed compared to low pressure.
JOURNAL OF GEOPHYSICAL RESEARCH-SOLID EARTH
(2021)
Article
Astronomy & Astrophysics
Julian B. Carlin, Andrew Melatos
Summary: This study introduces a new stress accumulation-relaxation meta-model for pulsar glitches, predicting glitch statistics through a history-dependent avalanche process. Unlike previous meta-models, the predictions of this model are inconsistent with current observations in terms of PDFs, auto-, and cross-correlations. The model also suggests the occurrence of aftershocks following large glitch events, which will be tested with future data from pulsar timing campaigns.
ASTROPHYSICAL JOURNAL
(2021)
Article
Astronomy & Astrophysics
Simon Guichandut, Andrew Cumming
Summary: Motivated by the recent observation by NICER of a type I X-ray burst from SAX J1808.4-3658 with a distinct pause feature during its rise, the study shows that such pauses can naturally occur in bursts ignited in a helium layer beneath a hydrogen-rich shell if enough energy is produced to eject the outer layers. The pause length is determined by the convection extent after ignition, while the luminosity change following the pause is influenced by the hydrogen gradient left behind. The results highlight the importance of convection treatment and favor strong mixing scenarios.
ASTROPHYSICAL JOURNAL
(2023)
Article
Biochemical Research Methods
Lucie K. Tintrop, Jana R. Lieske-Overgrand, Kaliyani Wickneswaran, Rukiyye Abis, Ruth Brunstermann, Maik A. Jochmann, Torsten C. Schmidt
Summary: This study introduces a method for simultaneous determination of fatty acids and fatty acid methyl esters using automated solvent-free solid-phase microextraction and isotope labeling in situ derivatization. Gas chromatography tandem-mass spectrometry with the chromatographic isotope effect and mass shift allows for selective differentiation of these two substance classes. The optimized derivatization conditions and standard addition calibration method provide accurate quantification of fatty acids and fatty acid methyl esters in different samples.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Piotr Paluch, Rafal Augustyniak, Mai-Liis Org, Kalju Vanatalu, Ats Kaldma, Ago Samoson, Jan Stanek
Summary: In nuclear magnetic resonance spectroscopy of proteins, methyl protons are important in studying dynamics, allosteric effects, and protein-protein interactions. This study addresses the challenge of assigning chemical shifts to methyl protons by using solid-state H-1-detected methods, fast magic-angle spinning, partial deuteration, and high-magnetic fields. The performance of different RF schemes for transferring coherence between methyl and backbone resonances is evaluated, and optimal parameters are determined through simulations. The concept of linearizing C-13 side chains by appropriate isotope labeling and resolution enhancement provided by 4D spectroscopy are also demonstrated.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Acoustics
Shravan Kottapalli, Avraham Hirschberg, Vinod Anantharaman, David M. J. Smeulders, Nicholas Waterson, Gunes Nakiboglu
Summary: This article investigates the turbulent wall pressure fluctuations caused by flow through single-hole sharp-square-edged orifices in a water filled pipe. Measurements and simulations show that the vena-contracta factors of the orifices are dependent on Reynolds numbers. The LES simulations provide a good prediction of the near-field hydrodynamic wall pressure fluctuations, while upstream and far downstream wall pressure fluctuations are dominated by acoustic pressure fluctuations.
JOURNAL OF SOUND AND VIBRATION
(2022)
Article
Chemistry, Multidisciplinary
Bin Zhou, Fei Shen, Zhiliang Hu, Songlin Wang, Xichao Ruan, Tianjiao Liang
Summary: A measurement technique was proposed to experimentally study stray neutrons inside neutron scattering instruments at CSNS. The feasibility of the method was demonstrated through verification experiments.
APPLIED SCIENCES-BASEL
(2022)
Article
Orthopedics
Josef Brunner, Maximilian Joergens, Maximilian Weigert, Hannah Kuempel, Nikolaus Degen, Julian Fuermetz
Summary: This study investigated the impact of rotation and flexion of the lower limb on radiological alignment parameters. The findings showed that rotation and flexion have a significant influence on two-dimensional alignment measurements in the coronal plane, especially when both are present.
KNEE SURGERY SPORTS TRAUMATOLOGY ARTHROSCOPY
(2023)
Article
Nuclear Science & Technology
Hattan Natto, Haori Yang
Summary: Two groups of Cherenkov glass detectors were produced, with different compositions and configurations. Wavelength shifting fibers were implemented in four samples to improve the light output. The objective was to test the detectors for neutron detection and observe the effect of WLS fibers on the detection process. Experimental and simulated results showed an increase in light output when WLS fibers were added.
NUCLEAR TECHNOLOGY
(2023)
Article
Biophysics
Kevin Pounot, Geoffrey W. Grime, Alessandro Longo, Michaela Zamponi, Daria Noferini, Viviana Cristiglio, Tilo Seydel, Elspeth F. Garman, Martin Weik, Vito Fodera, Giorgio Schiro
Summary: This study reveals the crucial role of zinc in insulin dynamics and aggregation kinetics at low pH, where zinc binding stabilizes the native form of insulin by facilitating hydration of this hydrophobic protein. Introducing new binding sites for zinc can improve insulin stability and tune its aggregation propensity.
BIOPHYSICAL JOURNAL
(2021)
Article
Physics, Multidisciplinary
Giorgio Schiro, Yann Fichou, Alex P. S. Brogan, Richard Sessions, Wiebke Lohstroh, Michaela Zamponi, Gerald J. Schneider, Francois-Xavier Gallat, Alessandro Paciaroni, Douglas J. Tobias, Adam Perriman, Martin Weik
Summary: The study revealed that solvent-free protein-polymer hybrids can replace hydration water, preserving protein structure and function, with dynamics similar to water's.
PHYSICAL REVIEW LETTERS
(2021)
Review
Biochemistry & Molecular Biology
Harshwardhan Poddar, Derren J. Heyes, Giorgio Schiro, Martin Weik, David Leys, Nigel S. Scrutton
Summary: Dynamic changes in protein structures are crucial for protein function and can be investigated with unprecedented temporal and spatial resolution using X-ray free electron lasers. Light-activated proteins are attractive targets for time-resolved structural studies, as they allow for visualization of early chemical changes and global structural changes.
Article
Biochemistry & Molecular Biology
Camilla B. Andersen, Yuichi Yoshimura, Janni Nielsen, Daniel E. Otzen, Frans A. A. Mulder
Summary: The study demonstrates that (-)-epigallocatechin gallate (EGCG) can reduce the toxicity of α-synuclein (α SN) oligomers by binding to both monomeric and oligomeric forms of α SN. EGCG binds to different regions of α SN with highest affinity for the monomeric form. Furthermore, kinetic data suggest a coupling between EGCG dimerization and α SN association.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
D. Sorigue, K. Hadjidemetriou, S. Blangy, G. Gotthard, A. Bonvalet, N. Coquelle, P. Samire, A. Aleksandrov, L. Antonucci, A. Benachir, S. Boutet, M. Byrdin, M. Cammarata, S. Carbajo, S. Cuine, R. B. Doak, L. Foucar, A. Gorel, M. Grunbein, E. Hartmann, R. Hienerwadel, M. Hilpert, M. Kloos, T. J. Lane, B. Legeret, P. Legrand, Y. Li-Beisson, S. L. Y. Moulin, D. Nurizzo, G. Peltier, G. Schiro, R. L. Shoeman, M. Sliwa, X. Solinas, B. Zhuang, T. R. M. Barends, J-P Colletier, M. Joffre, A. Royant, C. Berthomieu, M. Weik, T. Domratcheva, K. Brettel, M. H. Vos, I Schlichting, P. Arnoux, P. Mueller, F. Beisson
Summary: The study found that Fatty Acid Photodecarboxylase (FAP) exhibits efficient decarboxylation activity, primarily achieved through the reduction of the flavin chromophore and direct removal of carbon dioxide by the substrate carboxyl group. Essential residues R451 and C432 are crucial for substrate stabilization and charge transfer.
Article
Biochemistry & Molecular Biology
Jakob Toudahl Nielsen, Frans A. A. Mulder
Summary: CheSPI is a simple and efficient method that can accurately predict local structure and disorder, even in very small amounts of residual structure. It provides predictions for up to eight structural classes for structured regions and proteins, and generates intuitive numeric and graphical output.
JOURNAL OF BIOMOLECULAR NMR
(2021)
Editorial Material
Multidisciplinary Sciences
Frans A. A. Mulder
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Camilla Andersen, Anne Louise Gronnemose, Jannik N. Pedersen, Jan S. Nowak, Gunna Christiansen, Janni Nielsen, Frans A. A. Mulder, Daniel Erik Otzen, Thomas J. D. Jorgensen
Summary: This study found that the aggregation of alpha-synuclein is increased in the presence of lipid peroxidation products HNE and ONE. Furthermore, it was observed that ONE is more efficient than HNE in inducing alpha-synuclein oligomer formation.
Article
Chemistry, Physical
Falk Hoffmann, Frans A. A. Mulder, Lars Schaefer
Summary: Solution-state NMR relaxation experiments and molecular dynamics simulations have shown that while most entropy is contained within short-time dynamics, the slow dynamics of side chains on longer timescales significantly affects side-chain conformational entropy and must be considered for accurate extraction of thermodynamic properties.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
Allan R. E. Hansen, Kasper Enemark-Rasmussen, Frans A. A. Mulder, Pernille R. Jensen, Sebastian Meier
Summary: Electrochemical reduction allows for the capture and utilization of CO2 by converting it into small chemicals and fuels. However, there is a lack of well-established analytical standard operating procedures for accurately quantifying short-chain acids, aldehydes, and alcohols. The smallest organic compounds produced through electrochemical reduction of CO2 require slow NMR quantifications, which can be improved by using paramagnetic contrast agents or cooling water/DMSO for T-1-optimized measurements. H-1 NMR experiments commonly used in the study of biological mixtures are not suitable for quantitative analysis of T-1-optimized samples.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Biochemical Research Methods
Frank Gabel, Sylvain Engilberge, Emmanuelle Schmitt, Aurelien Thureau, Yves Mechulam, Javier Perez, Eric Girard
Summary: Small-angle X-ray scattering (SAXS) is an important tool in structural biology, providing information about the structure and interactions of biomolecules. However, the application of contrast-variation SAXS is limited by the range of solvent electron densities and the destabilizing effect of some co-solutes on biological systems.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Chemistry, Physical
Ahmed A. A. Ali, Falk Hoffmann, Lars Schaefer, Frans A. A. Mulder
Summary: Nuclear magnetic resonance (NMR) spin relaxation and molecular dynamics (MD) simulations are important methods for studying the internal dynamics of proteins. This study establishes a computational framework to extract cross correlation relaxation parameters of methyl groups in proteins from MD simulations and successfully obtains results consistent with experimental data.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemical Research Methods
Kyprianos Hadjidemetriou, Nicolas Coquelle, Thomas R. M. Barends, Elke De Zitter, Ilme Schlichting, Jacques-Philippe Colletier, Martin Weik
Summary: By combining various techniques, researchers have elucidated the catalytic mechanism of fatty-acid photodecarboxylase, which converts free fatty acids into hydrocarbon compounds. The study faced challenges and further experiments are needed to identify the photoproducts and their movements during the catalytic cycle.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Martin Weik, Tatiana Domratcheva
Summary: This review highlights recent advances in studying structural changes of light-sensitive proteins using time-resolved crystallography at X-ray free electron lasers and quantum chemical calculations.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Hamida Laroussi, Ariadna B. Juarez-Martinez, Aline Le Roy, Elisabetta Boeri Erba, Frank Gabel, Bernard de Massy, Jan Kadlec
Summary: Meiotic recombination in mice is initiated by DNA double-strand breaks (DSBs), catalyzed by the TOPOVIL complex. This complex's activity is regulated by meiotic factors such as REC114, MEI4, and IHO1, but the mechanism is not well understood. This study reveals the molecular details of these factors and their interactions, including REC114 forming homodimers, associating with MEI4 as a heterotrimer, and IHO1 forming tetramers. The study also shows that IHO1 directly interacts with REC114 and shares a binding surface with TOPOVIBL and another meiotic factor ANKRD31. These findings suggest the existence of a ternary IHO1-REC114-MEI4 complex and highlight the potential regulatory role of REC114 in mediating interactions with multiple partners.